Online source 6 YABBY genes
Part 1. The nucleotide sequences of SlYABBY gene family
Part 2. The protein sequences of SlYABBYs
Part 3. The protein sequences of AtYABBYs
Part 4. The YABBY domain sequences of AtYABBYs and SlYABBYs
Part 5. Alignment of amino acids in YABBY domains of AtYABBYs and SlYABBYs
Part 6. The paralogs in SlYABBY family
Part 7. The orthologs between AtYABYs and SlYABBYs
Part 8. The expression pattern of YABBY genes in wild tomato LA1589
Part 9. The RT-PCR primers
Part 10. Phylogenetic tree of the YABBY CDSs among Arabidopsis, cucumber, grape, poplar, potato, and
tomato
Part 11. Ks value and estimated divergence time of YABBY2 subfamily genes.
Part 12. Predicted CDSs matching between the segments of SL2.40ch06 and SL2.40ch11 containing
SlYABBY2a and FAS (SlYABBY2b) gene respectively
Part 13. The predicted genes in SL2.40ch06:41879001..42121000 containing SlYABBY2a.
Part 14.The predicted genes in SL2.40ch11:52133001..52357000 SlYABBY2b.
Part 15. Dot plot of two DNA sequences, SL2.40ch06:41879001..42121000 containing SlYABBY2a and
SL2.40ch11: 52133001..52357000 containing SlYABBY2b.
Part 16. Dot plot of two DNA sequences, tomato SL2.40ch06:41879001..42121000 containing SlYABBY2a and
Potato PGSC0003DMS000002348:230001..522000
Part 17. Dot plot of two DNA sequences, tomato SL2.40ch11:52133001..52357000 containing SlYABBY2b and
Potato PGSC0003DMS000000867:200001..503000
Part 1. The nucleotide sequences of SlYABBY gene family
>Solyc01g010240.2.1 genomic_reference:SL2.40ch01 gene_region:5028897-5031428
transcript_region:SL2.40ch01:5028897..5031428+ go_terms:GO:0005515,GO:0003700
functional_description:"CRABS CLAW (Fragment) (AHRD V1 ***- Q5EMM8_GOSHI); contains Interpro
domain(s) IPR006780 YABBY protein "
ATGTCTTCCTCATCTCCTAATTCCTCTTGTCTCAACTTATTGGAATCTGCTGATCATAAAATTAACACCATGGATCCTTCTGAACATCTTTG
CTATGTCCGTTGCAGTTTTTGTAACACTATACTCGCGGTGGGAATACCATGCAAGAAGTTGTTGGATACTGTGACAGTGAAATGTGGGCATT
GTGGTAATCTTTCCTTTTTAAGTAGTAGACCTCCAATTCAACCACAATTTTTTGATCACCAACCCATTCTTCAGCATCAAGATTTCTTCAAC
AATTTCAAGAAGGGACAGTCTTCATCTTCAAGTGAACCATCATCTCCAAAGGCACCTTTTGTTGTAAAACCTCCTGAGAAGAAGCACAGGCT
ACCATCTGCTTACAATCGGTTTATGAAGGATGAGATACAGCGTATTAAAGCAGCACATCCACAGATACCACATAGAGAAGCTTTCAGTGCAG
CAGCTAAAAATGTACATTCCAAATACTCCAAATGGGACCTTGGCTGA
>Solyc01g091010.2.1 genomic_reference:SL2.40ch01 gene_region:76475369-76478983
transcript_region:SL2.40ch01:76475369..76478983- go_terms:GO:0005515,GO:0003700
functional_description:"YABBY-like transcription factor CRABS CLAW-like protein (AHRD V1 **-*
Q6SRZ7_ANTMA); contains Interpro domain(s) IPR006780 YABBY protein "
ATGTCGTCTTCATCTGCTGCTTTTGCTCCGGACCACCACCTCCACCACCATCACCTCTCTCCTCCTTCAGGAGAACAACTCTGTTATGTCCA
ATGCAACTTTTGTGACACTGTTCTCGCGGTGAGTGTTCCTTGCTCAAGTTTCTTCAAAAATGTGACAGTAAGATGTGGTCATTGCACCAATC
TTCTCTCTGTCAACATTATTCTTCCCACTGCTGCTAATCAGCTTCATCTCCCACATTCTTTCTTTTCACCTCACAATCTTCTGGATGAGATT
CGGAATAATCCACCAAGTTTGTTGATGAATCAACAAATTAACCCAAATGAATCACTCATGCCAGTCCGAGGAGGAGTTGATGAAATTCCAAA
GCCACCAGTCGCAAACAGACCTCCGGAGAAGCGACAGAGAGTCCCATCTGCTTACAATCGATTCATCAAGGACGAGATCCAACGTATCAAAG
CTGGAAATCCCGATATAAGTCACAGGGAGGCCTTCAGTGCTGCTGCAAAGAATTGGGCCCATTTTCCACACATTCATTTCGGACTTATGCCT
GATCAACCCGTGAAGAAACCAAATGCATGTCAACAGGAAGGGGAGGATGTTCTGATGAAGGAAGGGTTTCTTGCTCCAGCAAACATTGGTGT
ATCTCCTTACTGA
>Solyc05g005240.1.1 evidence_code:10F0H1E0IEG genomic_reference:SL2.40ch05
gene_region:191257-193043 transcript_region:SL2.40ch05:191257..193043go_terms:GO:0005515,GO:0003700 functional_description:"YABBY-like transcription factor CRABS
CLAW-like protein (AHRD V1 **-* Q6SRZ7_ANTMA); contains Interpro domain(s) IPR006780 YABBY
protein "
ATGTCAACATTGAATAACCATTTGTTTGAACTCCAAGACACAATATGCTATGTGCAATGTGGCTATTGTACTACAATATTACTTGTTAGTGT
GCCATGCAGCAGCTTGTGCAACAAAGTAGTAACAGTGAGATGTGGGCATTGCACTACTCTCCTCTCTCTCAACTTGATTAAACCTTCTCTTC
ATCTCTTTGCTTCCTTCGACCAAACTCATCAGCCACCAGAAGTTGACAAGGATGAAACTGATGATGCTAATAAGAAGAATTCAAACTCAGAT
GAAGAAGATCAATTGGAGAATAATGTTCTTCCACTTAATCAAGTCGTCAATAAACCTCCAGAGAAGAGACAGAGAGCTCCTTCGGCTTATAA
TTGCTTTATCAAAGAAGAGATCAAGAGGCTGAAGACCCTATACCCCAACATGACTCACAAGCAAGCTTTCAGTACAGCAGCAAAAAATTGGG
CCCACTTTCCACCAAGTCAACATAGAGGAGGCTGTAGTCTTGGAGAGAGGAAAATGGCAAAGGTTTCTGCTGCAAGAAACTCCATGGTCCCA
AGAGATAGCAACGGTTTGATTCCTTGA
>Solyc05g012050.2.1 genomic_reference:SL2.40ch05 gene_region:5275528-5277367
transcript_region:SL2.40ch05:5275528..5277367- go_terms:GO:0003700
functional_description:"CRABS CLAW (Fragment) (AHRD V1 ***- Q5EMM8_GOSHI); contains Interpro
domain(s) IPR006780 YABBY protein "
ATGGATTATGTTCAATCTTCTGAGCATCTTTGCTACGTCCGTTGCAATTTTTGTAACACTGTTTTAGCGGTTGGAATTCCATACAAGAGGCT
AATGGATACTGTGACAGTGAAATGTGGCCATTGTAGCAATCTTTCATTTTTAACTACTAGACCTCCAATTCAAGGTCAATGCTTTGATCATC
AACCCAATATTCAGGGCTATTGTAGTGAATTAAAAAATAAGGGGCAAGCTTCATCATCTACCTCATCAACTTCTAGTGAACCTTTATCTCCA
AAGGCACCTTTTGTTGTAAAACCTCCTGAGAAGAAACACAGGCTTCCATCTGCCTACAATCGATTCATGAAGGAAGAGATACAACGTATCAA
ATCTGAAAATCCAGAGATACCACATAGAGAAGCTTTCAGTGCAGCTGCTAAAAATTGGGCTAGGTACCTTCCTAATCCACCAAATTCTGGAA
ATACCAACAATGTTTAG
>Solyc06g073920.2.1 genomic_reference:SL2.40ch06 gene_region:42038601-42044688
transcript_region:SL2.40ch06:42038601..42044688+ go_terms:GO:0003700
functional_description:"YABBY-like transcription factor CRABS CLAW-like protein (AHRD V1 **-*
Q6SRZ7_ANTMA); contains Interpro domain(s) IPR006780 YABBY protein "
ATGTCACTTGACATGACATATTCCTCCTCTTCCTCGGAACGTGTTTGCTATGTTCATTGCAACTTCTGCAGCACAATTCTTGCGGTTAGCGT
TCCATGCAACAGTATGATGACAATAGTGACAGTAAGGTGTGGACACTGCGCAAATTTGCTTTCTGTTAATATTGCACCTTCCCTTCAGTCTC
TCCCCATTCAAGATTTACAGAGACAAAATGAGTCAAGTATTGAAGATGGAATGAGTAGAGGTTATGGATCATCATCCTCTTCTACAAATTCA
TTTCACAGATTTTCTCCCATTCCTACTGATCATGATCAACCTAGATCCCCTCCTATTCGCGTACCGGAGAAAAGACAACGTGTTCCTTCTGC
CTACAATAGATTTATCAAGGAGGAGATCCAAAGGATAAAGGCAAGCAATCCTGATATTAGCCACAGAGAAGCATTTAGCACTGCTGCCAAAA
ATTGGGCACATTTCCCTCATATCCATTTTGGACTCAAGCTGGATGGCAACAAACAAACCAATAAATTGGATCATGCTGTTGCAGGAGAGGGT
CCTCAGAAAACAATTGGTCTCTATTAA
>Solyc07g008180.2.1 genomic_reference:SL2.40ch07 gene_region:2916878-2921216
transcript_region:SL2.40ch07:2916878..2921216+ go_terms:GO:0005515,GO:0003700
functional_description:"YABBY-like transcription factor CRABS CLAW-like protein (AHRD V1 **-*
Q6SRZ7_ANTMA); contains Interpro domain(s) IPR006780 YABBY protein "
ATGGCAAGTTGCATTGATGTTGCTTCTGATCAACTTTGCTATATCCCTTGCAACTTTTGCAATATTGTTCTTGCGGTGAGTGTTCCATGCAG
TAGCCTATTTGATATTGTGACTGTTCGTTGTGGACATTGCACAAATTTATGGTCCGTTAATATGGCAGCTGCATTTCAGTCCTCTTCTTCTG
CTTCGTGGCAAAATCATCAGGTTCCAAACTACACTGCTCCTGAGTATAGGATGGATTTTGGTTCATCAACCAAATGCAACATGAACAGGATG
TCAATGAGAACTCCAATCACAAACAATGTTCACGAGGAGAGGATTGTCAATCGACCTCCCGAGAAGAGGCAGAGAGTACCTTCTGCATATAA
TCAGTTCATAAAAGAAGAAATTCAGAGGATTAAAGCTAATAATCCAGATATCAGTCACAGGGAAGCATTTAGTACTGCTGCCAAAAATTGGG
CACACTTCCCTCATATTCACTTTGGACTCATGTTGGAGAGCAACAATCAAGCCAAACTTGCTTGTGGGAGCAGAAAACTATAA
>Solyc08g079100.2.1 genomic_reference:SL2.40ch08 gene_region:59908783-59911941
transcript_region:SL2.40ch08:59908783..59911941- go_terms:GO:0005515,GO:0003700
functional_description:"CRABS CLAW (Fragment) (AHRD V1 **-- Q5EMM8_GOSHI); contains Interpro
domain(s) IPR006780 YABBY protein "
ATGTCCTCTTCAAATAGCTTATCATTGGACCACCTTCCTCCTCCACCTCCTTCCGAGCAGCTCTGCTATGTCCATTGCAATGTTTGTGACAC
CGTCCTCGCGGTAAGTGTACCGTGCACAAGTTTGTTCAAAACTGTGACGGTTCGATGTGGACACTGCACTAATCTTTTGCCTGGATGGCTTT
TGCCTTCCACTAATCATCATCATCATCATTTTGGTCACACTTACTTCTCTCCTTCACACAATCTTCTGGATGAAATAAGCAATGCAACCCCA
AATTTCTTGATGAATCAGAGTAATTCTGCTCATGAATTTGTGCAGCTGCCTGCTCGACCTGGATTTGATGATCTTCCTAGACCACCACCCGT
TGTTAACAGACCTCCTGAGAAGAGACAGCGAGTCCCTTCTGCTTACAACCGATTCATCAAGGAAGAAATCCAACGCATAAAAGCAGGGAATC
CTGATATTAGCCACAGAGAAGCCTTCAGCGCCGCTGCGAAAAATTGGGCCCACTTTCCACACATTCAATTTGGTCTCATGCCTGATCAGACT
GTTAAGAGGACTAATGTGCGTCAGCAGGATGGAGAAGATGTTCTTACGAAAGATGGTTTGTTTAATACATCAGCCAATGTTAGTGTGTCTCC
TTACTGA
>Solyc11g071810.1.1 evidence_code:10F0H1E1IEG genomic_reference:SL2.40ch11
gene_region:52249470-52255656 transcript_region:SL2.40ch11:52249470..52255656functional_description:"CRABS CLAW (Fragment) (AHRD V1 **-- Q5EMM7_GOSHI); contains Interpro
domain(s) IPR006780 YABBY protein "
ATGTCATTCGATATGACTTTTTCTTCTTCACCTTCCTCAGAACGCGTTTGTTACTTGCAATGTAATTTTTGCAACACCATTCTTGCGGTTAG
TGTTCCATGCAGCAACATGTTAACCTTAGTGACAGTAAGATGTGGGCATTGTGCAAATATGCTTTCTGTTAATATTGGATCTTTAATTCAAG
CTCTACCCCTTCAAGATGTTCAAAAGCTGCAAAGGCAACAGTACACAAATGTTGAAAATAATTCTAGTAATTATAAAGCTTATGGTTCATCA
TCATCATCCTCTTCAAAGTTCAACAGATATTCTTCCATTGTTTCTCCTCAAATTGAACCTAAAATCCCTTCGATTCGTCCACCAGAGAAAAG
ACAACGTGTTCCTTCTGCGTACAACCGATTCATCAAGGAAGAGATTCAAAGGATCAAGGCCAGTAATCCTGATATTAGCCATCGTGAAGCTT
TTAGCACTGCTGCCAAAAATTGGGCACATTTTCCACATATTCACTTTGGACTCAAGCTGGAGGGCAACAAATAG
>Solyc12g009580.1.1 evidence_code:10F0H1E0IEG genomic_reference:SL2.40ch12
gene_region:2837633-2843798 transcript_region:SL2.40ch12:2837633..2843798go_terms:GO:0005515,GO:0003700 functional_description:"CRABS CLAW (Fragment) (AHRD V1 **-Q5EMM7_GOSHI); contains Interpro domain(s) IPR006780 YABBY protein "
ATGTCATCAAGCTACATTGATTCTACTAATTTTGAGAAACTTTGCTATATCCCTTGCAATTTTTGCAATATTGTTCTTGTGGTGAGTGTTCC
ATGCAGCAACTTGCTTGATATAGTGACAGTTAGATGTGGACATTGCACAAATTTGTGGTCCGTTAATATGGCTGCTGCATTTCACACCAATT
CTTGGCAAAATCATCTTCATCATCAGGTAGGAAACTACACTAATTCTCCTCATGATCAATACAAGGTAGATTTTGCTTCATCATCCATCACA
AACAACTCTACTCTTGAGGAGAGGAACGTAAATCGACCTCCGGAAAAGAGGCAACGAGGACCTTCTGCTTATAATCAGTTTATAAAAGAGGA
GATTCAAAGGATCAAGGCTAATAATCCAGATATCACTCATAGGGAAGCATTTAGTACTGCTGCTAAAAATTGGGCACACTTCCCTCACATTC
AGTTTGGCCTCATGTTAGAGACTGACAATCAAGCTAAACTTGGTGCTAGTGAGAACAAAGAAAAGCTTATAATGCATAGAGCTGCATTGCCA
AAAATAAAGACCTTCACCTTCTAA
Part 2. The protein sequences of SlYABBYs
>Solyc01g010240.2.1 genomic_reference:SL2.40ch01 gene_region:5028897-5031428
transcript_region:SL2.40ch01:5028897..5031428+ go_terms:GO:0005515,GO:0003700
functional_description:"CRABS CLAW (Fragment) (AHRD V1 ***- Q5EMM8_GOSHI); contains Interpro
domain(s) IPR006780 YABBY protein "
MSSSSPNSSCLNLLESADHKINTMDPSEHLCYVRCSFCNTILAVGIPCKKLLDTVTVKCGHCGNLSFLSSRPPIQPQFFDHQPILQHQDFFN
NFKKGQSSSSSEPSSPKAPFVVKPPEKKHRLPSAYNRFMKDEIQRIKAAHPQIPHREAFSAAAKNVHSKYSKWDLG*
>Solyc01g091010.2.1 genomic_reference:SL2.40ch01 gene_region:76475369-76478983
transcript_region:SL2.40ch01:76475369..76478983- go_terms:GO:0005515,GO:0003700
functional_description:"YABBY-like transcription factor CRABS CLAW-like protein (AHRD V1 **-*
Q6SRZ7_ANTMA); contains Interpro domain(s) IPR006780 YABBY protein "
MSSSSAAFAPDHHLHHHHLSPPSGEQLCYVQCNFCDTVLAVSVPCSSFFKNVTVRCGHCTNLLSVNIILPTAANQLHLPHSFFSPHNLLDEI
RNNPPSLLMNQQINPNESLMPVRGGVDEIPKPPVANRPPEKRQRVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNWAHFPHIHFGLMP
DQPVKKPNACQQEGEDVLMKEGFLAPANIGVSPY*
>Solyc05g005240.1.1 evidence_code:10F0H1E0IEG genomic_reference:SL2.40ch05
gene_region:191257-193043 transcript_region:SL2.40ch05:191257..193043go_terms:GO:0005515,GO:0003700 functional_description:"YABBY-like transcription factor CRABS
CLAW-like protein (AHRD V1 **-* Q6SRZ7_ANTMA); contains Interpro domain(s) IPR006780 YABBY
protein "
MSTLNNHLFELQDTICYVQCGYCTTILLVSVPCSSLCNKVVTVRCGHCTTLLSLNLIKPSLHLFASFDQTHQPPEVDKDETDDANKKNSNSD
EEDQLENNVLPLNQVVNKPPEKRQRAPSAYNCFIKEEIKRLKTLYPNMTHKQAFSTAAKNWAHFPPSQHRGGCSLGERKMAKVSAARNSMVP
RDSNGLIP*
>Solyc05g012050.2.1 genomic_reference:SL2.40ch05 gene_region:5275528-5277367
transcript_region:SL2.40ch05:5275528..5277367- go_terms:GO:0003700
functional_description:"CRABS CLAW (Fragment) (AHRD V1 ***- Q5EMM8_GOSHI); contains Interpro
domain(s) IPR006780 YABBY protein "
MDYVQSSEHLCYVRCNFCNTVLAVGIPYKRLMDTVTVKCGHCSNLSFLTTRPPIQGQCFDHQPNIQGYCSELKNKGQASSSTSSTSSEPLSP
KAPFVVKPPEKKHRLPSAYNRFMKEEIQRIKSENPEIPHREAFSAAAKNWARYLPNPPNSGNTNNV*
>Solyc06g073920.2.1 genomic_reference:SL2.40ch06 gene_region:42038601-42044688
transcript_region:SL2.40ch06:42038601..42044688+ go_terms:GO:0003700
functional_description:"YABBY-like transcription factor CRABS CLAW-like protein (AHRD V1 **-*
Q6SRZ7_ANTMA); contains Interpro domain(s) IPR006780 YABBY protein "
MSLDMTYSSSSSERVCYVHCNFCSTILAVSVPCNSMMTIVTVRCGHCANLLSVNIAPSLQSLPIQDLQRQNESSIEDGMSRGYGSSSSSTNS
FHRFSPIPTDHDQPRSPPIRVPEKRQRVPSAYNRFIKEEIQRIKASNPDISHREAFSTAAKNWAHFPHIHFGLKLDGNKQTNKLDHAVAGEG
PQKTIGLY*
>Solyc07g008180.2.1 genomic_reference:SL2.40ch07 gene_region:2916878-2921216
transcript_region:SL2.40ch07:2916878..2921216+ go_terms:GO:0005515,GO:0003700
functional_description:"YABBY-like transcription factor CRABS CLAW-like protein (AHRD V1 **-*
Q6SRZ7_ANTMA); contains Interpro domain(s) IPR006780 YABBY protein "
MASCIDVASDQLCYIPCNFCNIVLAVSVPCSSLFDIVTVRCGHCTNLWSVNMAAAFQSSSSASWQNHQVPNYTAPEYRMDFGSSTKCNMNRM
SMRTPITNNVHEERIVNRPPEKRQRVPSAYNQFIKEEIQRIKANNPDISHREAFSTAAKNWAHFPHIHFGLMLESNNQAKLACGSRKL*
>Solyc08g079100.2.1 genomic_reference:SL2.40ch08 gene_region:59908783-59911941
transcript_region:SL2.40ch08:59908783..59911941- go_terms:GO:0005515,GO:0003700
functional_description:"CRABS CLAW (Fragment) (AHRD V1 **-- Q5EMM8_GOSHI); contains Interpro
domain(s) IPR006780 YABBY protein "
MSSSNSLSLDHLPPPPPSEQLCYVHCNVCDTVLAVSVPCTSLFKTVTVRCGHCTNLLPGWLLPSTNHHHHHFGHTYFSPSHNLLDEISNATP
NFLMNQSNSAHEFVQLPARPGFDDLPRPPPVVNRPPEKRQRVPSAYNRFIKEEIQRIKAGNPDISHREAFSAAAKNWAHFPHIQFGLMPDQT
VKRTNVRQQDGEDVLTKDGLFNTSANVSVSPY*
>Solyc11g071810.1.1 evidence_code:10F0H1E1IEG genomic_reference:SL2.40ch11
gene_region:52249470-52255656 transcript_region:SL2.40ch11:52249470..52255656functional_description:"CRABS CLAW (Fragment) (AHRD V1 **-- Q5EMM7_GOSHI); contains Interpro
domain(s) IPR006780 YABBY protein "
MSFDMTFSSSPSSERVCYLQCNFCNTILAVSVPCSNMLTLVTVRCGHCANMLSVNIGSLIQALPLQDVQKLQRQQYTNVENNSSNYKAYGSS
SSSSSKFNRYSSIVSPQIEPKIPSIRPPEKRQRVPSAYNRFIKEEIQRIKASNPDISHREAFSTAAKNWAHFPHIHFGLKLEGNK*
>Solyc12g009580.1.1 evidence_code:10F0H1E0IEG genomic_reference:SL2.40ch12
gene_region:2837633-2843798 transcript_region:SL2.40ch12:2837633..2843798go_terms:GO:0005515,GO:0003700 functional_description:"CRABS CLAW (Fragment) (AHRD V1 **-Q5EMM7_GOSHI); contains Interpro domain(s) IPR006780 YABBY protein "
MSSSYIDSTNFEKLCYIPCNFCNIVLVVSVPCSNLLDIVTVRCGHCTNLWSVNMAAAFHTNSWQNHLHHQVGNYTNSPHDQYKVDFASSSIT
NNSTLEERNVNRPPEKRQRGPSAYNQFIKEEIQRIKANNPDITHREAFSTAAKNWAHFPHIQFGLMLETDNQAKLGASENKEKLIMHRAALP
KIKTFTF*
Part 3. The protein sequences of AtYABBYs
>AT1G08465.1 | Symbols: YAB2 | Plant-specific transcription factor YABBY family protein |
chr1:2676033-2679382 FORWARD LENGTH=184
MSVDFSSERVCYVHCSFCTTILAVSVPYASLFTLVTVRCGHCTNLLSLNIGVSLHQTSAPPIHQDLQPHRQHTTSLVTRKDCASSSRSTNNL
SENIDREAPRMPPIRPPEKRQRVPSAYNRFIKEEIQRIKACNPEISHREAFSTAAKNWAHFPHIHFGLKLDGNKKGKQLDQSVAGQKSNGYY
>AT1G23420.1 | Symbols: INO | Plant-specific transcription factor YABBY family protein |
chr1:8317423-8319104 FORWARD LENGTH=231
MTKLPNMTTTLNHLFDLPGQICHVQCGFCTTILLVSVPFTSLSMVVTVRCGHCTSLLSVNLMKASFIPLHLLASLSHLDETGKEEVAATDGV
EEEAWKVNQEKENSPTTLVSSSDNEDEDVSRVYQVVNKPPEKRQRAPSAYNCFIKEEIRRLKAQNPSMAHKEAFSLAAKNWAHFPPAHNKRA
ASDQCFCEEDNNAILPCNVFEDHEESNNGFRERKAQRHSIWGKSPFE
>AT1G69180.1 | Symbols: CRC | Plant-specific transcription factor YABBY family protein |
chr1:26007734-26008940 REVERSE LENGTH=181
MNLEEKPTMTASRASPQAEHLYYVRCSICNTILAVGIPLKRMLDTVTVKCGHCGNLSFLTTTPPLQGHVSLTLQMQSFGGSDYKKGSSSSSS
SSTSSDQPPSPSPPFVVKPPEKKQRLPSAYNRFMRDEIQRIKSANPEIPHREAFSAAAKNWAKYIPNSPTSITSGGHNMIHGLGFGEKK
>AT2G26580.1 | Symbols: YAB5 | plant-specific transcription factor YABBY family protein |
chr2:11303923-11306739 REVERSE LENGTH=164
MANSVMATEQLCYIPCNFCNIILAVNVPCSSLFDIVTVRCGHCTNLWSVNMAAALQSLSRPNFQATNYAVPEYGSSSRSHTKIPSRISTRTI
TEQRIVNRPPEKRQRVPSAYNQFIKEEIQRIKANNPDISHREAFSTAAKNWAHFPHIHFGLMLESNKQAKIA
>AT2G45190.1 | Symbols: AFO, FIL, YAB1 | Plant-specific transcription factor YABBY family protein
| chr2:18628450-18630552 REVERSE LENGTH=229
MSMSSMSSPSSAVCSPDHFSPSDHLCYVQCNFCQTILAVNVPYTSLFKTVTVRCGCCTNLLSVNMRSYVLPASNQLQLQLGPHSYFNPQDIL
EELRDAPSNMNMMMMNQHPTMNDIPSFMDLHQQHEIPKAPPVNRPPEKRQRVPSAYNRFIKEEIQRIKAGNPDISHREAFSAAAKNWAHFPH
IHFGLVPDNQPVKKTNMPQQEGEDNMVMKEGFYAPAAANVGVTPY
>AT4G00180.1 | Symbols: YAB3 | Plant-specific transcription factor YABBY family protein |
chr4:72804-75089 REVERSE LENGTH=240
MSSMSMSSSSAPAFPPDHFSSTDQLCYVHCSFCDTVLAVSVPPSSLFKTVTVRCGHCSNLLSVTVSMRALLLPSVSNLGHSFLPPPPPPPPP
NLLEEMRSGGQNINMNMMMSHHASAHHPNEHLVMATRNGRSVDHLQEMPRPPPANRPPEKRQRVPSAYNRFIKEEIQRIKAGNPDISHREAF
SAAAKNWAHFPHIHFGLMADHPPTKKANVRQQEGEDGMMGREGFYGSAANVGVAHN
Part 4. The YABBY domain sequences of AtYABBYs and SlYABBYs
>AtYABBY1
PDHFSPSDHLCYVQCNFCQTILAVNVPYTSLFKTVTVRCGCCTNLLSVNMRSYVLPASNQLQLQLGPHSYFNPQDILEELRDAPSNMNMMMM
NQHPTMNDIPSFMDLHQQHEIPKAPPVNRPPEKRQRVPSAYNRFIKEEIQRIKAGNPDISHREAFSAAAKNWAHFPHIHFGL
>AtYABBY2
MSVDFSSERVCYVHCSFCTTILAVSVPYASLFTLVTVRCGHCTNLLSLNIGVSLHQTSAPPIHQDLQPHRQHTTSLVTRKDCASSSRSTNNL
SENIDREAPRMPPIRPPEKRQRVPSAYNRFIKEEIQRIKACNPEISHREAFSTAAKNWAHFPHIHFGL
>AtYABBY3
PDHFSSTDQLCYVHCSFCDTVLAVSVPPSSLFKTVTVRCGHCSNLLSVTVSMRALLLPSVSNLGHSFLPPPPPPPPPNLLEEMRSGGQNINM
NMMMSHHASAHHPNEHLVMATRNGRSVDHLQEMPRPPPANRPPEKRQRVPSAYNRFIKEEIQRIKAGNPDISHREAFSAAAKNWAHFPHIHF
GL
>AtYABBY5
ANSVMATEQLCYIPCNFCNIILAVNVPCSSLFDIVTVRCGHCTNLWSVNMAAALQSLSRPNFQATNYAVPEYGSSSRSHTKIPSRISTRTIT
EQRIVNRPPEKRQRVPSAYNQFIKEEIQRIKANNPDISHREAFSTAAKNWAHFPHIHFGL
>AtINO
NHLFDLPGQICHVQCGFCTTILLVSVPFTSLSMVVTVRCGHCTSLLSVNLMKASFIPLHLLASLSHLDETGKEEVAATDGVEEEAWKVNQEK
ENSPTTLVSSSDNEDEDVSRVYQVVNKPPEKRQRAPSAYNCFIKEEIRRLKAQNPSMAHKEAFSLAAKNWAHFPPAHNKR
>AtCRC
SRASPQAEHLYYVRCSICNTILAVGIPLKRMLDTVTVKCGHCGNLSFLTTTPPLQGHVSLTLQMQSFGGSDYKKGSSSSSSSSTSSDQPPSP
SPPFVVKPPEKKQRLPSAYNRFMRDEIQRIKSANPEIPHREAFSAAAKNWAKYIPNS
>SlFAS
FSSSPSSERVCYLQCNFCNTILAVSVPCSNMLTLVTVRCGHCANMLSVNIGSLIQALPLQDVQKLQRQQYTNVENNSSNYKAYGSSSSSSSK
FNRYSSIVSPQIEPKIPSIRPPEKRQRVPSAYNRFIKEEIQRIKASNPDISHREAFSTAAKNWAHFPHIHFGL
>SlYABBY2a
TYSSSSSERVCYVHCNFCSTILAVSVPCNSMMTIVTVRCGHCANLLSVNIAPSLQSLPIQDLQRQNESSIEDGMSRGYGSSSSSTNSFHRFS
PIPTDHDQPRSPPIRVPEKRQRVPSAYNRFIKEEIQRIKASNPDISHREAFSTAAKNWAHFPHIHFGL
>SlYABBY1a
HHHLSPPSGEQLCYVQCNFCDTVLAVSVPCSSFFKNVTVRCGHCTNLLSVNIILPTAANQLHLPHSFFSPHNLLDEIRNNPPSLLMNQQINP
NESLMPVRGGVDEIPKPPVANRPPEKRQRVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNWAHFPHIHFGL
>SlYABBY1b
PPPPSEQLCYVHCNVCDTVLAVSVPCTSLFKTVTVRCGHCTNLLPGWLLPSTNHHHHHFGHTYFSPSHNLLDEISNATPNFLMNQSNSAHEF
VQLPARPGFDDLPRPPPVVNRPPEKRQRVPSAYNRFIKEEIQRIKAGNPDISHREAFSAAAKNWAHFPHIQFGL
>SlYABBY5a
SCIDVASDQLCYIPCNFCNIVLAVSVPCSSLFDIVTVRCGHCTNLWSVNMAAAFQSSSSASWQNHQVPNYTAPEYRMDFGSSTKCNMNRMSM
RTPITNNVHEERIVNRPPEKRQRVPSAYNQFIKEEIQRIKANNPDISHREAFSTAAKNWAHFPHIHFGL
>SlYABBY5b
IDSTNFEKLCYIPCNFCNIVLVVSVPCSNLLDIVTVRCGHCTNLWSVNMAAAFHTNSWQNHLHHQVGNYTNSPHDQYKVDFASSSITNNSTL
EERNVNRPPEKRQRGPSAYNQFIKEEIQRIKANNPDITHREAFSTAAKNWAHFPHIQFGL
>SlCRCb
MDYVQSSEHLCYVRCNFCNTVLAVGIPYKRLMDTVTVKCGHCSNLSFLTTRPPIQGQCFDHQPNIQGYCSELKNKGQASSSTSSTSSEPLSP
KAPFVVKPPEKKHRLPSAYNRFMKEEIQRIKSENPEIPHREAFSAAAKNWARYLPNPP
>SlINO
NHLFELQDTICYVQCGYCTTILLVSVPCSSLCNKVVTVRCGHCTTLLSLNLIKPSLHLFASFDQTHQPPEVDKDETDDANKKNSNSDEEDQL
ENNVLPLNQVVNKPPEKRQRAPSAYNCFIKEEIKRLKTLYPNMTHKQAFSTAAKNWAHFPPSQHRG
>SlCRCa
INTMDPSEHLCYVRCSFCNTILAVGIPCKKLLDTVTVKCGHCGNLSFLSSRPPIQPQFFDHQPILQHQDFFNNFKKGQSSSSSEPSSPKAPF
VVKPPEKKHRLPSAYNRFMKDEIQRIKAAHPQIPHREAFSAAAKNVHSKY
Part 5. Alignment of amino acids in YABBY domains of AtYABBYs and SlYABBYs
AtINO
--NHLFDLPGQICHVQCGFCTTILLVSVPFTSLS-MVVTVRCGHCTSLLSVN------LM
SlINO
--NHLFELQDTICYVQCGYCTTILLVSVPCSSLCNKVVTVRCGHCTTLLSLN------LI
AtYABBY1
PDHFSP--SDHLCYVQCNFCQTILAVNVPYTSLF-KTVTVRCGCCTNLLSVN--MRSYVL
AtYABBY3
PDHFSS--TDQLCYVHCSFCDTVLAVSVPPSSLF-KTVTVRCGHCSNLLSVTVSMRALLL
SlYABBY1a
HHHLSPPSGEQLCYVQCNFCDTVLAVSVPCSSFF-KNVTVRCGHCTNLLSVN-----IIL
SlYABBY1b
----PPPPSEQLCYVHCNVCDTVLAVSVPCTSLF-KTVTVRCGHCTNLLPGW-----LLP
SlYABBY5a
-SCIDVAS-DQLCYIPCNFCNIVLAVSVPCSSLF-DIVTVRCGHCTNLWSVN--MAAAFQ
SlYABBY5b
---IDSTNFEKLCYIPCNFCNIVLVVSVPCSNLL-DIVTVRCGHCTNLWSVN--MAAAFH
AtYABBY5
--ANSVMATEQLCYIPCNFCNIILAVNVPCSSLF-DIVTVRCGHCTNLWSVN--MAAALQ
SlFAS
--FSSSPSSERVCYLQCNFCNTILAVSVPCSNML-TLVTVRCGHCANMLSVN--IGSLIQ
SlYABBY2a
--TYSSSSSERVCYVHCNFCSTILAVSVPCNSMM-TIVTVRCGHCANLLSVN--IAPSLQ
AtYABBY2
--MSVDFSSERVCYVHCSFCTTILAVSVPYASLF-TLVTVRCGHCTNLLSLN--IGVSLH
ADE77109
---DLGIGAGHLCYIQCNYCSTVLAVNVPGSSLL-EIVPVRCGHCTSLLSVN--MGGLFQ
SlCRCb
--MDYVQSSEHLCYVRCNFCNTVLAVGIPYKRLM-DTVTVKCGHCSNLSFLT--TRPPIQ
SlCRCa
--INTMDPSEHLCYVRCSFCNTILAVGIPCKKLL-DTVTVKCGHCGNLSFLS--SRPPIQ
AtCRC
--SRASPQAEHLYYVRCSICNTILAVGIPLKRML-DTVTVKCGHCGNLSFLT--TTPPLQ
AtINO
SlINO
AtYABBY1
AtYABBY3
SlYABBY1a
SlYABBY1b
SlYABBY5a
SlYABBY5b
AtYABBY5
SlFAS
SlYABBY2a
AtYABBY2
ADE77109
SlCRCb
SlCRCa
AtCRC
KASFIPLHLLASLSHLDETGKEEVAATDGVEE--EAWKVNQEKENSPTTLVSSSDNED-KPS---LHLFASFDQTHQPPEVDKDETD---------DANKKNSNS-----DEEDQLE-P-ASNQLQLQLGPHSYFNPQDILEELRDAPSNMNM-MMMNQHPTMNDIPSFMDLHQQH-PSVSNLGHSFLPPPPPPPPPNLLEEMRSGGQNINMNMMMSHHASAHHPNEHLVMATRNGR
P--TAANQLHLPHSFFSP-HNLLDEIRNNPP----SLLMNQQINPNE-SLMPVRGGVD-S--TNHHHHHFGHTYFSPSHNLLDEISNATP----NFLMNQSNSAHEFVQLPARPGFD-SSSSASWQNHQVPNYTAP--------EYRMD-----FGSSTKCNMNRMSMRTPITNN--TNSWQNHLHHQVGNYTNSP-----HDQYKVD-----FASSS------------ITNNS-SLSRP---NFQATNYAVP--------EYGSS-----SRSHTKIP-------SRISTRT-ALPLQDVQKLQRQQYTNVENNSSNYKAYGSS-----SSSSSKFNRYS-----SIVSPQ-SLPIQDLQ---RQNESSIEDGMS--RGYGSS-----SSSTNSFHRFS-----PIPTDH-QTSAPPIHQDLQPHRQHTTSLVTR-KDCASS-----SRSTNNLSEN---------IDR-SSTPQEVEQSFNENNYSPSCPSQENKSCSSS-----SPKSRENSVIS-----GAESET-GQCFDHQPNIQG--YCSELKNKGQASSSTSS------TSSEPLS---------------PQFFDHQPILQHQDFFNNFK-KGQSSS-----------SSEPSS---------------GHVSLTLQMQSFG--GSDYKKGSSSSSSSST------SSDQPPS----------------
AtINO
SlINO
AtYABBY1
AtYABBY3
SlYABBY1a
SlYABBY1b
SlYABBY5a
SlYABBY5b
AtYABBY5
SlFAS
SlYABBY2a
AtYABBY2
ADE77109
SlCRCb
SlCRCa
AtCRC
-----EDVSRVYQVVNKPPEKRQRAPSAYNCFIKEEIRRLKAQNPSMAHKEAFSLAAKN-----NNVLPLNQVVNKPPEKRQRAPSAYNCFIKEEIKRLKTLYPNMTHKQAFSTAAKN------EIPKAP-PVNRPPEKRQRVPSAYNRFIKEEIQRIKAGNPDISHREAFSAAAKNSVDHLQEMPRPP-PANRPPEKRQRVPSAYNRFIKEEIQRIKAGNPDISHREAFSAAAKN------EIPKPP-VANRPPEKRQRVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKN------DLPRPPPVVNRPPEKRQRVPSAYNRFIKEEIQRIKAGNPDISHREAFSAAAKN------VHEERI--VNRPPEKRQRVPSAYNQFIKEEIQRIKANNPDISHREAFSTAAKN------TLEERN--VNRPPEKRQRGPSAYNQFIKEEIQRIKANNPDITHREAFSTAAKN------ITEQRI--VNRPPEKRQRVPSAYNQFIKEEIQRIKANNPDISHREAFSTAAKN------IEPKIP--SIRPPEKRQRVPSAYNRFIKEEIQRIKASNPDISHREAFSTAAKN------DQPRSP--PIRVPEKRQRVPSAYNRFIKEEIQRIKASNPDISHREAFSTAAKN------EAPRMP--PIRPPEKRQRVPSAYNRFIKEEIQRIKACNPEISHREAFSTAAKN-----VKPISTGLTDCGTTEKRQRAPSAYNRFIRAEIQRIKAVNPEISHREAFSAAAKN--------PKAP-FVVKPPEKKHRLPSAYNRFMKEEIQRIKSENPEIPHREAFSAAAKN--------PKAP-FVVKPPEKKHRLPSAYNRFMKDEIQRIKAAHPQIPHREAFSAAAKNV
--------PSPP-FVVKPPEKKQRLPSAYNRFMRDEIQRIKSANPEIPHREAFSAAAKN-
AtINO
SlINO
AtYABBY1
AtYABBY3
SlYABBY1a
SlYABBY1b
SlYABBY5a
SlYABBY5b
AtYABBY5
WAHFPPAHNKR
WAHFPPSQHRG
WAHFPHIHFGL
WAHFPHIHFGL
WAHFPHIHFGL
WAHFPHIQFGL
WAHFPHIHFGL
WAHFPHIQFGL
WAHFPHIHFGL
SlFAS
SlYABBY2a
AtYABBY2
ADE77109
SlCRCb
SlCRCa
AtCRC
WAHFPHIHFGL
WAHFPHIHFGL
WAHFPHIHFGL
WAHLGLML--WARYLPNPP-HSKY------WAKYIPNS---
Part 6. The paralogs in SlYABBY family
One paralog
The other paralog
Smith-Waterman
score
Overlap
Name
Length (aa)
Name
Length (aa)
Z-score
Bits
E Value
Identity
Similar
(aa)
SlCRCa
168
SlCRCb
158
544
712.7
138.1
6.9E-34
75.9%
88.3%
137
SlYABBY1a
218
SlYABBY1b
216
740
887.1
171.2
1.3E-43
66.5%
82.1%
224
SlYABBY2a
192
SlFAS
177
672
849.4
163.8
1.7E-41
72.3%
90.4%
177
191
645
736.1
142.9
3.4E-35
69.9%
84.4%
186
(SlYABBY2b)
SlYABBY5a
180
SlYABBY5b
Part 7. The orthologs between AtYABYs and SlYABBYs
SlYABBYs
AtYABBYs
Smith-Waterman
score
Overlap
Name
Length (aa)
Name
Length (aa)
Z-score
Bits
E Value
Identity
Similar
(aa)
SlCRCa
168
AtCRC
181
497
577.4
113.3
2.4E-26
64%
79.5%
161
SlCRCb
158
AtCRC
181
543
633.1
123.5
1.9E-29
66.7%
84.3%
159
SlINO
192
AtINO
231
496
606.8
119.3
5.4E-28
52.1%
70.4%
213
SlYABBY1a
218
AtYAB1
229
725
734.6
143.1
4.2E-35
64.5%
81.6%
234
SlYABBY1a
218
AtYAB3
240
685
700.5
136.9
3.3E-33
61.1%
75.8%
244
SlYABBY1b
216
AtYAB1
229
640
640.1
125.6
7.6E-30
58.2%
79.3%
232
SlYABBY1b
216
AtYAB3
240
637
636.7
125.1
1.2E-29
55.8%
75.6%
242
SlYABBY2a
192
AtYAB2
184
605
687.8
134
1.7E-32
64.6%
79.3%
198
SlFAS
177
AtYAB2
184
538
681.1
132.6
4E-32
63.5%
80.7%
181
SlYABBY5a
180
AtYAB5
164
668
807.3
155.8
3.7E-39
76.4%
86.2%
174
SlYABBY5b
191
AtYAB5
164
570
730.9
141.8
6.7E-35
69%
86.7%
158
(SlYABBY2b)
Part 8. The expression pattern of YABBY genes in wild tomato LA1589.
1, Root; 2, Shoot; 3, Stem; 4, Young leaf; 5, Mature leaf; 6, FL-<10dba; 7, FL-10dba; 8, FL-5dba; 9, FL-2dba; 10,
FL-anthesis; 11, Ovary-anthesis; 12, FR-2dpa; 13, FR-5dpa; 14, FR-10dpa; 15, FR-mature green; 16 FR- mature red. FL,
Flower; FR, Fruit; dba, day before anthesis; dpa, day post anthesis.
Part 9. The RT-PCR primers
Gene Name
Foward-Primer
Reverse-Primer
Size (bp)
SlCRCa
GGAATACCATGCAAGAAGTTG
GTTCTCACTTCTCAGCCAAG
394
SlCRCb
GCAAGCTTCATCATCTACCT
GGTAAGACCCAAACACAAAC
351
SlFAS (SlYABBY2a)
CCTTACAATCCTTTTGCTTC
TGTACTGTTGCCTTTGCAG
384
SlINO
CTTCATCTCTTTGCTTCCTTC
GTTGCTATCTCTTGGGACCA
384
SlYABBY1a
CCTCACAATCTTCTGGATGA
CAGTAAGGAGATACACCAATG
404
SlYABBY1b
AGAGGACTAATGTGCGTCAG
GTAGTGCTAAAGCAAAAAGTG
309
SlYABBY2a
CCTAGCTACATAACATGATG
GAATGGGAGAAAATCTGTGA
405
SlYABBY5a
CACTTTGGACTCATGTTGGAG
GATCATGATGGAGAAACCTCT
337
SlYABBY5b
CTCCTCATGATCAATACAAG
TGTTCTCACTAGCACCAAGT
288
eIF4α
GCACAACAGATTGAGAAGGT
CAAGGTCTCGTAAAGATCACA
471
Part 10. Phylogenetic tree of the YABBY CDSs among Arabidopsis, cucumber, grape, poplar, potato, and
tomato. This tree is unrooted tree and is depicted by using the CDS of gene BT123811 in Picea sitchensis as an
outgroup. Low bootstrap support (<50%) was not reported. Colors show species. Black, poplar; blue, Arabidopsis;
green, cucumber; orange, potato; purple, grape; red, tomato.
Part 11. Ks value and estimated divergence time of YABBY2 subfamily genes. The lower numbers indicate Ks
value among CDS of the YABBY2 subfamily genes and the upper numbers indicate the estimated divergence time
(million years) among YABBY2 subfamily genes. The Ks values were calculated using K-estimator 6.0 with Kimura-2p
as the multiple hits correcting method (Comeron 1999). Divergence time were estimated based on formula T = Ks/2r
70.0
AtYABBY2
SlYABBY2a
SlFAS (SlYABBY2b)
Potri.016G067300.1
PGSC0003DMT400015197
PGSC0003DMT400007731
GSVIVT01037533001
GSVIVT01022586001
Csa007814
AtYABBY2
using the divergence rate r = 6.5 × 10-9 mutations per synonymous site per year (Gaut et al, 1996).
93.8
77.6
71.6
63.7
110.0
72.4
67.7
72.1
62.8
68.2
61.7
80.4
70.9
78.8
60.9
114.8
117.5
55.0
116.9
117.5
76.2
84.8
66.9
75.9
83.3
41.0
115.5
10.6
42.9
87.0
48.1
5.9
98.8
86.9
Csa007814
1.0008
GSVIVT01022586001
1.2199
0.9372
GSVIVT01037533001
1.0083
0.8162
0.7923
PGSC0003DMT400007731
0.9311
0.8864
1.4922
0.9900
PGSC0003DMT400015197
0.8287
0.8020
1.5270
1.1029
0.5324
Potri.016G067300.1
1.4298
1.0457
0.7150
0.8695
1.5013
1.1304
SlFAS (SlYABBY2b)
0.9414
0.9211
1.5197
0.9867
0.1374
0.6252
1.2842
SlYABBY2a
0.8795
1.0243
1.5275
1.0831
0.5582
0.0768
1.1303
50.7
0.6595
Part 12. Predicted CDSs matching between the segments of SL2.40ch06 and SL2.40ch11 containing
SlYABBY2a and FAS (SlYABBY2b) gene respectively. SL2.40ch06, 41879000..42121000; SL2.40ch11,
52133000..52357000. Dashed lines indicate significant homology matches between specific predicted CDSs. Numbers
indicate specific predicted CDSs shown in Part 13 and Part 14.
Part 13. The predicted genes in SL2.40ch06:41879001..42121000
No.
Gene Locus
Gene transcript region
Gene functional description
1
Solyc06g073730.1.1
SL2.40ch06:41879453..41881270-
Ethylene insensitive 3 class transcription factor
2
Solyc06g073740.2.1
SL2.40ch06:41894196..41899465+
Beta-D-glucosidase
3
Solyc06g073750.2.1
SL2.40ch06:41900636..41903467+
Beta-D-glucosidase
4
Solyc06g073760.2.1
SL2.40ch06:41905608..41910016+
Beta-D-glucosidase
5
Solyc06g073770.1.1
SL2.40ch06:41914409..41914882+
Unknown Protein
6
Solyc06g073780.2.1
SL2.40ch06:41916196..41935528-
Structural maintenance of chromosomes protein 3
7
Solyc06g073790.2.1
SL2.40ch06:41938647..41940686-
40S ribosomal protein S11
8
Solyc06g073800.2.1
SL2.40ch06:41942028..41944004-
40S ribosomal protein S11
9
Solyc06g073810.2.1
SL2.40ch06:41946839..41953093-
Cellular nucleic acid-binding protein
10
Solyc06g073820.1.1
SL2.40ch06:41957492..41975936+
Ubiquitin carboxyl-terminal hydrolase family protein expressed
11
Solyc06g073830.1.1
SL2.40ch06:41978680..41979234-
Calmodulin-like protein
12
Solyc06g073840.2.1
SL2.40ch06:41984106..41992683+
Peptidyl-prolyl cis-trans isomerase D
13
Solyc06g073850.1.1
SL2.40ch06:41993432..41993875-
Unknown Protein
14
Solyc06g073860.1.1
SL2.40ch06:41998917..42000551+
RING-H2 zinc finger protein (Fragment)
15
Solyc06g073870.2.1
SL2.40ch06:42002858..42005584-
DNA-directed RNA polymerase II subunit RPB4
16
Solyc06g073880.2.1
SL2.40ch06:42008183..42009623+
RING-H2 zinc finger protein (Fragment)
17
Solyc06g073890.2.1
SL2.40ch06:42009395..42009879+
Zinc finger RING-type
18
Solyc06g073900.2.1
SL2.40ch06:42011100..42014951-
Unknown Protein
19
Solyc06g073910.2.1
SL2.40ch06:42017256..42019960+
Strictosidine synthase
20
Solyc06g073920.2.1
SL2.40ch06:42038601..42044688+
SlYABBY2, YABBY-like transcription factor
21
Solyc06g073930.2.1
SL2.40ch06:42048669..42061206-
Ubiquitin carboxyl-terminal hydrolase
22
Solyc06g073940.2.1
SL2.40ch06:42068722..42070616-
Unknown Protein
23
Solyc06g073950.2.1
SL2.40ch06:42090222..42095898+
DnaJ homolog subfamily C member 8
24
Solyc06g073960.2.1
SL2.40ch06:42095905..42107056-
Serine/threonine-protein phosphatase
25
Solyc06g073970.1.1
SL2.40ch06:42111866..42112939-
AT5G22070 protein (Fragment)
26
Solyc06g073980.2.1
SL2.40ch06:42117163..42120125+
Unknown Protein
Part 14.The predicted genes in SL2.40ch11:52133001..52357000
No.
Gene Locus
Gene transcript region
Gene functional description
1
Solyc11g071630.1.1
SL2.40ch11:52133392..52134005 -
Sensor histidine kinase LuxQ
2
Solyc11g071640.1.1
SL2.40ch11:52141513..52144602+
Beta-D-glucosidase
3
Solyc11g071650.1.1
SL2.40ch11:52146575..52151986+
Beta-D-glucosidase
4
Solyc11g071660.1.1
SL2.40ch11:52154367..52155974-
NF-kappa-B-activating protein
5
Solyc11g071670.1.1
SL2.40ch11:52157728..52159230+
Pentatricopeptide repeat-containing protein
6
Solyc11g071680.1.1
SL2.40ch11:52162376..52174213-
Serine/threonine protein kinase
7
Solyc11g071690.1.1
SL2.40ch11:52176483..52180827-
Cellular nucleic acid binding protein
8
Solyc11g071700.1.1
SL2.40ch11:52183260..52203855+
Ubiquitin carboxyl-terminal hydrolase family protein expressed
9
Solyc11g071710.1.1
SL2.40ch11:52204800..52207250+
DnaJ-like zinc-finger protein
10
Solyc11g071720.1.1
SL2.40ch11:52207795..52209357+
Acetyl esterase
11
Solyc11g071730.1.1
SL2.40ch11:52210463..52220734+
Kinesin-like protein
12
Solyc11g071740.1.1
SL2.40ch11:52221262..52221867-
Calmodulin-like protein
13
Solyc11g071750.1.1
SL2.40ch11:52223163..52223513-
Calmodulin-like protein
14
Solyc11g071760.1.1
SL2.40ch11:52225377..52225973-
Calmodulin-like protein
15
Solyc11g071770.1.1
SL2.40ch11:52229263..52232337-
Elongation factor Tu family protein
16
Solyc11g071780.1.1
SL2.40ch11:52235043..52235549-
Unknown Protein
17
Solyc11g071790.1.1
SL2.40ch11:52237076..52240112-
Unknown Protein
18
Solyc11g071800.1.1
SL2.40ch11:52240857..52244873-
Strictosidine synthase family protein
19
Solyc11g071810.1.1
SL2.40ch11:52249470..52255656-
SlFAS, SLYABBY2b, CRABS CLAW (Fragment)
20
Solyc11g071820.1.1
SL2.40ch11:52259863..52264687+
Receptor-like kinase
21
Solyc11g071830.1.1
SL2.40ch11:52265280..52268287-
Chaperone protein dnaj
22
Solyc11g071840.1.1
SL2.40ch11:52274253..52280254+
Calmodulin binding protein
23
Solyc11g071850.1.1
SL2.40ch11:52283425..52284495+
AT5G22070 protein (Fragment)
24
Solyc11g071860.1.1
SL2.40ch11:52290338..52292029+
Unknown Protein
25
Solyc11g071870.1.1
SL2.40ch11:52295316..52297648+
Ubiquitin-conjugating enzyme
26
Solyc11g071880.1.1
SL2.40ch11:52298447..52301148+
Receptor like kinase, RLK
27
Solyc11g071890.1.1
SL2.40ch11:52301894..52310067-
Outer envelope membrane protein
28
Solyc11g071900.1.1
SL2.40ch11:52311532..52311945+
Self-incompatibility protein (Fragment)
29
Solyc11g071910.1.1
SL2.40ch11:52312893..52321825+
GTP-binding family protein
30
Solyc11g071920.1.1
SL2.40ch11:52324269..52333682+
Serine/threonine-protein phosphatase
31
Solyc11g071930.1.1
SL2.40ch11:52334894..52341200-
DnaJ homolog subfamily C member 8
32
Solyc11g071940.1.1
SL2.40ch11:52348262..52349008+
Unknown Protein
33
Solyc11g071950.1.1
SL2.40ch11:52350625..52356685+
Unknown Protein
Part 15. Dot plot of two DNA sequences, SL2.40ch06:41879001..42121000 containing SlYABBY2a and
SL2.40ch11: 52133001..52357000 containing SlYABBY2b. Dot plot made by Advanced PipMaker (Schwartz et al.
2000).
Part 16. Dot plot of two DNA sequences, tomato SL2.40ch06:41879001..42121000 containing SlYABBY2a and
Potato PGSC0003DMS000002348:230001..522000. Dot plot made by Advanced PipMaker (Schwartz et al.
2000).
Part 17. Dot plot of two DNA sequences, tomato SL2.40ch11:52133001..52357000 containing SlYABBY2b and
Potato PGSC0003DMS000000867:200001..503000. Dot plot made by Advanced PipMaker (Schwartz et al.
2000).
References
Comeron JM (1999) K-Estimator: calculation of the number of nucleotide substitutions per site and the confidence
intervals. Bioinformatics 15 (9):763-764
Gaut BS, Morton BR, McCaig BC, Clegg MT (1996) Substitution rate comparisons between grasses and palms:
Synonymous rate differences at the nuclear gene Adh parallel rate differences at the plastid gene rbcL. P Natl
Acad Sci USA 93 (19):10274-10279
Schwartz S, Zhang Z, Frazer KA, Smit A, Riemer C, Bouck J, Gibbs R, Hardison R, Miller W (2000) PipMaker--a web
server for aligning two genomic DNA sequences. Genome Res 10 (4):577-586