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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...taacacttttctttggcaatggaaatgtattaagatatagctgtgacatgctgatttgcctttgaattatggctaaaataactcatcaataccctgacagGTTTTGGATATGATTAACAACCCACACTATCTGTATCGGATGACCATCCTCCATGCAATTTCTCTCCTTGCCCCTGTTATGGGCCCAGAAATTACATGCT

Basic information

species Vitis vinifera
transcript Vv17s0000g03870.t01
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv17s0000g03870.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GRMZM2G102858_T01 (Zea mays), 3'ss of exon 10
--taacacttttctttggcaatggaaatgtattaagatatagctgtgacat-gctgatttgcctttgaattatgg--ctaaaataactcatcaataccctgacagGTTTTGGATATGATTAACAACCCACACTATCTGTATCGGATGACCATCCTCCATGCAATTTCTCTCCTTGCCCCTGTTATGGGCCCAGAAATTACATGCT
  |||      | || |  |||  || |   | | | |  |    | | ||       |||  |   |||  |     |   | | ||| |  |||  ||   |||||||||| | ||| ||||||||||| |||||||||||||||||||   | || || |||||| | || || ||||| ||||| || || || |||||| 
ggtaaagagggtattgg--aataaaatttactcatggttaattaattatatcaacagattgattgaaaatctttatattgtcaaatctcttttatattct---agGTTTTGGAGAAGATAAACAACCCACATTATCTGTATCGGATGACCACTTTGCAAGCTATTTCTTTGCTAGCTCCTGTCATGGGTCCTGATATCACATGCC

upper sequence: Vv17s0000g03870.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GLYMA07G10000.1 (Glycine max), 3'ss of exon 9
-taacacttttctttggcaatggaaatgtattaagatatagctgtgacatgctgatttgcctttgaattatggctaaaataactcatcaataccctgacagGTTTTGGATATGATTAACAACCCACACTATCTGTATCGGATGACCATCCTCCATGCAATTTCTCTCCTTGCCCCTGTTATGGGCCCAGAAATTACATGCT
 | | | | |    ||     |||     ||  |      |   | | |||||         || | |  |     ||| || |  |  || |  || ||||||||||| ||| |||   | ||||| ||||||||||||||||| ||| | || ||||||||||| || || |||||| ||||| | || ||||| |  |
atgaaattatatgatgatccaggaggaccatggattccatgaaattatatgctctcaaagtatttactatttatctaaacaagtattgtatcctttg-cagGTTTTGGACATGGTTACTGATCCACATTATCTGTATCGGATGACAATCTTACAAGCAATTTCTCTACTAGCTCCTGTTCTGGGCTCGGAGATTACTTCTT
















Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|349825185|gb|FQ415732.1|FQ415732
EST:     TTGCAGAGGAATTTGGCCCAGATTGGGCAATGCAGCACATAATTCCACAG                         GTTTTGGATATGATTAACAATCCACACTATCTGCATCGGATGACCATCCTC
genomic: TTGCAGAGGAATTTGGCCCAGATTGGGCAATGCAGCACATAATTCCACAGgtctttctga ... accctgacagGTTTTGGATATGATTAACAACCCACACTATCTGTATCGGATGACCATCCTC
EST: gi|352769560|gb|FQ468488.1|FQ468488
EST:     TTGCAGAGGAATTTGGCCCAGATTGGGCAATGCAGCACATAATTCCACAG                         GTTTTGGATATGATTAACAACCCACACTATCTGTATCGGATGACCATCCTC
genomic: TTGCAGAGGAATTTGGCCCAGATTGGGCAATGCAGCACATAATTCCACAGgtctttctga ... accctgacagGTTTTGGATATGATTAACAACCCACACTATCTGTATCGGATGACCATCCTC
EST: gi|352776768|gb|FQ472655.1|FQ472655
EST:     TTGCAGAGGAATTTGGCCCAGATTGGGCAATGCAGCACATAATTCCACAG                         GTTTTGGATATGATTAACAACCCACACTATCTGTATCGGATGACCATCCTC
genomic: TTGCAGAGGAATTTGGCCCAGATTGGGCAATGCAGCACATAATTCCACAGgtctttctga ... accctgacagGTTTTGGATATGATTAACAACCCACACTATCTGTATCGGATGACCATCCTC
EST: gi|27584295|gb|CB006990.1|CB006990
EST:     CATAATTCCACAG                         GTTTTGGATATGATTAACAACCCACACTATCTGTATCGGATGACCATCCTC
genomic: CATAATTCCACAGgtctttctga ... accctgacagGTTTTGGATATGATTAACAACCCACACTATCTGTATCGGATGACCATCCTC
EST: gi|352763870|gb|FQ465320.1|FQ465320
EST:     GCAGCACATAATTCCACAG                         GTTTTGGATATGATTAACAACCCACACTATCTGTATGGGATGACCATCCTC
genomic: GCAGCACATAATTCCACAGgtctttctga ... accctgacagGTTTTGGATATGATTAACAACCCACACTATCTGTATCGGATGACCATCCTC
EST: gi|110414406|gb|EC980237.1|EC980237
EST:     TTGCAGAGGAATTTGGCCCAGATTGGGCAATGCAGCACATAATTCCACAG                         GTTTTGGATATGATTAACAACCCACACTATCTGTATCGGATGACCATCCTC
genomic: TTGCAGAGGAATTTGGCCCAGATTGGGCAATGCAGCACATAATTCCACAGgtctttctga ... accctgacagGTTTTGGATATGATTAACAACCCACACTATCTGTATCGGATGACCATCCTC
EST: gi|30134721|gb|CB920059.1|CB920059
EST:     TTGCAGAGGAATTTGGCCCAGATTGGGCAATGCAGCACATAATTCCACAG                         GTTTTGGATATGATTAACAACCCACACTATCTGTATCGGATGACCATCCTC
genomic: TTGCAGAGGAATTTGGCCCAGATTGGGCAATGCAGCACATAATTCCACAGgtctttctga ... accctgacagGTTTTGGATATGATTAACAACCCACACTATCTGTATCGGATGACCATCCTC
EST: gi|352787200|gb|FQ477820.1|FQ477820
EST:     TTGCAGAGGAATTTGGCCCAGATTGGGCAATGCAGCACATAATTCCACAG                         GTTTTGGATATGATTAACAATCCACACTATCTGTATCGGATGACCATCCTC
genomic: TTGCAGAGGAATTTGGCCCAGATTGGGCAATGCAGCACATAATTCCACAGgtctttctga ... accctgacagGTTTTGGATATGATTAACAACCCACACTATCTGTATCGGATGACCATCCTC
EST: gi|22012824|gb|BQ797858.1|BQ797858
EST:     TTGCAGAGGAATTTGGCCCAGATTGGGCAATGCAGCACATAATTCCACAG                         GTTTTGGATATGATTAACAACCCACACTATCTGTATCGGATGACCATCCTC
genomic: TTGCAGAGGAATTTGGCCCAGATTGGGCAATGCAGCACATAATTCCACAGgtctttctga ... accctgacagGTTTTGGATATGATTAACAACCCACACTATCTGTATCGGATGACCATCCTC
EST: gi|33404973|gb|CF210600.1|CF210600
EST:     TTGCAGAGGAATTTGGCCCAGATTGGGCAATGCAGCACATAATTCCACAG                         GTTTTGGATATGATTAACAACCCACACTATCTGTATCGGATGACCATCCTC
genomic: TTGCAGAGGAATTTGGCCCAGATTGGGCAATGCAGCACATAATTCCACAGgtctttctga ... accctgacagGTTTTGGATATGATTAACAACCCACACTATCTGTATCGGATGACCATCCTC
EST: gi|110691608|gb|EE069902.1|EE069902
EST:     TTGCAGAGGAATTTGGCCCAGATTGGGCAATGCAGCACATAATTCCACAG                         GTTTTGGATATGATTAACAACCCACACTATCTGTATCGGATGACCATCCTC
genomic: TTGCAGAGGAATTTGGCCCAGATTGGGCAATGCAGCACATAATTCCACAGgtctttctga ... accctgacagGTTTTGGATATGATTAACAACCCACACTATCTGTATCGGATGACCATCCTC
EST: gi|110399866|gb|EC966397.1|EC966397
EST:     TTGCAGAGGAATTTGGCCCAGATTGGGCAATGCAGCACATAATTCCACAG                         GTTTTGGATATGATTAACAACCCACACTATCTGTATCGGATGACCATCCTC
genomic: TTGCAGAGGAATTTGGCCCAGATTGGGCAATGCAGCACATAATTCCACAGgtctttctga ... accctgacagGTTTTGGATATGATTAACAACCCACACTATCTGTATCGGATGACCATCCTC
EST: gi|33405058|gb|CF210685.1|CF210685
EST:     TTGCAGAGGAATTTGGCCCAGATTGGGCAATGCAGCACATAATTCCACAG                         ATCTTGGATATGATTAACAACCCACACTATCTGTATCGGATGACCATCCTC
genomic: TTGCAGAGGAATTTGGCCCAGATTGGGCAATGCAGCACATAATTCCACAGgtctttctga ... accctgacagGTTTTGGATATGATTAACAACCCACACTATCTGTATCGGATGACCATCCTC
EST: gi|110429193|gb|EC995682.1|EC995682
EST:     TTGCAGAGGAATTTGGCCCAGATTGGGCAATGCAGCACATAATTCCACAG                         GTTTTGGATATGATTAACAACCCACACTATCTGTATCGGATGACCATCCTC
genomic: TTGCAGAGGAATTTGGCCCAGATTGGGCAATGCAGCACATAATTCCACAGgtctttctga ... accctgacagGTTTTGGATATGATTAACAACCCACACTATCTGTATCGGATGACCATCCTC
EST: gi|22012767|gb|BQ797801.1|BQ797801
EST:     TTGCAGAGGAATTTGGCCCAGATTGGGCAATGCAGCACATAATTCCACAG                         GTTTTGGATATGATTAACAACCCACACTATCTGTATCGGATGACCATCCTC
genomic: TTGCAGAGGAATTTGGCCCAGATTGGGCAATGCAGCACATAATTCCACAGgtctttctga ... accctgacagGTTTTGGATATGATTAACAACCCACACTATCTGTATCGGATGACCATCCTC
EST: gi|110697249|gb|EE074074.1|EE074074
EST:     TTGCAGAGGAATTTGGCCCAGATTGGGCAATGCAGCACATAATTCCACAG                         GTTTTGGATATGATTAACAACCCACACTATCTGTATCGGATGACCATCCTC
genomic: TTGCAGAGGAATTTGGCCCAGATTGGGCAATGCAGCACATAATTCCACAGgtctttctga ... accctgacagGTTTTGGATATGATTAACAACCCACACTATCTGTATCGGATGACCATCCTC
EST: gi|351031302|gb|FQ445327.1|FQ445327
EST:     TTGCAGAGGAATTTGGCCCAGATTGGGCAATGCAGCACATAATTCCACAG                         GTTTTGGATATGATTAACAATCCACACTATCTGTATCGGATGACCATCCTC
genomic: TTGCAGAGGAATTTGGCCCAGATTGGGCAATGCAGCACATAATTCCACAGgtctttctga ... accctgacagGTTTTGGATATGATTAACAACCCACACTATCTGTATCGGATGACCATCCTC
EST: gi|71866595|gb|DT015650.1|DT015650
EST:     TTGCAGAGGAATTTGGCCCAGATTGGGCAATGCAGCACATAATTCCACAG                         GTTTTGGATATGATTAACAACCCACACTATCTGTATCGGAT
genomic: TTGCAGAGGAATTTGGCCCAGATTGGGCAATGCAGCACATAATTCCACAGgtctttctga ... accctgacagGTTTTGGATATGATTAACAACCCACACTATCTGTATCGGAT
EST: gi|110428387|gb|EC994857.1|EC994857
EST:     TTGCAGAGGAATTTGGCCCAGATTGGGCAATGCAGCACATAATTCCACAG                         GTTTTGGATATGATTAACAACCCACACTATCTGTATCGGATGACCATCCTC
genomic: TTGCAGAGGAATTTGGCCCAGATTGGGCAATGCAGCACATAATTCCACAGgtctttctga ... accctgacagGTTTTGGATATGATTAACAACCCACACTATCTGTATCGGATGACCATCCTC
EST: gi|30300336|gb|CB977130.1|CB977130
EST:     TTGCAGAGGAATTTGGCCCAGATTGGGCAATGCAGCACATAATTCCACAG                         GTTTTGGATATGATTAACAACCCACACTATCTGTATCGGATGACCATCCTC
genomic: TTGCAGAGGAATTTGGCCCAGATTGGGCAATGCAGCACATAATTCCACAGgtctttctga ... accctgacagGTTTTGGATATGATTAACAACCCACACTATCTGTATCGGATGACCATCCTC
EST: gi|110388878|gb|EC953676.1|EC953676
EST:     TTGCAGAGGAATTTGGCCCAGATTGGGCAATGCAGCACATAATTCCACAG                         GTTTTGGATATGATTAACAACCCACACTATCTGTATCGGATGACCATCCTC
genomic: TTGCAGAGGAATTTGGCCCAGATTGGGCAATGCAGCACATAATTCCACAGgtctttctga ... accctgacagGTTTTGGATATGATTAACAACCCACACTATCTGTATCGGATGACCATCCTC
EST: gi|110411876|gb|EC977604.1|EC977604
EST:     TTGCAGAGGAATTTGGCCCAGATTGGGCAATGCAGCACATAATTCCACAG                         GTTTTGGATATGATTAACAACCCACACTATCTGTATCGGATGACCATCCTC
genomic: TTGCAGAGGAATTTGGCCCAGATTGGGCAATGCAGCACATAATTCCACAGgtctttctga ... accctgacagGTTTTGGATATGATTAACAACCCACACTATCTGTATCGGATGACCATCCTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acatgctgatttgcctttgaattatggctaaaataactcatcaataccctgacagGTTTTGGATATGATTAACAACCCACACTATCTGTATCGGATGACCATCCTCCATGCAATTTCTCTCCTTGCCCCTGTTATGGGCCCAGAAATTACATGCT
                              aaataac  putative branch site (score: 2)
               tttgaattat  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
taacacttttctttggcaatggaaatgtattaagatatagctgtgacatgctgatttgcctttgaattatggctaaaataactcatcaataccctgacagGTTTTGGATATGATTAACAACCCACACTATCTGTATCGGATGACCATCCTCCATGCAATTTCTCTCCTTGCCCCTGTTATGGGCCCAGAAATTACATGCT

- - - - - - - - -aatggaa
- - - - - - - - - - - - - - - - - - - - - - -acatgct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tatggct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaataa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctcatca