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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgatctagtttttgtagtctagtattataggaatatctaattcatttcacttattctggatgctgagtttatcatctggtgtttggttttgacaaacagATAATACCCGACAAGTGTAGATATGAAGTATTGTCAACCAAAATTGAAATCCGACTTGCAAAAGCTGAAGAAATTCATTGGACTTCTCTTGAATTCAGCA

Basic information

species Vitis vinifera
transcript Vv16s0050g01510.t01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv16s0050g01510.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA09G23980.1 (Glycine max), 3'ss of exon 6
---ttgatctagtttttgtagtctagtattataggaatatctaattcatttcacttattctggatgctgagtttatcat-ctggtgtttggttttgacaaacagATAATACCCGACAAGTGTAGATATGAAGTATTGTCAACCAAAATTGAAATCCGACTTGCAAAAGCTGAAGAAATTCATTGGACTTCTCTTGAATTCAGCA
   || | ||  | | | | || ||   |  |||   |   |   | |||    |  ||||| ||   | || |||  |  || | |||||||||   |||||||| |||||   ||| |||  ||||||||| ||||| |||||||||||||| || ||||||||||| |||   ||||| ||||| ||||| ||||||| ||
atgttaaactcctctatatggttta---tcttagtgtttgttttgttattctgttacttctgtatag-gtgtatattgtgttgatctttggttttcttaaacagATCATACCTTCCAATTGTCAATATGAAGTTTTGTCCACCAAAATTGAAATTCGTCTTGCAAAAGCAGAACCTATTCACTGGACATCTCTAGAATTCACCA

upper sequence: Vv16s0050g01510.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA16G29450.2 (Glycine max), 3'ss of exon 6
--ttgatctagtttttgtagtctagtattataggaatatctaattcatttcacttattctggatgctgagtttatcat-ctggtgtttggttttga-caaacagATAATACCCGACAAGTGTAGATATGAAGTATTGTCAACCAAAATTGAAATCCGACTTGCAAAAGCTGAAGAAATTCATTGGACTTCTCTTGAATTCAGCA
  || | ||  ||| | | || ||   |  |||   |   |   | |||    |  ||||| |||  | || |||  |  || | |||||||||   |||||||||  ||||   ||| ||  |||||||||| ||||| |||||||||||||| || ||||| ||||| |||   ||||| ||||| ||||| ||||||| ||
atttaaactcctttatatggttta---tcttagtgtttgttttgttattctgttacttctgtatga-gtgtatattgtgttgatctttggttttcttcaaacagATTGTACCTTCCAATTGCCGATATGAAGTTTTGTCCACCAAAATTGAAATTCGCCTTGCGAAAGCAGAACCTATTCACTGGACATCTCTAGAATTCACCA
















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|110712988|gb|EE088514.1|EE088514
EST:     TGTTCCTGGTGATGTTGCATATCATTTTCAAC-TCGCTTATTTGGNAAAG                         ATAATACC-GACAAGTGTAGATATGAAGTATTGGTCA-CCAAA-TTGAAA
genomic: TGTTCCTGGTGATGTTGCATATCATTTTCAACCTCGCTTATTTGG-AAAGgtaaggctca ... tgacaaacagATAATACCCGACAAGTGTAGATATGAAGTATTG-TCAACCAAAATTGAAA
EST: gi|71859342|gb|DT008397.1|DT008397
EST:     ATGTTCCTGGTGATGTTGCATATCATTTTCAACCTCGCTTATTTGGAAAG                         ATAATACCCGACAAGTGTAGATATGAAGTATTGTCAACCAAAATTGAAATC
genomic: ATGTTCCTGGTGATGTTGCATATCATTTTCAACCTCGCTTATTTGGAAAGgtaaggctca ... tgacaaacagATAATACCCGACAAGTGTAGATATGAAGTATTGTCAACCAAAATTGAAATC
EST: gi|29782866|gb|CB348559.2|CB348559
EST:     ATGTTCCTGGTGATGTTGCATATCATTTTCAACCTCGCTTATTTGGAAAG                         ATAATACCCGACAAGTGTAGATATGAAGTATTGTCAACCAAAATTGAAATC
genomic: ATGTTCCTGGTGATGTTGCATATCATTTTCAACCTCGCTTATTTGGAAAGgtaaggctca ... tgacaaacagATAATACCCGACAAGTGTAGATATGAAGTATTGTCAACCAAAATTGAAATC
EST: gi|29783203|gb|CB349232.2|CB349232
EST:     ATGTTCCTGGTGATGTTGCATATCATTTTCAACCTCGCTTATTTGGAAAG                         ATAATACCCGACAAGTGTAGATATGAAGTATTGTCAACCAAAATTGAAATC
genomic: ATGTTCCTGGTGATGTTGCATATCATTTTCAACCTCGCTTATTTGGAAAGgtaaggctca ... tgacaaacagATAATACCCGACAAGTGTAGATATGAAGTATTGTCAACCAAAATTGAAATC
EST: gi|110694395|gb|EE071465.1|EE071465
EST:     ATGTTCCTGGTGATGTTGCATATCATTTTCAACCTCGCTTATTTGGAAAG                         A-AATACCCGACAAGTGTAGATATGAAGTATTGTTCA-CCAAA-TTGAAAT
genomic: ATGTTCCTGGTGATGTTGCATATCATTTTCAACCTCGCTTATTTGGAAAGgtaaggctca ... tgacaaacagATAATACCCGACAAGTGTAGATATGAAGTATTGT-CAACCAAAATTGAAAT
EST: gi|110421576|gb|EC987874.1|EC987874
EST:     ATGTTCCTGGTGATGTTGCATATCATTTTCAACCTCGCTTATTTGGAAAG                         ATAATACCCGACAAGTGTAGATATGAAGTATTGTCAACCAAAATTGAAATC
genomic: ATGTTCCTGGTGATGTTGCATATCATTTTCAACCTCGCTTATTTGGAAAGgtaaggctca ... tgacaaacagATAATACCCGACAAGTGTAGATATGAAGTATTGTCAACCAAAATTGAAATC
EST: gi|110686508|gb|EE064228.1|EE064228
EST:     ATGTTCCTGGTGATGTTGCATATCATTTTCAACCTCGCTTATTTGGAAAG                         ATAATACCCGACAAGTGTAGATATGAAGTATTGTCAACCAAAATTGAAATC
genomic: ATGTTCCTGGTGATGTTGCATATCATTTTCAACCTCGCTTATTTGGAAAGgtaaggctca ... tgacaaacagATAATACCCGACAAGTGTAGATATGAAGTATTGTCAACCAAAATTGAAATC
EST: gi|32271506|gb|CD720665.1|CD720665
EST:     ATGTTCCTGGTGATGTTGCATACCATTTTCAACCTCGCTTATTTGGAAAG                         ATAATACCCGACAAGTGTAGATATGAAGTATTGTCAACCAAAATTGAAATC
genomic: ATGTTCCTGGTGATGTTGCATATCATTTTCAACCTCGCTTATTTGGAAAGgtaaggctca ... tgacaaacagATAATACCCGACAAGTGTAGATATGAAGTATTGTCAACCAAAATTGAAATC
EST: gi|46917631|gb|CN546960.1|CN546960
EST:     ATGTTCCTGGTGATGTTGCATATCATTTTCAACCTCGCTTATTTGGAAAG                         ATAATACCCGACAAGTGTAGATATGAAGTATTGTCAACCAAAATTGAAATC
genomic: ATGTTCCTGGTGATGTTGCATATCATTTTCAACCTCGCTTATTTGGAAAGgtaaggctca ... tgacaaacagATAATACCCGACAAGTGTAGATATGAAGTATTGTCAACCAAAATTGAAATC
EST: gi|110729024|gb|EE105164.1|EE105164
EST:     ATGTTCCTGGTGATGTTGCATATCATTTTCAACCTCGCTTATTTGGAAAG                         ATAATACCCGACNAGTGTAGATATGAAGTATTGTCACCCAAAATTGAA-TC
genomic: ATGTTCCTGGTGATGTTGCATATCATTTTCAACCTCGCTTATTTGGAAAGgtaaggctca ... tgacaaacagATAATACCCGACAAGTGTAGATATGAAGTATTGTCAACCAAAATTGAAATC
EST: gi|28969441|gb|CB348474.1|CB348474
EST:     ATGTTCCTGGTGATGTTGCATATCATTTTCAACCTCGCTTATTTGGAAAG                         ATAATACCCGACAAGTGTAGATATGAAGTATTGTCAACCAAAATTGAAATC
genomic: ATGTTCCTGGTGATGTTGCATATCATTTTCAACCTCGCTTATTTGGAAAGgtaaggctca ... tgacaaacagATAATACCCGACAAGTGTAGATATGAAGTATTGTCAACCAAAATTGAAATC
EST: gi|110364112|gb|EC927758.1|EC927758
EST:     ATGTTCCTGGTGATGTTGCATATCATTTTCAACCTCGCTTATTTGGAAAG                         ATAATACCCGACAAGTGTAGATATGAAGTATTGTCAACCAAAATTGAAATC
genomic: ATGTTCCTGGTGATGTTGCATATCATTTTCAACCTCGCTTATTTGGAAAGgtaaggctca ... tgacaaacagATAATACCCGACAAGTGTAGATATGAAGTATTGTCAACCAAAATTGAAATC
EST: gi|77581747|gb|DV219826.1|DV219826
EST:     ATGTTCCTGGTGATGTTGCATATCATTTTCAACCTCGCTTATTTGGAAAG                         ATAATACCCGACAAGTGTAGATATGAAGTATTGTCAACCAAAATTGAAATC
genomic: ATGTTCCTGGTGATGTTGCATATCATTTTCAACCTCGCTTATTTGGAAAGgtaaggctca ... tgacaaacagATAATACCCGACAAGTGTAGATATGAAGTATTGTCAACCAAAATTGAAATC
EST: gi|110687406|gb|EE064790.1|EE064790
EST:     ATGTTCCTGGTGATGTTGCATATCATTTTCAACCTCGCTTATTTGGAAAG                         ATAATACCCGACAAGTGTAGAT
genomic: ATGTTCCTGGTGATGTTGCATATCATTTTCAACCTCGCTTATTTGGAAAGgtaaggctca ... tgacaaacagATAATACCCGACAAGTGTAGAT
EST: gi|110693950|gb|EE070628.1|EE070628
EST:     ATGTTCCTGGTGATGTTGCATATCATTTTCAACCTCGCTTATTTGGAAAG                         ATA-TACCCGACAAGTGTAGATATGAAGTATTGTCAACCAAAATTTGAA-T
genomic: ATGTTCCTGGTGATGTTGCATATCATTTTCAACCTCGCTTATTTGGAAAGgtaaggctca ... tgacaaacagATAATACCCGACAAGTGTAGATATGAAGTATTGTCAACCAAAATT-GAAAT
EST: gi|110711614|gb|EE088295.1|EE088295
EST:     TGTTCCTGGTGATGTTGCATATCATTTTCAACCTCGCTTATTTGGAAAAG                         ATA-TACC-GACNAGTGTAGA
genomic: TGTTCCTGGTGATGTTGCATATCATTTTCAACCTCGCTTATTTGGAAA-Ggtaaggctca ... tgacaaacagATAATACCCGACAAGTGTAGA
EST: gi|32249238|gb|CD715057.1|CD715057
EST:     ATGTTCCTGGTGATGTTGCATACCATTTTCAACCTCGCTTATTTGGAAAG                         ATAATACCCGACAAGTGTAGATATGAAGTATTGTCAACCAAAATTGAAATC
genomic: ATGTTCCTGGTGATGTTGCATATCATTTTCAACCTCGCTTATTTGGAAAGgtaaggctca ... tgacaaacagATAATACCCGACAAGTGTAGATATGAAGTATTGTCAACCAAAATTGAAATC
EST: gi|110732977|gb|EE108734.1|EE108734
EST:     TGTTTCTGGTGATNGT-GCATATCATTTTCAACCTCGCTTATTTGGAAAG                         A-AATACCCCGACA-GTGTAGATATGAAGTATTGTCAACCAAAATTGAAAT
genomic: TGTTCCTGGTGAT-GTTGCATATCATTTTCAACCTCGCTTATTTGGAAAGgtaaggctca ... tgacaaacagATAATACCC-GACAAGTGTAGATATGAAGTATTGTCAACCAAAATTGAAAT
EST: gi|110723197|gb|EE100235.1|EE100235
EST:     ATGTTCCTGGTGATGTTGCATATCATTTTCAACCTCGCTTATTTGGAAAG                         ATA-TACCCGACNAGTGTAGATATGAAGTATTGTCAAC
genomic: ATGTTCCTGGTGATGTTGCATATCATTTTCAACCTCGCTTATTTGGAAAGgtaaggctca ... tgacaaacagATAATACCCGACAAGTGTAGATATGAAGTATTGTCAAC
EST: gi|161718657|gb|FC067946.1|FC067946
EST:     ATGTTCCTGGTGATGTTGCATATCATTTTCAACCTCGCTTATTTGGAAAG                         ATA-TACCCGACA
genomic: ATGTTCCTGGTGATGTTGCATATCATTTTCAACCTCGCTTATTTGGAAAGgtaaggctca ... tgacaaacagATAATACCCGACA
EST: gi|110383861|gb|EC948264.1|EC948264
EST:     ATGTTCCTGGTGATGTTGCATATCATTTTCAACCTCGCTTATTTGGAAAG                         ATAATACCCGACAAGTGTAGATATGAAGTATTGTCAACCAAAATTGAAATC
genomic: ATGTTCCTGGTGATGTTGCATATCATTTTCAACCTCGCTTATTTGGAAAGgtaaggctca ... tgacaaacagATAATACCCGACAAGTGTAGATATGAAGTATTGTCAACCAAAATTGAAATC
EST: gi|110426741|gb|EC993160.1|EC993160
EST:     ATGTTCCTGGTGATGTTGCATATCATTTTCAACCTCGCTTATTTGGAAAG                         ATAATACCCGACAAGTGTAGATATGAAGTATTGTCAACCAAAATTGAAATC
genomic: ATGTTCCTGGTGATGTTGCATATCATTTTCAACCTCGCTTATTTGGAAAGgtaaggctca ... tgacaaacagATAATACCCGACAAGTGTAGATATGAAGTATTGTCAACCAAAATTGAAATC
EST: gi|71873209|gb|DT022264.1|DT022264
EST:     TGTTCCTGGTGATGTTGCATATCATTTTCAACCCTCGCT-ATTTGGGAAG                         ATAATACCCGACAAGTGTAGATATGAAG
genomic: TGTTCCTGGTGATGTTGCATATCATTTTCAACC-TCGCTTATTTGGAAAGgtaaggctca ... tgacaaacagATAATACCCGACAAGTGTAGATATGAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttcacttattctggatgctgagtttatcatctggtgtttggttttgacaaacagATAATACCCGACAAGTGTAGATATGAAGTATTGTCAACCAAAATTGAAATCCGACTTGCAAAAGCTGAAGAAATTCATTGGACTTCTCTTGAATTCAGCA
                                          ttttgac  putative branch site (score: 3)
                       tttatcat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttgatctagtttttgtagtctagtattataggaatatctaattcatttcacttattctggatgctgagtttatcatctggtgtttggttttgacaaacagATAATACCCGACAAGTGTAGATATGAAGTATTGTCAACCAAAATTGAAATCCGACTTGCAAAAGCTGAAGAAATTCATTGGACTTCTCTTGAATTCAGCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - -aggaata
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - ggatgct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgtttgg