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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tctattttcacctttcttccagcccacatgctagatgtgtttgataaatctttttaaacccttgagaagtgtgttcattttctgcttaacgtgtatgcagAAAAAGAAAGAGTGTTTTGCATCATGCCTCTTTGTCTGTTACGATTTAATTCGGCCAGACGTTGTCCTTGAGCTTGCATGGATGAACAATATGATCGACT

Basic information

species Vitis vinifera
transcript Vv06s0004g06860.t01
intron # 27
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv06s0004g06860.t01 (Vitis vinifera), 3'ss of exon 27
lower sequence: GRMZM2G057576_T02 (Zea mays), 3'ss of exon 25
-tctattttca--cctttcttccagcccacatgctagatgtgtttgataaatctttttaaacccttgagaagt-gtgttcattttctgctta----------------acgtgta-tgcagAAAAAGAAAGAGTGTTTTGCATCATGCCTCTTTGTCTGTTACGATTTAATTCGGCCAGACGTTGTCCTTGAGCTTGCATGGATGAACAATATGATCGACT
 | |  ||  |  || || |    ||  |     | |  ||   | ||  |    | || ||     | |  |  || |    ||||| |||                |  |||| || ||   |||||||| |||||||| || ||||||||  | || |||||  | || |||||||| || |  ||||||||||||||||||||||| ||| | ||||
gtttggttcgaacccattgtattggctgatgatatgggagtagctaattcaatactatatacagcaaaaagcttatgcttgcattctgattagtaaacacatccaatcatatgtaatgtagGGTAAGAAAGAATGTTTTGCTTCTTGCCTCTTCATTTGCTACGACCTGATCCGGCCAGATGTGGCTCTTGAGCTTGCATGGATGAACAACATGGTGGACT

upper sequence: Vv06s0004g06860.t01 (Vitis vinifera), 3'ss of exon 27
lower sequence: GLYMA01G38580.1 (Glycine max), 3'ss of exon 27
--------------------------------------------------------------------------tctattttcacctttcttccagcccacatg--ctagatgtg--tttgataaat-ctttttaaacccttgagaagtgtgttcattttctgcttaacg-------tgtat------gcagAAAAAGAAAGAGTGTTTTGCATCATGCCTCTTTGTCTGTTACGATTTAATTCGGCCAGACGTTGTCCTTGAGCTTGCATGGATGAACAATATGATCGACT
                                                                           || ||  ||   | |    | ||  | |    ||||  |   |||| |   | |||| |  |||          ||  |  | || |  |||||        | |||      ||||  ||||||||||||||||||||||||||||||||||||||| ||| | || |||||||| ||||  ||||||||  | ||||||||||||||||| || |
gtgtttattttcttgtccttttccttaagatatcaaactccagtattcgtaaattagatactaactaggttagaccttttggcatagtgcagtgaccctgcttcacttagaaattattttgctgctttctttcttcacctccagtgctggttcttttcttttaattaacaaagggattatattgatttgcagGGAAAGAAAGAGTGTTTTGCATCATGCCTCTTTGTCTGTTATGATATTATACGGCCAGATGTTGCTCTTGAGCTATCTTGGATGAACAATATGATTGATT

upper sequence: Vv06s0004g06860.t01 (Vitis vinifera), 3'ss of exon 27
lower sequence: GLYMA11G06720.1 (Glycine max), 3'ss of exon 27
----------------------------------------------------------------------------------tctattttcacctttcttccagcccacatgctagatgtgtttgataaat-ctttttaaacccttgagaagtgtgttcattttctgcttaacg-------tgtat------gcagAAAAAGAAAGAGTGTTTTGCATCATGCCTCTTTGTCTGTTACGATTTAATTCGGCCAGACGTTGTCCTTGAGCTTGCATGGATGAACAATATGATCGACT
                                                                                   |    | ||| ||    |     ||| |   | |||  |||| |   | ||||    |||      |   || ||  | |  |  |||||        | |||      ||||  ||||||||||||||||||||||||||||||||||||||| ||| | ||  ||||||| ||||  |||||||| || ||||||||||||||||| || |
gtgtttattttcttgtccttttccttaagatctcaaactctggtattcgtaaattagatactaactaggttagacccttttggcatagtgcactttgaccctgcttcacttag-aaatgattttgctgctttctttcctcacctcccgcaccagtttttctctcttaattaacaaagggattatattgatttgcagGGAAAGAAAGAGTGTTTTGCATCATGCCTCTTTGTCTGTTATGATATTATATGGCCAGATGTTGCTCTTGAGCTAGCTTGGATGAACAATATGATTGATT

upper sequence: Vv06s0004g06860.t01 (Vitis vinifera), 3'ss of exon 27
lower sequence: GLYMA14G37510.1 (Glycine max), 3'ss of exon 25
tctattttcacctttcttccagcccacatgctagatgtgtttgataaatctttttaaacccttgagaag----tgtgttcattttctgcttaacgtgtatgcagAAAAAGAAAGAGTGTTTTGCATCATGCCTCTTTGTCTGTTACGATTTAATTCGGCCAGACGTTGTCCTTGAGCTTGCATGGATGAACAATATGATCGACT
      |||||||  | |          ||  |    | |||| |   |  |||||||   |    |||    | |||| || || | |      | | | ||| | |||||||| ||||||||||| ||||||||||||||||| ||| |||| |||||||| ||||  |||||||| || ||||||||||||||||| || |
---tgcttcacctcacctttgttttctttgtcatgcttctttggtct-taattttaaattttaacaaaggagttatgttaatattattccctgtatctttccagGAGAAGAAAGAATGTTTTGCATCTTGCCTCTTTGTCTGTTATGATATAATACGGCCAGATGTTGCTCTTGAGCTAGCTTGGATGAACAATATGATTGATT

upper sequence: Vv06s0004g06860.t01 (Vitis vinifera), 3'ss of exon 27
lower sequence: GLYMA02G39360.1 (Glycine max), 3'ss of exon 27
tctattttcacctttcttccagcccacat-gctagatgtgtttgataaatctttttaaacccttgagaagt-gtgttcattttctgcttaacgtgtatgcagAAAAAGAAAGAGTGTTTTGCATCATGCCTCTTTGTCTGTTACGATTTAATTCGGCCAGACGTTGTCCTTGAGCTTGCATGGATGAACAATATGATCGACT
   |  |   | ||  || |      | | | | |   |  ||  ||| | |   |||    || |  |||  ||||||| || | | |    | | | |||   ||||| || ||||||||||| |||||||| |||||||| ||| |||| |||||||| ||||  |||||||| || ||||||||||||||||| || |
--cacctcacctttgttttctttgtgcttcgttggtcttaatttttaattttaactaagtagttaattagttatgttcatattattccttgtatctttccagGGGAAGAAGGAATGTTTTGCATCTTGCCTCTTCGTCTGTTATGATATAATACGGCCAGATGTTGCTCTTGAGCTAGCTTGGATGAACAATATGATTGATT

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|30251298|gb|CB969031.1|CB969031
EST:     CTGGGGATCGTGAACCTGCAGAGGAGTTGCTTGTTTATTTCATTGAGCAG                         AAAAAGAAAGAGTGTTTTGCATCATGCCTCTTTGTCTGTTACGATTTAATT
genomic: CTGGGGATCGTGAACTTGCAGAGGAGTTGCTTGTTTATTTCATTGAGCAGgtatgagtca ... gtgtatgcagAAAAAGAAAGAGTGTTTTGCATCATGCCTCTTTGTCTGTTACGATTTAATT
EST: gi|30252228|gb|CB969779.1|CB969779
EST:     GCTTGTTTATTTCATTGAGCAG                         AAAAAGAAAGAGTGTTTTGCATCATGCCTCTTTGTCTGTTACGATTTAATT
genomic: GCTTGTTTATTTCATTGAGCAGgtatgagtca ... gtgtatgcagAAAAAGAAAGAGTGTTTTGCATCATGCCTCTTTGTCTGTTACGATTTAATT
EST: gi|30252045|gb|CB968684.1|CB968684
EST:     CTGGGGATCGTGAACCTGCAGAGGAGTTGCTTGTTTATTTCATTGAGCAG                         AAAAAGAAAGAGTGTTTTGCATCATGCCTGATCGTCTGTTACGATTTAATT
genomic: CTGGGGATCGTGAACTTGCAGAGGAGTTGCTTGTTTATTTCATTGAGCAGgtatgagtca ... gtgtatgcagAAAAAGAAAGAGTGTTTTGCATCATGCCTCTTTGTCTGTTACGATTTAATT
EST: gi|349826023|gb|FQ415828.1|FQ415828
EST:     CTGGGGATCGTGAACTTGCAGAGGAGTTGCTTGTTTATTTCATTGAGCAG                         AAAAAGAAAGAGTGTTTTGCATCATGCCTCTNTGTCTGTTACGATTTAATT
genomic: CTGGGGATCGTGAACTTGCAGAGGAGTTGCTTGTTTATTTCATTGAGCAGgtatgagtca ... gtgtatgcagAAAAAGAAAGAGTGTTTTGCATCATGCCTCTTTGTCTGTTACGATTTAATT
EST: gi|30251483|gb|CB969216.1|CB969216
EST:     GCTTGTTTATTTCATTGAGCAG                         AAAAAGAAAGAGTGTTTTGCATCATGCCTCTTTGTCTGTTACGATTTAATT
genomic: GCTTGTTTATTTCATTGAGCAGgtatgagtca ... gtgtatgcagAAAAAGAAAGAGTGTTTTGCATCATGCCTCTTTGTCTGTTACGATTTAATT
EST: gi|30252223|gb|CB969774.1|CB969774
EST:     GCTTGTTTATTTCATTGAGCAG                         AAAAAGAAAGAGTGTTTTGCATCATGCCTCTTTGTCTGTTACGATTTAATT
genomic: GCTTGTTTATTTCATTGAGCAGgtatgagtca ... gtgtatgcagAAAAAGAAAGAGTGTTTTGCATCATGCCTCTTTGTCTGTTACGATTTAATT
EST: gi|351040418|gb|FQ434551.1|FQ434551
EST:     CTGGGGATCGTGAACTTGCACAGGAGTTGCTTGTTTATTTCATTGAGCAT                         AAAAAGAAAGAGTGTTTTGCATCATGCCTCTTTGTCTGTTACGATTTAATT
genomic: CTGGGGATCGTGAACTTGCAGAGGAGTTGCTTGTTTATTTCATTGAGCAGgtatgagtca ... gtgtatgcagAAAAAGAAAGAGTGTTTTGCATCATGCCTCTTTGTCTGTTACGATTTAATT
EST: gi|110699699|gb|EE076936.1|EE076936
EST:     CTGGGGATCGTGAACTTGCAGAGGAGTTGCTTGTTTATTTCATTGAGCAG                         AAAAAGAAAGAGTGTTTTGCATCATGCCTCTTTGTCTGTTACGATTTAATT
genomic: CTGGGGATCGTGAACTTGCAGAGGAGTTGCTTGTTTATTTCATTGAGCAGgtatgagtca ... gtgtatgcagAAAAAGAAAGAGTGTTTTGCATCATGCCTCTTTGTCTGTTACGATTTAATT
EST: gi|30251472|gb|CB969205.1|CB969205
EST:     GCTTGTTTATTTCATTGAGCAG                         AAAAAGAAAGAGTGTTTTGCATCATGCCTCTTTGTCTGTTACGATTTAATT
genomic: GCTTGTTTATTTCATTGAGCAGgtatgagtca ... gtgtatgcagAAAAAGAAAGAGTGTTTTGCATCATGCCTCTTTGTCTGTTACGATTTAATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaatctttttaaacccttgagaagtgtgttcattttctgcttaacgtgtatgcagAAAAAGAAAGAGTGTTTTGCATCATGCCTCTTTGTCTGTTACGATTTAATTCGGCCAGACGTTGTCCTTGAGCTTGCATGGATGAACAATATGATCGACT
                                      gcttaac  putative branch site (score: 3)
     tttttaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tctattttcacctttcttccagcccacatgctagatgtgtttgataaatctttttaaacccttgagaagtgtgttcattttctgcttaacgtgtatgcagAAAAAGAAAGAGTGTTTTGCATCATGCCTCTTTGTCTGTTACGATTTAATTCGGCCAGACGTTGTCCTTGAGCTTGCATGGATGAACAATATGATCGACT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - tcttcca
- - - - - - - - - - -gcccaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaccct