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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagttgttgcttcattcactctgcactttgtatagctttagatggggtcagttgtgaatatctccttttgacctaatcttgactatgctgttgaattaattctctttatgttgatagGGACTTCACAAATCCATCTCTGCCTTCAGAGCAGAAAGGCAGATCTTCACAG

Basic information

species Vitis vinifera
transcript Vv18s0072g00310.t01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv18s0072g00310.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA10G36770.1 (Glycine max), 3'ss of exon 8
gtgagttgttgcttcattcactctgcactttgtatagctttagatggggtcagttgtgaatatctccttttgacctaatcttgactatgctgttgaattaattctctttatgttgatagGGACTTCACAAATCCATCTCTGCCTTCAGAGCAGAAAGGCAGATCTTCACAG
             | ||||| || |   ||  | |   | |   |  | |   | || ||| |||  ||   | ||  |  ||||  ||||| ||| ||  ||   | |   || | |||||||||||||| |||  ||| ||  ||||||||||||||||| ||||||| 
------------gtgattcagtcag---ttattgtgtttctgtttttgtttgctagttaatctctttttgacatcttgttatgacattgctgctgactttgttgcatct---ttcacagGGACTTCACAAACCCAAATCTCCCCACAGAGCAGAAAGGCAGACCTTCACAA

upper sequence: Vv18s0072g00310.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA16G27970.1 (Glycine max), 3'ss of exon 7
gtgagttgttgcttcattcactctgcactttgtatagctttagatggggtcagttgtgaatatctccttttgacctaatcttgactatgctgttgaattaattctctttatgttg-atagGGACTTCACAAATCCATCTCTGCCTTCAGAGCAGAAAGGCAGATCTTCACAG
             | | ||| |  |  |||| | ||  | |  ||    ||| || | ||  |   || ||    |||  |||       | ||  | | | | |  | || |   | |||||||||||||| ||   ||||||| |||||||||||||  |||||||||| 
------------gtgactcagttggttctttctttatttatttat----tcattttttaacttaatctcttt-tataacattgtaatcattatt--actgagtttactcatatcccacagGGACTTCACAAACCCTAATCTGCCTACAGAGCAGAAAGGTCGATCTTCACAA

upper sequence: Vv18s0072g00310.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA20G30820.1 (Glycine max), 3'ss of exon 9
gtgagttgttgcttcattcactctg-cactttgtatagctttagatggggtcagttgtgaatatctccttttgacctaatct-tgactatgctgttgaattaattctctttatgttgatagGGACTTCACAAATCCATCTCTGCCTTCAGAGCAGAAAGGCAGATCTTCACAG
                 | | |||| || ||  | |   | |   |  | |   ||||  || |||  ||   | ||  | | | ||  || || ||| || |||   | |   || | |||||||||||||| |||  ||| ||| ||||||||||||| ||| ||||||| 
----------------gtgattctgtcagttcttgtgtttctttttttgtttgcttgttgatctctttttgacatcttgtttatcacattgttgctgactttatttcatct---ttcacagGGACTTCACAAACCCAAATCTCCCTACAGAGCAGAAAGGAAGACCTTCACAA

upper sequence: Vv18s0072g00310.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA02G08870.2 (Glycine max), 3'ss of exon 3
gtgagttgttgcttcattcactctgcactttgtatagctttagatggggtcagttgtgaatatctccttttgacctaatcttgactatgctgttgaattaattctctttatgttg-atagGGACTTCACAAATCCATCTCTGCCTTCAGAGCAGAAAGGCAGATCTTCACAG
       ||  ||   ||   |||  | ||| | ||    |  ||    |   || | | |   ||| ||| |    ||  | |  ||  | ||  | | | | |  | |||||  | |||||||||||||| ||   ||||||| |||||||||||||  |||||||||| 
-------gtgactcagttggttcttta-tttatttattcattcattcattttttt-taacttgatcccttttataacattgtaataat--tatt--actgagtttactcatgttccacagGGACTTCACAAACCCTAATCTGCCTACAGAGCAGAAAGGTCGATCTTCACAA

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|351025264|gb|FQ434277.1|FQ434277
EST:     CAAACCTTGATGAGTTACAAGTGAACTACAATAATGAGCGCTCTAG                         GGACTTCACAAATCCATCTCTGCCTTCAGAGCAGAAAGGCAGATCTTCACA
genomic: CAAACCTTGATGAGTTACAAGTGAACTACAATAATGAGCGCTCTAGgtgagttgtt ... atgttgatagGGACTTCACAAATCCATCTCTGCCTTCAGAGCAGAAAGGCAGATCTTCACA
EST: gi|110387338|gb|EC951996.1|EC951996
EST:     CCTTGATGAGTTACAAGTGAACTACAATAATGAGCGCTCTAG                         GGACTTCACAAATCCATCTCTGCCTTCAGAGCAGAAAGGCAGATCTTCACA
genomic: CCTTGATGAGTTACAAGTGAACTACAATAATGAGCGCTCTAGgtgagttgtt ... atgttgatagGGACTTCACAAATCCATCTCTGCCTTCAGAGCAGAAAGGCAGATCTTCACA
EST: gi|349827659|gb|FQ422527.1|FQ422527
EST:     CAAACCTTGATGAGTTACAAGTGAACTACAATAATGAGCGCTCTAG                         GGACTTCACAAATCCATCTCTGCCTTCAGAGCAGAAAGGCAGATCTTCACA
genomic: CAAACCTTGATGAGTTACAAGTGAACTACAATAATGAGCGCTCTAGgtgagttgtt ... atgttgatagGGACTTCACAAATCCATCTCTGCCTTCAGAGCAGAAAGGCAGATCTTCACA
EST: gi|351014018|gb|FQ434170.1|FQ434170
EST:     CCTTGATGAGTTACAAGTGAACTACAATAATGAGCGCTCTAG                         GGACTTCACAAATCCATCTCTGCCTTCAGAGCAGAAAGGCAGATCTTCACA
genomic: CCTTGATGAGTTACAAGTGAACTACAATAATGAGCGCTCTAGgtgagttgtt ... atgttgatagGGACTTCACAAATCCATCTCTGCCTTCAGAGCAGAAAGGCAGATCTTCACA
EST: gi|349825575|gb|FQ419492.1|FQ419492
EST:     CAAACCTTGATGAGTTACAAGTGAACTACAATAATGAGCGCTCTAG                         GGACTTCACAAATCCATCTCTGCCTTCAGAGCAGAAAGGCAGATCTTCACA
genomic: CAAACCTTGATGAGTTACAAGTGAACTACAATAATGAGCGCTCTAGgtgagttgtt ... atgttgatagGGACTTCACAAATCCATCTCTGCCTTCAGAGCAGAAAGGCAGATCTTCACA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tccttttgacctaatcttgactatgctgttgaattaattctctttatgttgatagGGACTTCACAAATCCATCTCTGCCTTCAGAGCAGAAAGGCAGATCTTCACAG
                               aattaat  putative branch site (score: 3)
                                     ttctctttat  CT-rich tract
                               aattaattctctttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagttgttgcttcattcactctgcactttgtatagctttagatggggtcagttgtgaatatctccttttgacctaatcttgactatgctgttgaattaattctctttatgttgatagGGACTTCACAAATCCATCTCTGCCTTCAGAGCAGAAAGGCAGATCTTCACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT