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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtataatgaagtttgctggcacacatcaaaattttggctttaatttgtagccattatgcctaatggtgcttcccttacatttttttatcgcatgtagAATTTTCTTTTCAAGTCAACCAAAGAGGACTCGCCTTTGAAGGCCACGGATTTTGGTCTATCAGACTTCATAAAGCCTG

Basic information

species Vitis vinifera
transcript Vv04s0023g03420.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv04s0023g03420.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os02g03410.1 (Oryza sativa), 3'ss of exon 4
gtataa--tgaa-gtttgctggcacacatcaa--aattttggctttaatttgtagccattatgcctaatggtgcttccct-tacatttttttatcgcatgtagAATTTTCTTTTCAAGTCAACCAAAGAGGACTCGCCTTTGAAGGCCACGGATTTTGGTCTATCAGACTTCATAAAGCCTG
||| ||  |||| | || |     |    |||  | | |    |||  |       |||||   || | |     |     |  |  | ||| ||      |||| || |||||||| |||||||| |||||||| ||||| ||||| || ||||||||||| |||||||||||||| || |
gtagaaattgaacgctttcaatgtcttggcaattagtgtacattttggtgatatttcattacttctcaggtcatgtaagaatgtacctattt-tccttcccagAACTTCCTTTTCAAATCAACCAAGGAGGACTCACCTTTAAAGGCAACAGATTTTGGTCTGTCAGACTTCATAAAACCAG

upper sequence: Vv04s0023g03420.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G365035_T01 (Zea mays), 3'ss of exon 4
gtataatgaagtttgctggcacacatcaaaattttggctttaat--ttgtagccattatgccta----atggtgcttcccttacatttttttatcgcatgtagAATTTTCTTTTCAAGTCAACCAAAGAGGACTCGCCTTTGAAGGCCACGGATTTTGGTCTATCAGACTTCATAAAGCCTG
      |  | | ||   | | |    | |||  || | | |||  | || || | ||    |     |    |  |  || | | | || | | |  ||||||| || || ||||| ||||  || |||||||||||  | ||||| || ||||||||||| |||||||||||||| || |
-----gtatactctgaaagtataagatagaatcctgtcataaatagtagttgctaatacctttttattaaaaggagtagctaataatcttat-tggtgtgtagAACTTCCTATTCAAATCAAAAAAGGAGGACTCGCCCCTTAAGGCTACAGATTTTGGTCTTTCAGACTTCATAAAACCAG

upper sequence: Vv04s0023g03420.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA01G37100.1 (Glycine max), 3'ss of exon 5
gtataatgaagtttgctggcacacatcaaaattttggctttaatttgtagccattatgcctaatggtgcttcccttacatttttttatcgcatgtagAATTTTCTTTTCAAGTCAACCAAAGAGGACTCGCCTTTGAAGGCCACGGATTTTGGTCTATCAGACTTCATAAAGCCTG
||||  | ||||| ||| ||| |  |    | | ||| |||  | | | || | ||| | | |   |  | | |||                || |||||||||||||||||||||||||||| || || ||||| ||||| || ||||||||| | || || |||||||| ||||
gtatggtcaagttcgctagcatatctacgcaatatggatttg-tatat-gctactatacattaaaattttcctctt----------------tgcagAATTTTCTTTTCAAGTCAACCAAAGAAGATTCACCTTTAAAGGCTACCGATTTTGGTTTGTCTGATTTCATAAAACCTG

upper sequence: Vv04s0023g03420.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA16G23870.1 (Glycine max), 3'ss of exon 6
gtataatgaagtttgctggcacacatcaaaattttggctttaatttgtagccattatgcctaatggtgcttcccttacatt----tttttatcg---catgtagAATTTTCTTTTCAAGTCAACCAAAGAGGACTCGCCTTTGAAGGCCACGGATTTTGGTCTATCAGACTTCATAAAGCCTG
|||| || |||     | ||| |  |   || ||||  |  |||  | | | ||  | |   ||| |        || |||    |||||| |    | || ||||||||||||| || ||||||||||| || || ||||| |||||||| ||||||||| | ||||| |||||||| ||||
gtatgatcaagcacatttgcatatctgccaaatttgtgtgaaatgag-atctatactactagatgctatacataatatattaatatttttacctattcttgcagAATTTTCTTTTTAAATCAACCAAAGAAGATTCACCTTTAAAGGCCACTGATTTTGGTTTGTCAGATTTCATAAAACCTG

upper sequence: Vv04s0023g03420.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA11G08180.1 (Glycine max), 3'ss of exon 5
gtataatgaagtttgctggcacacatcaaaattttggctttaatttgtagccattatgcctaatggtgcttcccttacatttttttatcgcatgtagAATTTTCTTTTCAAGTCAACCAAAGAGGACTCGCCTTTGAAGGCCACGGATTTTGGTCTATCAGACTTCATAAAGCCTG
|| |  | ||||||||||||| |  |    | | |||  ||    ||||   ||| | |   ||      |     |  |||  |  | ||||| |||||||||||||||||||||||||||| || || ||||| ||||| || ||||||||| | || || || ||||| ||||
gtgtggtcaagtttgctggcatatctacgcaatatggagttg---tgta---attttactctata-----tattaaatttttcctctttgcatgcagAATTTTCTTTTCAAGTCAACCAAAGAAGATTCACCTTTAAAGGCTACCGATTTTGGTTTGTCTGATTTTATAAAACCTG

upper sequence: Vv04s0023g03420.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA02G05440.1 (Glycine max), 3'ss of exon 4
gtataatgaagtttgctggcacacatcaaaattttggctttaatttgtagccattatgcctaatggtgcttcccttac--atttttttatcg---catgtagAATTTTCTTTTCAAGTCAACCAAAGAGGACTCGCCTTTGAAGGCCACGGATTTTGGTCTATCAGACTTCATAAAGCCTG
|||| || |||     | ||| |  |   || ||||   | || |   | | ||  | |   ||| |   |     |   || |||||| |    | || ||||||||||||| || |||| |||||| || || ||||| |||||||| ||||||||| | ||||| |||||||| ||||
gtatgatcaagcacatttgcatatctgccaaatttg-tgtgaactgagatctatactactagatgctatataatagattaatgtttttacctattcttgcagAATTTTCTTTTTAAATCAATCAAAGAAGATTCACCTTTAAAGGCCACAGATTTTGGTTTGTCAGATTTCATAAAACCTG

upper sequence: Vv04s0023g03420.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AT2G17890.1 (Arabidopsis thaliana), 3'ss of exon 4
gtataatgaagtttgctggcaca--catcaaaattttggctttaatttgtagccattatgcctaatggtgcttcccttacatttttttatcgcatgtagAATTTTCTTTTCAAGTCAACCAAAGAGGACTCGCCTTTGAAGGCCACGGATTTTGGTCTATCAGACTTCATAAAGCCTG
       | || ||  |  | |   |||||   || ||  | |   | || |   |||| |  ||   |  ||   |   | |  | | || ||   |||||||||| ||||| |||||| |||| || |||||| | || || || ||||| ||| |||| |||||||||||||| |
-------gtagcttaattactccatcatcatgtttctgaatgtgtatagttggttttattcacaagtattgttttttactaatcatct-tctcaaacagAATTTTCTGTTCAAATCAACCGAAGAAGATTCGCCTCTAAAAGCTACTGATTTCGGTTTATCTGACTTCATAAAGCCAG

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|161714014|gb|FC064089.1|FC064089
EST:     CAGCTGAGTGTCATTTACATGGTCTGGTACACCGTGACATGAAACCAGAG                         AATTTTCTTTTCAAGTCAACCAAAGAGGACTCGCCTTTGAAGGCCACGGAT
genomic: CAGCTGAGTGTCATTTACATGGTCTGGTACACCGTGACATGAAACCAGAGgtataatgaa ... tcgcatgtagAATTTTCTTTTCAAGTCAACCAAAGAGGACTCGCCTTTGAAGGCCACGGAT
EST: gi|71864824|gb|DT013879.1|DT013879
EST:     CAGCTGAGTGTCATTTACATGGTCTGGTACACCGTGACATGAAACCAGAG                         AATTTTCTTTTCAAGTCAACCAAAGAGGACTCGCCTTTGAAGGCCACGGAT
genomic: CAGCTGAGTGTCATTTACATGGTCTGGTACACCGTGACATGAAACCAGAGgtataatgaa ... tcgcatgtagAATTTTCTTTTCAAGTCAACCAAAGAGGACTCGCCTTTGAAGGCCACGGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atttgtagccattatgcctaatggtgcttcccttacatttttttatcgcatgtagAATTTTCTTTTCAAGTCAACCAAAGAGGACTCGCCTTTGAAGGCCACGGATTTTGGTCTATCAGACTTCATAAAGCCTG
                             cccttac  putative branch site (score: 3)
                          cttcccttacattttt  CT-rich tract
                                ttacatttttttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtataatgaagtttgctggcacacatcaaaattttggctttaatttgtagccattatgcctaatggtgcttcccttacatttttttatcgcatgtagAATTTTCTTTTCAAGTCAACCAAAGAGGACTCGCCTTTGAAGGCCACGGATTTTGGTCTATCAGACTTCATAAAGCCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG