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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttctctcatgcacacacacacacacacacagtattgttctttcttatcaactgaggacaggatgtcagatgacttactcaattggatgatggggtcttagGTATTGGCAGAGGATGAAAACAATGTCAAGGCATTATTTAGACGAGGAAAAGCTAGAGCAGAACTTGGGCAAACAGATGCTGCCCGTGAGGACTTCAGTA

Basic information

species Vitis vinifera
transcript Vv13s0064g00580.t01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv13s0064g00580.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: LOC_Os11g05090.1 (Oryza sativa), 3'ss of exon 6
--ttctctcatgcacacacacacacacacacagtattgttctttcttatcaactgaggacaggatgtcagatgacttactcaattggatgatggggtcttagGTATTGGCAGAGGATGAAAACAATGTCAAGGCATTATTTAGACGAGGAAAAGCTAGAGCAGAACTTGGGCAAACAGATGCTGCCCGTGAGGACTTCAGTA
    ||  | ||   |  ||  ||     | | | ||   |  | ||  | |    | | |   | |    ||  | |   | |   |          | |||| ||||||||||||||||||||||| || ||||| || |||||||||||||| ||||| |||||||| || |||||  | ||  | |||||||||   |
gtaactgacctggcaattcat-caagtgaagaatttttccccctttttccgaaaccgaataat-tattgactggatgatgaactcataatcctattcttcagGTGTTGGCAGAGGATGAAAACAATGTGAAAGCATTGTTCAGACGAGGAAAAGCAAGAGCTGAACTTGGTCAGACAGAATCAGCGAGGGAGGACTTCCTGA

upper sequence: Vv13s0064g00580.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: LOC_Os12g05090.1 (Oryza sativa), 3'ss of exon 6
---ttctctcatgcacacacacacacacacacagtattgttctttcttatcaactgaggacaggatgtcagatgacttactcaattggatgatggggtctt--agGTATTGGCAGAGGATGAAAACAATGTCAAGGCATTATTTAGACGAGGAAAAGCTAGAGCAGAACTTGGGCAAACAGATGCTGCCCGTGAGGACTTCAGTA
   ||   |  || |   |  |||  ||     | ||||  | ||   || |    |  | || ||  | ||| |  |  |||| || || ||    |  |  |||| ||| |||||||||||||||| || || || || || |||||||||||||||||||| |||||||| ||||||||  | ||  | |||||||||   |
gattttggttttgtattgattcacggacctgttg-attgaccatttgaataag--aatcaaagaattgctgatca--tgatcaactgcataatctcattcttcagGTGTTGTCAGAGGATGAAAACAACGTGAAAGCGTTGTTCAGACGAGGAAAAGCTAGAGCTGAACTTGGTCAAACAGAATCAGCAAGGGAGGACTTCCTGA

upper sequence: Vv13s0064g00580.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA09G36250.1 (Glycine max), 3'ss of exon 7
-ttctctcatgcacacacacacacacacacagtattgttctttcttatcaactgaggacaggatgtc-agatgacttactcaattggatgatggggtcttagGTATTGGCAGAGGATGAAAACAATGTCAAGGCATTATTTAGACGAGGAAAAGCTAGAGCAGAACTTGGGCAAACAGATGCTGCCCGTGAGGACTTCAGTA
    |   |    |   |  | |   | | | | || |||    ||||    |    | || |  || |    | | |    ||||| ||||    |   ||||| |||  |||||||| |||||||| ||||| |||||||| ||||| || |||||||||  |||||||||||||||||||||| | || || ||    |
aaggtaaaaccatctggctgatattgaaataatctt-ttccacattatgttttactcatagtacatccatgaaagtcaagtcattgg-tgatccacttgcagGTACTGGGTGAGGATGAGAACAATGTGAAGGCGTTATTTAGGCGAGGTAAGGCTAGAGCAACACTTGGGCAAACAGATGCTGCCAGGGAAGATTTTCTAA

upper sequence: Vv13s0064g00580.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA12G01080.1 (Glycine max), 3'ss of exon 6
ttctctcatgcacacacacacacacacacagtattgttctttcttatcaactgaggacaggatgtcagatgacttactcaattggatgatggggtct-tagGTATTGGCAGAGGATGAAAACAATGTCAAGGCATTATTTAGACGAGGAAAAGCTAGAGCAGAACTTGGGCAAACAGATGCTGCCCGTGAGGACTTCAGTA
 |  || ||    | | |  |     |||| ||| || |   | |   |    ||     | ||    |     |  | || |  |||||||    |  ||||| |||  |||||||| |||||||| |||||||||||||| ||||| || |||||||||| |||||||||||| ||| ||||| | || || ||    |
ctggctgatattgaaataatcttttccacattatagtacaaccatgaaagtcaagtcattggtgatccact-tgtgtttaactttatgatggaacttgcagGTACTGGGTGAGGATGAGAACAATGTGAAGGCATTATTTAGGCGAGGTAAGGCTAGAGCAGCACTTGGGCAAACGGATACTGCCAGGGAAGATTTTCTAA

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|110404958|gb|EC970485.1|EC970485
EST:     ATAAAGCTGAAGCGCTACGAAGAAGCCATTGGTCAATGCAGCATT                         GTATTGGCAGAGGATGAAAACAATGTCAAGGCATTATTTAGACGAGGAAAA
genomic: ATAAAGCTGAAGCGCTACGAAGAAGCCATTGGTCAATGCAGCATTgtatgtataa ... ggggtcttagGTATTGGCAGAGGATGAAAACAATGTCAAGGCATTATTTAGACGAGGAAAA
EST: gi|110732252|gb|EE107386.1|EE107386
EST:     AAGCGCTACGAAGAAGCCATTGGTCAATGCAGCATT                         GTATTGGCAGAGGATGAAAACAATGTCAAGGCATTATTTAGACGAGGAAAA
genomic: AAGCGCTACGAAGAAGCCATTGGTCAATGCAGCATTgtatgtataa ... ggggtcttagGTATTGGCAGAGGATGAAAACAATGTCAAGGCATTATTTAGACGAGGAAAA
EST: gi|110385321|gb|EC949833.1|EC949833
EST:     ATCAGGACGATGAAAATGAAATAGTTACTGAAAATGCAGCATTTGTGCATGGGGAACCTCTTCAAGATGGTACGGGTCCTCCAAAAGTTGATTCTGAAGTGGAAGTTCTTCATGAGAAA
genomic: ATCAGGACGATGAAAATGAAATAGTTACTGAAAATGCAGCATTTGTGCATGGGGAACCTCTTCAAGATGGTACGGGTCCTCCAAAAGTTGATTCTGAAGTGGAAGTTCTTCATGAGAAA
EST: gi|30304226|gb|CB981020.1|CB981020
EST:     ATCAGGACGATGAAAATGAAATAGTTACTGAAAATGCAGCATTTGTGCATGGGGAACCTCTTCAAGATGGTACGGGTCCTCCAAAAGTTGATTCTGAAGTGGAAGTTCTTCATGAGAAA
genomic: ATCAGGACGATGAAAATGAAATAGTTACTGAAAATGCAGCATTTGTGCATGGGGAACCTCTTCAAGATGGTACGGGTCCTCCAAAAGTTGATTCTGAAGTGGAAGTTCTTCATGAGAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atcaactgaggacaggatgtcagatgacttactcaattggatgatggggtcttagGTATTGGCAGAGGATGAAAACAATGTCAAGGCATTATTTAGACGAGGAAAAGCTAGAGCAGAACTTGGGCAAACAGATGCTGCCCGTGAGGACTTCAGTA
                         gacttac  putative branch site (score: 2)
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttctctcatgcacacacacacacacacacagtattgttctttcttatcaactgaggacaggatgtcagatgacttactcaattggatgatggggtcttagGTATTGGCAGAGGATGAAAACAATGTCAAGGCATTATTTAGACGAGGAAAAGCTAGAGCAGAACTTGGGCAAACAGATGCTGCCCGTGAGGACTTCAGTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - ctcatgc
- - - - - -acacaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -caggatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tggatga