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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtctggtcgaaatgaatttttcccaaccacattttctatccagtgaatgattctcagttcaataattttatgttttttaatcatactctagGTTATATTGACACCAACCCACCTTGCTATTGTGATGGAATATGCCTCTGGAGGAGAGCTCTTTGAGCGGATATGCAATGCCGGCCGGTTCAGTGAGGATG

Basic information

species Vitis vinifera
transcript Vv03s0063g01080.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv03s0063g01080.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os03g55600.1 (Oryza sativa), 3'ss of exon 2
gtctggtcgaaatgaatttttcccaaccacattttctatccagtgaatgattctcagttcaataattttatgttttttaatcata---ctctagGTTATATTGACACCAACCCACCTTGCTATTGTGATGGAATATGCCTCTGGAGGAGAGCTCTTTGAGCGGATATGCAATGCCGGCCGGTTCAGTGAGGATG
     ||      | || ||    |  | |||| ||||       | | | | |   | ||  ||   || ||| | || ||||    ||  ||||||| || || ||||| || ||||||||||| ||||||||||||||||| || ||||| || ||| | || || ||    |  ||||||||||| ||||
-----gtaagtcaggatcttcatgacgctcattctctagttcaccattcaatattt-tccagcaaaaataagttctcta-tcatgtatctacagGTTATTTTAACCCCAACTCATCTTGCTATTGTCATGGAATATGCCTCTGGTGGTGAGCTTTTCGAGAGAATTTGTAAGAATGTACGGTTCAGTGAAGATG

upper sequence: Vv03s0063g01080.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G138861_T01 (Zea mays), 3'ss of exon 3
gtctggtcgaaatgaatttttcccaaccacattttctatccagtgaatgattctcagttcaataattttatgttttttaatcatactctagGTTATATTGACACCAACCCACCTTGCTATTGTGATGGAATATGCCTCTGGAGGAGAGCTCTTTGAGCGGATATGCAATGCCGGCCGGTTCAGTGAGGATG
            ||| ||          |   | | | |||   ||||  | |   ||| || | |||| | || ||   |     |||||||||| || ||||| ||||| ||||||||||| ||||||||||||||||| || ||||| |||||| ||||||| ||   ||  || |||||||| ||||
-----------gtgagttgggattg-tgatgctgtttctccccagaat--tccattgttaaacatttttttattcttctttgtatgtctagGTTATTTTAACACCGACCCATCTTGCTATTGTCATGGAATATGCCTCTGGCGGTGAGCTTTTTGAGAGGATATGTAAGAACGTGCGATTCAGTGAAGATG

upper sequence: Vv03s0063g01080.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G171435_T01 (Zea mays), 3'ss of exon 2
gtctggtcgaaatgaatttttcccaaccacattttctatccagtgaatgattctcagttcaataattttatgttttttaatcatactctagGTTATATTGACACCAACCCACCTTGCTATTGTGATGGAATATGCCTCTGGAGGAGAGCTCTTTGAGCGGATATGCAATGCCGGCCGGTTCAGTGAGGATG
        ||  ||   || |        |  |||||  ||    | | |||    ||| || | ||||    ||| |    ||| |||||||||| || ||||| ||||| ||||||||||| ||||||||||||||||| || ||||| |||||| | ||||| ||   ||  || |||||||| ||||
------gtgagttgggattgt----gatgctgtttctcccccagaattcattt---gttaaacacttttgaaatttctttgtata-tctagGTTATTTTAACACCGACCCATCTTGCTATTGTCATGGAATATGCCTCTGGCGGTGAGCTTTTTGAGAGAATATGTAAGAACGTGCGATTCAGTGAAGATG

upper sequence: Vv03s0063g01080.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA02G15330.1 (Glycine max), 3'ss of exon 2
gtctggtcgaaatgaatttttcccaaccacattttctatccagtgaatgattctcagttcaataattttatgttttttaatcat-actctagGTTATATTGACACCAACCCACCTTGCTATTGTGATGGAATATGCCTCTGGAGGAGAGCTCTTTGAGCGGATATGCAATGCCGGCCGGTTCAGTGAGGATG
            | || ||||   ||   | | | ||||    |       ||| ||    ||  |||  |  ||||   |    ||| |||||||||||||||||||| ||  | || ||||||||||||||||| |||||||||||||| |||||| | ||||||||||| ||  |||||||||||||||
-------gtgtgtaaactttt---aatgtcttatcctatttctt---cctatcttagaaatattgtttagtccttttctgttgcgactttagGTTATATTGACACCAACACATTTGGCAATTGTGATGGAATATGCTTCTGGAGGAGAGCTATTTGAGAGAATATGCAATGCAGGGAGGTTCAGTGAGGATG

upper sequence: Vv03s0063g01080.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA07G33120.1 (Glycine max), 3'ss of exon 2
gtctggtcgaaatgaatttttcccaaccacattttctatccagtgaatgattctcagttcaataattttatgttttttaatcatactctagGTTATATTGACACCAACCCACCTTGCTATTGTGATGGAATATGCCTCTGGAGGAGAGCTCTTTGAGCGGATATGCAATGCCGGCCGGTTCAGTGAGGATG
     ||  |||    |  |  |  | |  ||||  |      | ||  ||    | || | ||||     ||||| | ||   ||| |||||||||||||| ||||| ||  | || ||||||||||||||||| |||||||||||||| |||||| | ||||||||||| ||  |||||||||||||||
---gtgtgcaaacccctaatgtctgatcctatttctttctatcttaaaaat----attttattaatc----gttttctgatgtgactttagGTTATATTGACCCCAACACATTTAGCAATTGTGATGGAATATGCTTCTGGAGGAGAGCTATTTGAGAGAATATGCAATGCAGGAAGGTTCAGTGAGGATG

upper sequence: Vv03s0063g01080.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA20G01240.1 (Glycine max), 3'ss of exon 2
gtctggtcgaaatgaatttttcccaaccacattttctatccagtgaatgattctcagttcaat--aattttatgttttttaatcatactctagGTTATATTGACACCAACCCACCTTGCTATTGTGATGGAATATGCCTCTGGAGGAGAGCTCTTTGAGCGGATATGCAATGCCGGCCGGTTCAGTGAGGATG
|| || ||   |     | | | || |||   | |  | | | |   |  | |    |  | |  |||||  | |  ||   |   | | ||||| |||||||| || || ||  | ||||||||||||||||| || |||||||||||| | |||||||||||||||||||| || ||||| ||||||||||
gtttgttctcgaaactctgtacacatccaatgtcttcacctatttcttcctacctgatgtattttaatttattctcattctctgcaagtgtagGTAATATTGACCCCTACACATTTGGCTATTGTGATGGAATACGCTTCTGGAGGAGAGTTATTTGAGCGGATATGCAATGCAGGACGGTTTAGTGAGGATG

upper sequence: Vv03s0063g01080.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA07G29500.1 (Glycine max), 3'ss of exon 2
--------------gtctggtcgaaatgaatttttcccaaccacattttctatccagtgaatgattctcagttcaataattttatgttttttaatcatactctagGTTATATTGACACCAACCCACCTTGCTATTGTGATGGAATATGCCTCTGGAGGAGAGCTCTTTGAGCGGATATGCAATGCCGGCCGGTTCAGTGAGGATG
               ||||  || |   |||   |     | |  |  ||   ||  | | |||     | || ||| | ||    || | |     ||   ||| | ||||| || || || ||  | |||||||||||||| || || ||||| |||||| | |||||||||||||||||||| || ||||| ||||| ||||
gtttgttctctgaactctgtacgcatccaatgcctta-gcctatttcctcctacctataactgagatatattttaattagttctcattctctgcaagta---tagATCATATTAACCCCTACACATTTGGCTATTGTGATGGAGTACGCTTCTGGGGGAGAGTTATTTGAGCGGATATGCAATGCAGGACGGTTTAGTGAAGATG

upper sequence: Vv03s0063g01080.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT4G33950.1 (Arabidopsis thaliana), 3'ss of exon 2
------------gtctggtcgaaa-tgaatttttcccaaccacattttctatccagtgaatgattctcagttcaataattttatgttttttaatcatactctagGTTATATTGACACCAACCCACCTTGCTATTGTGATGGAATATGCCTCTGGAGGAGAGCTCTTTGAGCGGATATGCAATGCCGGCCGGTTCAGTGAGGATG
             |||  |  ||  ||  || ||   |   ||||||||     |   || ||       ||| ||||||| ||     |||    | ||  |||||||||| |||||||||||  | || ||||| ||||||||||| ||||||||||| || || ||||| || |||||||| ||||| ||||| || || |
gtttgttttcaactctcttttaagctgttttcttattattaacattttcaggaaaaaaaagga------attctataatttaat---ccttaggattgcttcagGTTATATTAACACCAACCCATTTAGCCATTGTTATGGAATATGCATCTGGAGGAGAACTTTTCGAGCGAATCTGCAATGCAGGCCGCTTCAGCGAAGACG

upper sequence: Vv03s0063g01080.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: PP1S116_98V6.1 (Physcomitrella patens), 3'ss of exon 2
---------------------------------------------------------------gtctggtcg---aaatgaatttttcccaaccacattttct--atccagtgaatgattctcagttcaataattttatgttttttaatcatactctagGTTATATTGACACCAACCCACCTTGCTATTGTGATGGAATATGCCTCTGGAGGAGAGCTCTTTGAGCGGATATGCAATGCCGGCCGGTTCAGTGAGGATG
                                                                 ||||  |     ||||| |||    |   |||||      |   | || |   ||   ||| | | |  ||   ||  || ||   || |  || | || ||||| ||||||||| | || |||||||||||||||||  |||| |||||||| |||||||| || || || || | |||||||||||| ||||
gtgatcattctagactttttgattttttattattattaatttttttttccctgaacttgtagaccctgggtgtgtggatgaactttctggattgacattactggaagatattggacatttaggagtactaaagctt---gtacttgaac--tatttcagATCATGTTGACTCCAACCCACTTGGCCATTGTGATGGAATATGCTGCTGGTGGAGAGCTGTTTGAGCGAATTTGTAAAGCAGTCCGGTTCAGTGAAGATG

upper sequence: Vv03s0063g01080.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: PP1S218_59V6.1 (Physcomitrella patens), 3'ss of exon 2
--------------------------------------------------gtctggtcgaaatgaatttttcccaaccacattttctatccagtgaatgattctcagttcaataattttatgttttttaatcat---actctagGTTATATTGACACCAACCCACCTTGCTATTGTGATGGAATATGCCTCTGGAGGAGAGCTCTTTGAGCGGATATGCAATGCCGGCCGGTTCAGTGAGGATG
                                                  | | ||||| |   |   | | || ||   | |  |     | ||  | ||| |   ||   ||   ||     |  || |  |   | |  |||| ||  |||| ||||||||  | |||||||| |||||||||||  |||| ||||| || |||||||| || || || || ||||| |||||||| ||||
gtgagaaacctacacatatttcttattattccaagggtctcaagatttgtggccggtcgca-caatgatgtacctactggactaac--atgattgtcttattgtacattttgtagcattgaaactcgtacttgtttcatttcagGTCATGCTGACTCCAACCCATTTGGCTATTGTTATGGAATATGCTGCTGGTGGAGAACTTTTTGAGCGAATCTGTAACGCAGGCCGCTTCAGTGAAGATG

upper sequence: Vv03s0063g01080.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: PP1S113_72V6.1 (Physcomitrella patens), 3'ss of exon 2
--------------------------------gtctggtcgaaatgaatttttcccaaccacattttctatccag---tgaatgattctc-------agttcaataattttatgttttttaatcatac--tctagGTTATATTGACACCAACCCACCTTGCTATTGTGATGGAATATGCCTCTGGAGGAGAGCTCTTTGAGCGGATATGCAATGCCGGCCGGTTCAGTGAGGATG
                                |     | | |||  ||||| |      | || ||||  |  |   ||  |   || |       | |||   | |  ||  | || |  || |    |  |||| || ||||| || |||||  | || |||||||||||||||||  | || |||||||| |||||||| || || ||||| || |||||||| || ||||
gtgtgaaagaagcagctctttcgtattttgcagaggttttggaatctattttgcatggataaatattctggcatgacatggttagctccctgttacaaattctggagtgctaaatcttgtgctcgtttcattcagGTCATGTTGACCCCGACCCATTTGGCCATTGTGATGGAATATGCGGCGGGTGGAGAGCTGTTTGAGCGAATTTGTAATGCTGGTCGGTTCAGCGAAGATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatccagtgaatgattctcagttcaataattttatgttttttaatcatactctagGTTATATTGACACCAACCCACCTTGCTATTGTGATGGAATATGCCTCTGGAGGAGAGCTCTTTGAGCGGATATGCAATGCCGGCCGGTTCAGTGAGGATG
                                      ttttaat  putative branch site (score: 3)
                   agttcaataattttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtctggtcgaaatgaatttttcccaaccacattttctatccagtgaatgattctcagttcaataattttatgttttttaatcatactctagGTTATATTGACACCAACCCACCTTGCTATTGTGATGGAATATGCCTCTGGAGGAGAGCTCTTTGAGCGGATATGCAATGCCGGCCGGTTCAGTGAGGATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG