Sequence
atgc intronic sequence ATGC exonic sequence...aaaaagaaaaaaaaaattggtttatctaggtaatctgtctattggagttaaaattttaaattagttacattctcttgatactcctttttggtaattgcagGCTACCATTGGGATTGATTTTTTGTCTAAAACGATGTACCTTGAGGATCGAACAATTCGTTTGCAGCTTTG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv00s0665g00040.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA11G38110.1 (Glycine max), 3'ss of exon 1
aaaaagaaaaaaaaaattggtttatctaggtaatctgtctattggagttaaaattttaaattagttacattctcttgatactcct---ttttggtaattgcagGCTACCATTGGGATTGATTTTTTGTCTAAAACGATGTACCTTGAGGATCGAACAATTCGTTTGCAGCTTTG
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-atcttcttcgtaaatttgttttgcatttgaatctttacgatctcccttcccccttttcct--gctagggtcttgacaaatttctagatcatcaaaatttcagGCTACTATTGGTATTGACTTCTTGTCAAAAACAATGTACCTTGAAGATCGAACAGTTCGTTTGCAGCTTTG
upper sequence: Vv00s0665g00040.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA18G02040.1 (Glycine max), 3'ss of exon 1
aaaaagaaaaaaaaaattggtttatctag-gtaatctgtctattggagttaaaattttaaattagttacattctcttgatactcctttttggt---aattgcagGCTACCATTGGGATTGATTTTTTGTCTAAAACGATGTACCTTGAGGATCGAACAATTCGTTTGCAGCTTTG
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--aattatcttcttcgtaaatttgttttgcacaatgtttccatctcccttcccccttttcct--gctagggtcttgacaaatttcttgatcatcaaaatttcagGCTACTATTGGTATTGACTTCTTGTCAAAAACAATGTACCTTGAAGATCGAACAGTTCGTCTGCAGCTTTG
upper sequence: Vv00s0665g00040.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA08G14390.1 (Glycine max), 3'ss of exon 1
aaaaagaaaaaaaaaattggtttatctaggtaatctgtctattggagttaaaattttaaat--tagttacattctcttgatactcctttttggtaattgcagGCTACCATTGGGATTGATTTTTTGTCTAAAACGATGTACCTTGAGGATCGAACAATTCGTTTGCAGCTTTG
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gtttccttggtatatatttttttgttctgtcaagg-atccacaatttttattcttcctgctgctagatg-gctgacaaaatattttgttatctaaatttcagGCAACTATTGGTATTGACTTTTTGTCAAAAACAATGTACCTTGAAGATAGAACTGTTCGCTTGCAGCTTTG
upper sequence: Vv00s0665g00040.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA05G31200.1 (Glycine max), 3'ss of exon 1
aaaaagaaaaaaaaaattggtttatctaggtaatctgtctattggagttaaaattttaaa-----ttagttacattctcttgatactcctttttggta-----attgcagGCTACCATTGGGATTGATTTTTTGTCTAAAACGATGTACCTTGAGGATCGAACAATTCGTTTGCAGCTTTG
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--------ttgttttcttggtatatttttttattccatcaac--gattcacaatttttatgcttcctgctgctagactgctgacaaaattttttgttatgtaaatttcagGCAACTATTGGTATTGACTTTTTGTCAAAAACAATGTACCTTGAAGATAGAACTGTTCGCCTGCAGCTTTG
upper sequence: Vv00s0665g00040.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: AT5G10260.1 (Arabidopsis thaliana), 3'ss of exon 1
-----------------------------------------------------------------------aaaaagaaaaaaaaaattggttt-atctaggtaatctgtctattggagttaaaattttaaattagttacattctcttgatactcctt-tttggtaattgcagGCTACCATTGGGATTGATTTTTTGTCTAAAACGATGTACCTTGAGGATCGAACAATTCGTTTGCAGCTTTG
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gttggatcattttcttctatcccatctcgatcaaaattaattttgatccattgtctgtgagatccacgatcctgttgctgtaatgaatggatcagattcagaattgctagaaactcatagcattgtgttcattggatcaaattctgatattagttatggtgtttttgttgcagGCAACCATTGGAATTGATTTTTTGTCAAAAACAATGTACCTTGAGGATAGGACTGTTCGTCTCCAACTATG
upper sequence: Vv00s0665g00040.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: AT4G39890.1 (Arabidopsis thaliana), 3'ss of exon 1
-aaaaagaaaaaaaaaattggtttatctaggtaat-ctgtctattggagttaaaattttaaattagttacattctcttgatactcctttttggtaattgcagGCTACCATTGGGATTGATTTTTTGTCTAAAACGATGTACCTTGAGGATCGAACAATTCGTTTGCAGCTTTG
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tcttattatgatcaagatcgatgatgctaagcactgttgcttctttgctttcttagtt--agtcattaagcctttatttgtgttctctctgactctctgcagCCTACCATTGGAATCGATTTTCTATCGAAAACAATGTACCTCGAAGATCGAACAGTTCGTTTGCAGCTATG
upper sequence: Vv00s0665g00040.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: AT2G22290.1 (Arabidopsis thaliana), 3'ss of exon 1
-aaaaagaaaaaaaaaattggtttatctaggtaatctgtctattggagttaaaattttaaattagttacattctcttgatactcctttttggtaattgcagGCTACCATTGGGATTGATTTTTTGTCTAAAACGATGTACCTTGAGGATCGAACAATTCGTTTGCAGCTTTG
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tagatcatgtagatacaatgctgaatgtaaatt-tcttttagttgtagtaatcttcacaaaatttatacattagtctcataaatctttgtttcattcacagGCTACTATTGGAATTGACTTCTTATCGAAAACAATGTACCTTGAAGATCGAACTGTTCGTCTGCAGCTATG
upper sequence: Vv00s0665g00040.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: PP1S346_29V6.1 (Physcomitrella patens), 3'ss of exon 2
------------------------------------------------------------------------------------------aaaaagaaaaaaaaaattggtttatctaggtaatctgtctattggagttaaaattttaaattagttacattctcttgatactcctttttggtaattgcagGCTACCATTGGGATTGATTTTTTGTCTAAAACGATGTACCTTGAGGATCGAACAATTCGTTTGCAGCTTTG
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gtgagattcttttttatcctctcatctgtgtataatagacttttactcgtaatccctgcagcttctgtgtgatttcattcaccatctttcaaagagatatagaaaat----atacattggtaattttgagaatacact--agacttgattttgaagaattaattatg----tcttgtttgatt-cgacagGCAACCATCGGTATTGATTTTCTCTCTAAGACCATGTACCTTGAGGATCGTACCGTGCGACTACAGCTCTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agttaaaattttaaattagttacattctcttgatactcctttttggtaattgcagGCTACCATTGGGATTGATTTTTTGTCTAAAACGATGTACCTTGAGGATCGAACAATTCGTTTGCAGCTTTG
tcttgat putative branch site (score: 4)
aaattttaaattagtt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aaaaagaaaaaaaaaattggtttatctaggtaatctgtctattggagttaaaattttaaattagttacattctcttgatactcctttttggtaattgcagGCTACCATTGGGATTGATTTTTTGTCTAAAACGATGTACCTTGAGGATCGAACAATTCGTTTGCAGCTTTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- aaagaaa
- - - aaaaaaa
- - - - - - - - - - - - - - - - - - - ctattgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cattctc