Sequence
atgc intronic sequence ATGC exonic sequence...tcgttgcctaaaaatttgctgcatactttgttaggttgtgatgcattcatgttattctttgtctgattaaaaggtattctgctctttctgtctaattcagGCATCTAGCCCGTTGCAAGTGAAGTATGCAGATGGCGAGTTGGAAAGGCTAG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv07s0104g01150.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA10G02700.3 (Glycine max), 3'ss of exon 1
tcgttgcctaaaaatttgctgcatactttgttaggttgtgatgcattcatgttattctttgtctgattaaaaggtattctgctctttctgtctaattcagGCATCTAGCCCGTTGCAAGTGAAGTATGCAGATGGCGAGTTGGAAAGGCTAG
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caattgctgacattattgacatctttgcataataactatggtgagatggtattactattctcctgattgggaagcatcttattttttgtgtccaattcagGCATCTAGTCCGTTGCAAGTGAAGTATGCAGATGGTGAATTGGAAAGATTAG
upper sequence: Vv07s0104g01150.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA02G17090.1 (Glycine max), 3'ss of exon 2
tcgttgcctaaaaatttgctgcatactttgttaggttgtgatgcatt--catgttattctttgtctgattaaaaggtattctgctctttctgtctaattcagGCATCTAGCCCGTTGCAAGTGAAGTATGCAGATGGCGAGTTGGAAAGGCTAG
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--attgctgacattattgacatctttgcttaataactatggtgtgatgacatagtactattctcctgattgggaagcatcctattttttgtgtccaattcagGCATCTAGTCCGTTACAAGTGAAGTATGCAGATGGCGAATTGGAAAGATTAG
upper sequence: Vv07s0104g01150.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA03G36650.2 (Glycine max), 3'ss of exon 2
------tcgttgcctaaaaatttgctgcatactttgttaggttgtgatgcattcatgttattctttgtctgattaaaaggtattctgctctttc-tgtctaattcagGCATCTAGCCCGTTGCAAGTGAAGTATGCAGATGGCGAGTTGGAAAGGCTAG
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ttggtaataatgttgaggaagttattgc---tttagtaaccatgtgatatg---atactattctcattctgatttggaa-catcctgtttttctgtgtccaattcagGCATCTAGTCCATTACAAGTGAAGTATGCAGATGGGGAGTTGGAAAGATTAG
upper sequence: Vv07s0104g01150.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA19G39300.1 (Glycine max), 3'ss of exon 2
tcgttgcctaaaaatttgctgcatac-tttgttaggttgtgatgcatt--catgttattctttgtctgattaaaaggtattctgctctttc-tgtctaattcagGCATCTAGCCCGTTGCAAGTGAAGTATGCAGATGGCGAGTTGGAAAGGCTAG
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---ttagtaataatgttgtggaagatatttctttagtaacgatgtgatatgatattattctcattctgatttggaa-catcctgtttttctgtgtccatttcagGCATCTAGTCCATTACAAGTGAAGTATGCAGATGGCGAGCTGGAAAGATTAG
upper sequence: Vv07s0104g01150.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT1G03457.2 (Arabidopsis thaliana), 3'ss of exon 2
---------tcgttgcctaaaaatttgctgcatactttgttaggttgtgatgcattcatgttattctttgtctgattaaaaggtattctgctctttctgtctaattcagGCATCTAGCCCGTTGCAAGTGAAGTATGCAGATGGCGAGTTGGAAAGGCTAG
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tttctgtggccggtatctgaacattagg---atgctta--tgggctatg-tacactcttatccctctct--cgaattatagaattcact-ttcttatgatatgtttcagGCATCTAGTCCGTTGCAAGTTAAGTATGCAGATGGCGAGTTGGAAAGACTAG
upper sequence: Vv07s0104g01150.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT4G03110.1 (Arabidopsis thaliana), 3'ss of exon 2
--tcgttgcctaaaaatttgctgcatactttgttaggttgtgatgcattcatgttattctttgtctgattaaaaggtattctgctctttctgtctaattcagGCATCTAGCCCGTTGCAAGTGAAGTATGCAGATGGCGAGTTGGAAAGGCTAG
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catggttgtttcagtgtgttcttcggccttttgactgtaacatttaggatgcttagatccttgtcaggtctctaactaactttttcttttggtt--gctcagGCTAACAGTCTATTGCAAGTAAAGTATGCAGATGGCGAATTAGAAAGGCTAG
upper sequence: Vv07s0104g01150.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: PP1S12_239V6.1 (Physcomitrella patens), 3'ss of exon 4
tcgttgcctaaaaatttgctgcatactttgttaggttgtgatgcattcatgttattctttgtctgattaaaa---ggtattctgctctttctgtctaatt-cagGCATCTAGCCCGTTGCAAGTGAAGTATGCAGATGGCGAGTTGGAAAGGCTAG
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--aaagtccatgcatgtttaatgtttgcagcttaccttccatatattcac--caattggagacccgtaaaattctgatttactgatacatttctggaatgatagGTAGCCAGTCCCTTGCAAGTGAAGTATGCTGATGGCGAGATGGAACGATTAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttcatgttattctttgtctgattaaaaggtattctgctctttctgtctaattcagGCATCTAGCCCGTTGCAAGTGAAGTATGCAGATGGCGAGTTGGAAAGGCTAG
gtctaat putative branch site (score: 3)
ttctgctctttctgtc CT-rich tract
ttattcttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tcgttgcctaaaaatttgctgcatactttgttaggttgtgatgcattcatgttattctttgtctgattaaaaggtattctgctctttctgtctaattcagGCATCTAGCCCGTTGCAAGTGAAGTATGCAGATGGCGAGTTGGAAAGGCTAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - taaaaat
- - - - - - - - - - gcatact
- - - - - - - - - - - - - - - - -ggttgtg
- - - - - - - - - - - - - - - - - - - - - gcattca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -attaaaa