Sequence
atgc intronic sequence ATGC exonic sequence...aacctctgtgtgtctgtgcaaaggatcatgaaccatgtgcctttctcttgcttgtctctaaaggatgtgtgggatctaacttcggcccctggtttctcagGTTGGAGATTTTGGACTGGCAAGGTGGCAGCCAGATGGAGACATGGGAGTGGAAACACGAATAATTGGAACATTTGG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv11s0016g02430.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: LOC_Os01g41870.1 (Oryza sativa), 3'ss of exon 6
aacctctgtgtgtctg-tgcaaaggatcatgaaccatgtgcctttctcttgcttgtctctaaaggatgtgtgggatctaacttcggcccctggtttctcagGTTGGAGATTTTGGACTGGCAAGGTGGCAGCCAGATGGAGACATGGGAGTGGAAACACGAATAATTGGAACATTTGG
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acctaatgtctgttgaactcgattgtataggcatcttgtattcttgttaacttcacaatcctaagataag-gttgtaagtctttcaataatgttctgacagGTTGGAGATTTTGGGTTGGCACGATGGCAACCTGATGGTGACATGGGTGTTGACACGAGAGTAATTGGAACATTCGG
upper sequence: Vv11s0016g02430.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA05G36280.1 (Glycine max), 3'ss of exon 5
-------------------------------------------------------------------------aacctctgtgtgtctgtgcaaaggatcatgaaccatgtgcct---ttctcttgcttgtctctaaaggatgtgtgggatctaacttcggcccctggtt--tctcagGTTGGAGATTTTGGACTGGCAAGGTGGCAGCCAGATGGAGACATGGGAGTGGAAACACGAATAATTGGAACATTTGG
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gtacgtctcattcttcaatttcaaaaatggactaatgagtgttcacataatggtttcatatgctgtttagagcaattact-tacttctgtttaaagattgcttatctatgaagccatatgttcataactatgcttttagg-tatgttttataatatgaaatgtcttaattaattttagGTAGGAGATTTTGGACTAGCAAGGTGGCAGCCAGATGGAGACATGGGTGTGGAAACCAGGGTGATAGGAACATTTGG
upper sequence: Vv11s0016g02430.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA08G03340.2 (Glycine max), 3'ss of exon 4
--------------------------------------------------------------------------aacctctgtgtgtctgtgcaaaggat--catgaaccatgtgcctttctcttgcttgt-ctctaaaggatgtgtgggatctaacttcggcccctggtttctcagGTTGGAGATTTTGGACTGGCAAGGTGGCAGCCAGATGGAGACATGGGAGTGGAAACACGAATAATTGGAACATTTGG
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gtacgtcttattcttcaatttcaaaaatggactgatgagtgttcacattaatggtttcatatgctttatacagcaatgact-tacttctgtttgaagattgctttctatgaagcaatatgttcataactatgcttttaggtatgtttgaaaatatgaaatgtctcaaataattttagGTAGGAGATTTTGGACTAGCAAGGTGGCAGCCAGATGGAGACATGGGTGTGGAAACCAGGGTCATAGGAACATTTGG
upper sequence: Vv11s0016g02430.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: PP1S336_36V6.1 (Physcomitrella patens), 3'ss of exon 6
--------aacctctgtgtgtctgtgcaaaggatcatgaaccatgtgcctttctcttgcttgt---ctctaaaggatgtgtgg-----gatctaacttcggcccctggtttctcagGTTGGAGATTTTGGACTGGCAAGGTGGCAGCCAGATGGAGACATGGGAGTGGAAACACGAATAATTGGAACATTTGG
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gtatgcatcgtagcagaaattcttttcaattcaagtagttccatttcctactcctaagctggcagattcttacacttgagtagtcattgagagaagttttgttctttggatatcagGTGGGAGATTTTGGACTCGCAAGATGGCAGCCAGACGGACATTGTGGTGTGGAGACCAGGGTTATTGGCACTTTCGG
upper sequence: Vv11s0016g02430.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: PP1S59_359V6.1 (Physcomitrella patens), 3'ss of exon 5
aacctctgtgtgtctgtgcaaaggatcatgaaccatgtgcctttctcttgcttgtctctaaagg-atgtgtgggatctaacttcggcccctg-----------gtttct-------cagGTTGGAGATTTTGGACTGGCAAGGTGGCAGCCAGATGGAGACATGGGAGTGGAAACACGAATAATTGGAACATTTGG
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---gtatgtggcgttccacacactgtttcgaacggtaaatgtttctgtttattgtctgaatggccacatgcctattcctaatgtggttaccgacagcacaagtgttttttggatatcagGTTGGAGATTTTGGACTTGCAAGATGGCAACCAGATGGACATTGTGGTGTGGAGACCAGGGTTATTGGCACCTTCGG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcttgcttgtctctaaaggatgtgtgggatctaacttcggcccctggtttctcagGTTGGAGATTTTGGACTGGCAAGGTGGCAGCCAGATGGAGACATGGGAGTGGAAACACGAATAATTGGAACATTTGG
atctaac putative branch site (score: 2)
tttctc putative PPT
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aacctctgtgtgtctgtgcaaaggatcatgaaccatgtgcctttctcttgcttgtctctaaaggatgtgtgggatctaacttcggcccctggtttctcagGTTGGAGATTTTGGACTGGCAAGGTGGCAGCCAGATGGAGACATGGGAGTGGAAACACGAATAATTGGAACATTTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- cctctgt
- - - - - tgtctgt
- - - - - - - - - caaagga
- - - - - - - - - -aaaggat
- - - - - - - - - - - - - catgaac
- - - - - - - - - - - - - - - - -catgtgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gtgtggg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cggcccc
