Sequence
atgc intronic sequence ATGC exonic sequencegtatgctccaaccccatcattttacttaacaaaattattcttcatacataataaattaataataatgttgataaagaataacgataaatgatgatgaacaagagttaattaaaataaatgactggttttgatgaaacagGTAAAAGGAGAAATCACATACAATGGACATAAACTTAATGAGTTTGAGCCTAGAAAAACTTCAGCATACATTAGCCAAAATGATGTTCATGTTGGAGAAA
Basic information
species | Glycine max |
transcript | GLYMA08G21540.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA08G21540.2 (Glycine max), 3'ss of exon 3
lower sequence: AT3G16340.1 (Arabidopsis thaliana), 3'ss of exon 3
gtatgctccaaccccatcattttacttaacaaaattattcttcatacataataaattaataataatgttgataaagaataacgataaatgatgatgaacaagagttaattaaaataaatgactggttttgatgaaacagGTAAAAGGAGAAATCACATACAATGGACATAAACTTAATGAGTTTGAGCCTAGAAAAACTTCAGCATACATTAGCCAAAATGATGTTCATGTTGGAGAAA
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------------------------------------------------------gttaa--ataatacacattatgattattgattacacattctagaaaaaaagagact----taaattattaatgaaaatgga-cagGTGACAGGGAGAGTAACATACAATGGGCATGGATTGGAAGAGTTTGTGCCACAGAAAACATCAGCATACATAAGCCAAAACGATGTTCATGTTGGAGTCA
upper sequence: GLYMA08G21540.2 (Glycine max), 3'ss of exon 3
lower sequence: Vv09s0002g03640.t01 (Vitis vinifera), 3'ss of exon 3
gtatgctccaaccccatcattttacttaacaaaattattcttcatacataataaattaat--aataatgttgataaagaataacgataaatgatgatgaacaagagttaattaaaataaatgactggttttgatgaaacagGTAAAAGGAGAAATCACATACAATGGACATAAACTTAATGAGTTTGAGCCTAGAAAAACTTCAGCATACATTAGCCAAAATGATGTTCATGTTGGAGAAA
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------gtcagttttcatattttgc---atgggctcacatcttacaaaaaattagcttgtttggtaagtctaaaagtatataatatgatataatattaattactcatc--ttataatag-taattaatttgcatggaacagGTCAGAGGGGAAGTGACTTATAATGGCCATAGGCTCAATGAATTTGTGCCACAGAAGACATCGGCATACATTAGCCAAAATGATGTTCACATAGGAGAAA
upper sequence: GLYMA08G21540.2 (Glycine max), 3'ss of exon 3
lower sequence: Vv09s0002g03550.t01 (Vitis vinifera), 3'ss of exon 3
gtatgctccaaccccatcattttacttaacaaaattattcttcatacataataaattaat--aataatgttgataaagaataacgataaatgatgatgaacaagagttaattaaaataaatgactggttttgatgaaacagGTAAAAGGAGAAATCACATACAATGGACATAAACTTAATGAGTTTGAGCCTAGAAAAACTTCAGCATACATTAGCCAAAATGATGTTCATGTTGGAGAAA
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------gtcagttttcatattttgc---atgggctcacatcttataaaaaattagcttgtttggtaagtctaaaagtatataatatgatataatattaattactcatc--ttataatac-taattaatttgcatggaacagGTCAGAGGGGAAGTGACTTATAATGGGCATAGGCTAAATGAATTTGTGCCACAGAAGACATCGGCATACATTAGCCAAAATGATGTTCACATAGGAGAAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.taaatgatgatgaacaagagttaattaaaataaatgactggttttgatgaaacagGTAAAAGGAGAAATCACATACAATGGACATAAACTTAATGAGTTTGAGCCTAGAAAAACTTCAGCATACATTAGCCAAAATGATGTTCATGTTGGAGAAA
ttttgat putative branch site (score: 4)
aacaagagttaattaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgctccaaccccatcattttacttaacaaaattattcttcatacataataaattaataataatgttgataaagaataacgataaatgatgatgaacaagagttaattaaaataaatgactggttttgatgaaacagGTAAAAGGAGAAATCACATACAATGGACATAAACTTAATGAGTTTGAGCCTAGAAAAACTTCAGCATACATTAGCCAAAATGATGTTCATGTTGGAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA