Sequence
atgc intronic sequence ATGC exonic sequencegtgagtgttataaatacttcatttttattctaggagtcataaataaagccgagctgatgtgtttcttgtctgtgcaacccactctcagGTTATCAGCAGAGTTGGTGACCTTGTGGGCATCAAATACTTCCCTGCAGAAACACCAAAGATTGCTGGAGCTGATCATGATAAGCTGGAGTAGGAATCAA
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G157249_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os11g31640.1 (Oryza sativa), 3'ss of exon 11
gtgagtgttataaatacttcatttt----tattctaggagtcataaataaagccgagctgatgtgtttcttgtctgtgcaacccactctcagGTTATCAGCAGAGTTGGTGACCTTGTGGGCATCAAATACTTCCCTGCAGAAACACCAAAGATTGCTGGAGCTGATCATGATAAGCTGGAGTAGGAATCAA
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gtgagtgctttcgtttgttaattttcggctgttcacatatgtttaaacggattccaattcacattgttctcatgtttgtaatccactc--agGTTATCAGCAGAGTTGGTGATCTTGTGGGCATCAAGTACTTCCCTGCGGAGCCGCCAAAGATTGCTGAAGCTGATCACGATAAGCTGGAGTAAATGATGA
upper sequence: GRMZM2G157249_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA16G26210.1 (Glycine max), 3'ss of exon 11
---gtgagtgttataa-atacttcatttt----tattctaggagtcataaataaagccgagctgatgtgtttcttgtctgtg----caacccactctcagGTTATCAGCAGAGTTGGTGACCTTGTGGGCATCAAATACTTCCCTGCAGAAACACCAAAGATTGCTGGAGCTGATCATGATAAGCTGGAGTAGGAATCAA
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attttgtttgttttgatatacttcttacagggattttgtttaaatttgctatttccatgatatgttgtgttaatttgctatgatcttctttctttcttagGTTATTAGCAGAGTGGGTGATCTTGTTGGCATAAAATACTTCCCTGCTGAACCAACAAAGCAGCAACAAGAAGGGGGTAAAACTGTGAAGTTTGATTGAG
upper sequence: GRMZM2G157249_T01 (Zea mays), 3'ss of exon 4
lower sequence: Vv14s0068g01300.t01 (Vitis vinifera), 3'ss of exon 11
------gtgagtgttataaatacttcatttttatt-ctaggagtcata-aataaa---gccgagctgatgtgtttcttgtctgtgcaacccactct--cagGTTATCAGCAGAGTTGGTGACCTTGTGGGCATCAAATACTTCCCTGCAGAAACACCAAAG--ATTGCTGGAGCTGATCATGATAAG-CTGGAGTAGGAATCAA
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ttcagaaattgtgttgctcttgtttcggatccatggttatgagtcttttaatgggtgtgctccatccatg-gttacacacttaaacagtttcttttgtcagGTTATCAGCCGAGTTGGCGATCTTGTTGGTATAAAATACTTCCCTGCGCAGCCCAAGGAGCAGCAACAAGAGGAAAAAACATCAAAACTGGACTGAAAGT---
upper sequence: GRMZM2G157249_T01 (Zea mays), 3'ss of exon 4
lower sequence: Vv17s0000g00500.t01 (Vitis vinifera), 3'ss of exon 12
------------gtgagtgt-tataaatacttcatttttattctaggagtcataaataaagccg-agctgatgtgtttcttgtctgtgcaacccactctcagGTTATCAGCAGAGTTGGTGACCTTGTGGGCATCAAATACTTCCCTGCAGAAACACCAAAG--ATTGCTGGAGCTGATCATGAT-AAGCTGGAGTAGGAATCAA
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tttaataataatgtgtacacacaaaaatactccattg--acacagaattttggtagtgtggttgtaaccaattttcttattggaccttctggtttttgtcagGTTATCAGCCGAGTTGGTGACCTAGTGGCCATAAAGTATTTCCCTGCTGAGCCCAGGAAGCAACAGCTGGAGGAAGGCAGAGTGAAACTGGAGTGAAAGA--- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gagtcataaataaagccgagctgatgtgtttcttgtctgtgcaacccactctcagGTTATCAGCAGAGTTGGTGACCTTGTGGGCATCAAATACTTCCCTGCAGAAACACCAAAGATTGCTGGAGCTGATCATGATAAGCTGGAGTAGGAATCAA
agctgat putative branch site (score: 4)
cccactctc putative PPT
ataaataaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagtgttataaatacttcatttttattctaggagtcataaataaagccgagctgatgtgtttcttgtctgtgcaacccactctcagGTTATCAGCAGAGTTGGTGACCTTGTGGGCATCAAATACTTCCCTGCAGAAACACCAAAGATTGCTGGAGCTGATCATGATAAGCTGGAGTAGGAATCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA