Sequence
atgc intronic sequence ATGC exonic sequence...cacaattgaataaacagccataatactcccttcaaaaattgaactttcagcaaatgactaaactaaagatcaggattattttacaattttttggtgatagTTTAAGAGGGTTGAGAGTATGTAAAAATGATGTAGTTGTGGCTGGTGGCATGGAAAGAATGTCTAATGCGCCTAAATACCTAGTAGATGCAAC
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv18s0089g00570.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: LOC_Os09g07830.1 (Oryza sativa), 3'ss of exon 4
--cacaattgaataaacagccata----atactcccttcaaaaattgaactttcagcaaatgactaaactaaagatcaggattattttacaattttt-tggtgatagTTTAAGAGGGTTGAGAGTATGTAAAAATGATGTAGTTGTGGCTGGTGGCATGGAAAGAATGTCTAATGCGCCTAAATACCTAGTAGATGCAAC
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gttacagttcatgaggcagcctttctataaattctgttcaagaaattatattt-acctgatca-tgggcttgtttttatttcctttctgcagCGACAATGTTTGCAGCACAGTCAATTCTAT--TGGGCATCAATGATATTGTTGTAGCCGGTGGCATGGAAAGCATGTCTAATGCTCCAAAATACATTGCTGA------
upper sequence: Vv18s0089g00570.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM5G866758_T02 (Zea mays), 3'ss of exon 4
--------cacaattgaataaacagccata-atactcccttcaaaaattgaactttcagcaaatgactaaactaaagatcaggattattttacaattttttggtgata-gTTT--AAGAGGGTTGA---GAGTATGTAAAAATGATGTAGTTGTGGCTGGTGGCATGGAAAGAATGTCTAATGCGCCTAAATACCTAGTAGATGCAAC
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gtttgaatcgaatttatctgtctgtccttgtgtactctgctcagagttcacagaagtgagagattacctgaccatgctcttgttttcctttcctatatgcagCTACTATGTTTGCAGCACAGTCAATTCAATTGGGTATCAATGATATTGTTGTGGCTGGTGGCATGGAAAGCATGTCCAATGCCCCAAAGTACATTGCTGA------
upper sequence: Vv18s0089g00570.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA07G39870.1 (Glycine max), 3'ss of exon 4
---cacaattgaataaacagccataatactcccttcaaaaattgaactttcagcaaatga--ctaaact--aaagatcaggattattttacaattttttggtgatagTTTAAGAGGGTTGAGAGTATGTAAAAATGATGTAGTTGTGGCTGGTGGCATGGAAAGAATGTCTAATGCGCCTAAATACCTAGTAGATGCAAC
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gtatgctgtttttcttgttgatttggaagggtattccactattcccacttaaatatatgaattttaattggaagggtccttgtcattgca-gCTACCATGCTTGCAGCACTCACCA--TACAATTTGGTCTCAATGATGTTGTTGTGGCTGGTGGTATGGAAAGCATGTCTAATGCACCTAAGTACCTTGCAGA------
upper sequence: Vv18s0089g00570.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA17G00910.1 (Glycine max), 3'ss of exon 4
--------cacaattgaataaacagccataatactcccttcaaaaattgaactttcagcaaatga--ctaaactaaagatcaggattattttacaattttt-tggtgatagTTTAAGAGGGTTGAGAGTATGTAAAAATGATGTAGTTGTGGCTGGTGGCATGGAAAGAATGTCTAATGCGCCTAAATACCTAGTAGATGCAAC
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gtatgttctttttttgttgttgttgatttggaagggtattccagtattcccacttaaatatatgaattttaattggaagggtccttttcattgcagCTACCATGCTTGCAGCACTCACCA--TACAATTCGGTCTCAATGATGTTGTTGTGGCTGGTGGTATGGAAAGCATGTCAAATGCACCTAAGTACATTGCGGA------ atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttcagcaaatgactaaactaaagatcaggattattttacaattttttggtgatagTTTAAGAGGGTTGAGAGTATGTAAAAATGATGTAGTTGTGGCTGGTGGCATGGAAAGAATGTCTAATGCGCCTAAATACCTAGTAGATGCAAC
aactaaa putative branch site (score: 2)
tttttt putative PPT
aggattattttacaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
cacaattgaataaacagccataatactcccttcaaaaattgaactttcagcaaatgactaaactaaagatcaggattattttacaattttttggtgatagTTTAAGAGGGTTGAGAGTATGTAAAAATGATGTAGTTGTGGCTGGTGGCATGGAAAGAATGTCTAATGCGCCTAAATACCTAGTAGATGCAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - -gaataaa
- - - - - - - cagccat
- - - - - - - - - - - - - -cccttca
- - - - - - - - - - - - - - - - - -aaattga
- - - - - - - - - - - - - - - - - - - - - - - tcagcaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaactaa