Sequence
atgc intronic sequence ATGC exonic sequence...ccaagtttagcaaagttagcattaaattttctattggttatgtgtagctatttagtgattgattgtctcaacctcctctttctgatgttatttattgcagCTTCCTCCTGAATGGATAGATCAGTTTGAGTCAGGCATTCAG
Basic information
species | Glycine max |
transcript | GLYMA06G36190.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA06G36190.1 (Glycine max), 3'ss of exon 4
lower sequence: AT5G53900.2 (Arabidopsis thaliana), 3'ss of exon 4
ccaagtttagcaaagttagcattaaatttt--ctattggttatgtgtagctatttagtgattgattgtctcaacctcctctttctgat--gttatttattgcagCTTCCTCCTGAATGGATAGATCAGTTTGAGTCAGGCATTCAG
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-------gtacgttttcaatcttaaattttattttttggttagatgtagaaatttatgatcctgatggct-accttacacttaaaagtcaaaaatttattgcagCTTCCTCCAGAATGGACCGACCAATTCGAATCAGGCATTCAG
upper sequence: GLYMA06G36190.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv19s0014g02320.t01 (Vitis vinifera), 3'ss of exon 4
------------------------------------------------------------------------------------ccaagtttagcaaagtt--agcattaaattttctattg-gttatgt-gtagctattta---gtgattgattgtctcaacctcctctttctgatgttatttattgcagCTTCCTCCTGAATGGATAGATCAGTTTGAGTCAGGCATTCAG
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gtaagtaggagaacctcaaacacaaacgttctcttttgattgggtatttgataaaactaattaccattgtgtgggcaaatagtgggtgatttgataaatttggagaaatgggttctttttggcatcatgtcgtggtctattatatgttaatgattgatgatgttcttagcttttggttgaattaattgcagCTTCCTCCTGAATGGACCGATCAGTTTGAGTCAGGCATTCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agctatttagtgattgattgtctcaacctcctctttctgatgttatttattgcagCTTCCTCCTGAATGGATAGATCAGTTTGAGTCAGGCATTCAG
ttctgat putative branch site (score: 3)
tgatgttatttatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ccaagtttagcaaagttagcattaaattttctattggttatgtgtagctatttagtgattgattgtctcaacctcctctttctgatgttatttattgcagCTTCCTCCTGAATGGATAGATCAGTTTGAGTCAGGCATTCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
- - - - - - - - - - - - - - - - - -ggttatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - gtgattg