Sequence
atgc intronic sequence ATGC exonic sequencegtgagaattttatatcttcaatcagattgagattgacttaattgcttatctaggctactattctcactccataactatgatagcttcgggttccataacatgatgtgtttctcaaaaaatgatatgatatgatgcagATAAAATGGATTTGCCCTACTGCTCCTACCCGTCCTGTGGCGATACTTGGTGGTTTTCCCTGCACTGCAT
Basic information
species | Glycine max |
transcript | GLYMA13G43990.2 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA13G43990.2 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os01g42690.2 (Oryza sativa), 3'ss of exon 3
gtgagaattttatatcttcaatcagattgagattgacttaattgcttatctaggctactattctcactccataactatgatagcttcgggttccataacatgatgtgtttctcaaaaaatgatatgata-tgatgcagATAAAATGGATTTGCCCTACTGCTCCTACCCGTCCTGTGGCGATACTTGGTGGTTTTCCCTGCACTGCAT
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-----------------------aggttagccatagc--aattttttaaaaagatttttagcaatagcat-tgttcatgctagttctaagtttattaac----------tctcaagc--ttataccatccttatgcagATCAAATGGATTTGCCCTACTGCACCAACACGCCCTGTTGCTGCTTTCGGTGGATTCCCTTGCACAGCAT
upper sequence: GLYMA13G43990.2 (Glycine max), 3'ss of exon 4
lower sequence: Vv09s0002g06010.t01 (Vitis vinifera), 3'ss of exon 4
gtgagaattttatatcttcaatcagattgagattgacttaattgcttatctaggctactattctcactccataactatgatagcttcgggttccataacatgatgtgtttctcaaaaaatgatatgatatgatgcagATAAAATGGATTTGCCCTACTGCTCCTACCCGTCCTGTGGCGATACTTGGTGGTTTTCCCTGCACTGCAT
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-----------------------------------------------------------gtaaggatttgtttttttaaattgcttttgggcttataaaaccacaaatcttactgt---tcaaattctatgatgcagATAAAATGGATTTGTCCAACTGCTCCTACTCGTCCTGTTGCAGTACTCGGTGGATTTCCTTGCACTGCAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gcttcgggttccataacatgatgtgtttctcaaaaaatgatatgatatgatgcagATAAAATGGATTTGCCCTACTGCTCCTACCCGTCCTGTGGCGATACTTGGTGGTTTTCCCTGCACTGCAT
ccataac putative branch site (score: 3)
aaaaaatgatatgata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagaattttatatcttcaatcagattgagattgacttaattgcttatctaggctactattctcactccataactatgatagcttcgggttccataacatgatgtgtttctcaaaaaatgatatgatatgatgcagATAAAATGGATTTGCCCTACTGCTCCTACCCGTCCTGTGGCGATACTTGGTGGTTTTCCCTGCACTGCAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG