Sequence
atgc intronic sequence ATGC exonic sequence...attcattactgttttttaatctttatttaaataaaactcgtgtgtgctagctataacttttttgggctagctaggaattacatggttaacttttgtgcagCAACATATATTACATAAATGATAATTTGGATAAGAGGACTTGGACTTATATCTTTGGAGCATGTTGTGCCACCACTGTATTTATCCCTTCCTTCCACAAC
Basic information
species | Glycine max |
transcript | GLYMA04G00640.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA04G00640.1 (Glycine max), 3'ss of exon 3
lower sequence: AT2G21050.1 (Arabidopsis thaliana), 3'ss of exon 3
attcattactgttttttaatctttatttaaataaaactcgtgtgtgctagctataacttttttgggctagctaggaattacatggttaacttttgtgcagCAACATATATTACATAAATGATAATTTGGATAAGAGGACTTGGACTTATATCTTTGGAGCATGTTGTGCCACCACTGTATTTATCCCTTCCTTCCACAAC
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-----------------gtactttatataccaattctttcttcaggaaaatgagactaatgatgtagtggtttaatggtaagtgaatgtgttgt-tgcagCAACATATATTACATAAATGATAATCTGGACAAGAGGACATGGACATACATATTTGGAGCATGTTGTGCAACCACAGTCTTTATTCCTTCCTTCCACAAC
upper sequence: GLYMA04G00640.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv03s0038g02140.t01 (Vitis vinifera), 3'ss of exon 3
----------------------------------------------------------attcattactgttttttaatctttatttaaata--aaactcgtgtgtgctagctataacttttttgggctagctaggaatt-------acatggt-taacttttgt-gcagCAACATATATTACATAAATGATAATTTGGATAAGAGGACTTGGACTTATATCTTTGGAGCATGTTGTGCCACCACTGTATTTATCCCTTCCTTCCACAAC
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gcatctccctctctccctccctatcctcctcctactactactctctctctctctctctctctttctctgtctcttgttttttcttcacccaccacatttttttttcctttctttacaataaacaaagatctgaggcattttctgcaactgggcatgtcgtttgttgcagCAACATATATTACATAAATGATAATCTGGACAAGAGGACATGGACTTACATCTTCGGAGCCTGCTGTGCCACCACAGTCTTTATTCCTTCATTCCACAAC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gctagctataacttttttgggctagctaggaattacatggttaacttttgtgcagCAACATATATTACATAAATGATAATTTGGATAAGAGGACTTGGACTTATATCTTTGGAGCATGTTGTGCCACCACTGTATTTATCCCTTCCTTCCACAAC
ggttaac putative branch site (score: 3)
cttttgt CT-rich tract
tataactttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
attcattactgttttttaatctttatttaaataaaactcgtgtgtgctagctataacttttttgggctagctaggaattacatggttaacttttgtgcagCAACATATATTACATAAATGATAATTTGGATAAGAGGACTTGGACTTATATCTTTGGAGCATGTTGTGCCACCACTGTATTTATCCCTTCCTTCCACAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - aaataaa
- - - - - - - - - - - - - - - - - - - -gtgtgtg