Sequence
atgc intronic sequence ATGC exonic sequencegtatgttctaatgctctatcctgaactccatgtattctccttaaattattcatgcactaaatgatgaaccgatctttgattttcaaagcattattctagttttatttttcttaatttattcagGTTGCACTCCTCTTCATTGGGCTGCTATTAGGGGCAACTTGGAGGCCAGTACCGTGTTAGTACAGGCTGGCAAGAAGGAAGATCTTATGGTGACTGATAA
Basic information
species | Glycine max |
transcript | GLYMA13G23230.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA13G23230.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os06g43680.1 (Oryza sativa), 3'ss of exon 4
gtatgttctaa--tgctctatcctga--actccatgtattctccttaaattattcatgc--actaaatgatgaaccg-atctttgatt------------ttcaaagcattattctagttttatttttcttaatttattc--agGTTGCACTCCTCTTCATTGGGCTGCTATTAGGGGCAACTTGGAGGCCAGTACCGTGTTAGTACAGGCTGGCAAGAAGGAAGATCTTATGGTGACTGATAA
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gcatgtgctaaatttatctatttccattattacctgtactgctgtgcacataacagtgtaaaccaatggcttagccatatctccaattatatcagtacacttcagagcatgagatttacttctttactacaatgctgcccctagGTTGTACCCCTTTACATTGGGCTGCTATTAGGGGGAACCTGGAGGCATGCACTGTGCTAGTTCAGGCTGGCAAAAAGGATGACTTGATGGTGAAGGATAA
upper sequence: GLYMA13G23230.1 (Glycine max), 3'ss of exon 5
lower sequence: AT5G20350.1 (Arabidopsis thaliana), 3'ss of exon 4
gtatgttctaatgctctatcctgaactccatgtattctccttaaattattcatgcactaaatgatgaaccgatctttgattttcaaagcattattctagttttatttttcttaatttattcagGTTGCACTCCTCTTCATTGGGCTGCTATTAGGGGCAACTTGGAGGCCAGTACCGTGTTAGTACAGGCTGGCAAGAAGGAAGATCTTATGGTGACTGATAA
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-----------------gtggttacaaacatattttttttttaaatcttctttgtttattttcttagattaactatacgtttctaa--catcttctccgttatattgattctg--ttat-cagGTTGCACTCCTCTGCATTGGGCTGCCATCCGAGGTAATTTGGAGGCTTGCACTGTCTTGGTGCAGGCTGGAAAGAAAGAGGATTTGATGATTACTGACAA
upper sequence: GLYMA13G23230.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv11s0118g00470.t01 (Vitis vinifera), 3'ss of exon 4
gtatgttctaatgctctatcctgaactccatgtattctcctt---------aaattattcat-gcactaaatgatgaaccgatctttgat---tttcaaagcattat--tctagttttatttttcttaattta--ttcagGTTGCACTCCTCTTCATTGGGCTGCTATTAGGGGCAACTTGGAGGCCAGTACCGTGTTAGTACAGGCTGGCAAGAAGGAAGATCTTATGGTGACTGATAA
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gtatgctttgatgctcagtaccttaattcattttttttttttcctgaaggaatatttttctttgtagaaacttaccattttatatctagaatatctcatattatcatcctcttgctcttgtttccacattgtaacttcagGTTGTACACCTCTCCATTGGGCTGCTATTAGGGGCAACTTAGAGGCATGCACAGTGTTAGTGCAGGCTGGGAAGAAGGAGGACCTAATGATGACCGACAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ccgatctttgattttcaaagcattattctagttttatttttcttaatttattcagGTTGCACTCCTCTTCATTGGGCTGCTATTAGGGGCAACTTGGAGGCCAGTACCGTGTTAGTACAGGCTGGCAAGAAGGAAGATCTTATGGTGACTGATAA
tcttaat putative branch site (score: 3)
tttattc CT-rich tract
aaagcattattctagt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgttctaatgctctatcctgaactccatgtattctccttaaattattcatgcactaaatgatgaaccgatctttgattttcaaagcattattctagttttatttttcttaatttattcagGTTGCACTCCTCTTCATTGGGCTGCTATTAGGGGCAACTTGGAGGCCAGTACCGTGTTAGTACAGGCTGGCAAGAAGGAAGATCTTATGGTGACTGATAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA