Sequence
atgc intronic sequence ATGC exonic sequencegtatatacacacacatatatagacatatataattaacaactctacactactattaatgtttttttcagcaccctctatatatgttattaatttctcagtttcttcattaagtaggtcttaaaactttctgagtttttttattaattatatgttcataatttcatgatgtgtgcttagGCCTTCAGAGGTGTGGAAAGAGTTGCAGATTAAGATGGATAAATTATCTAAGACCTGATTTGAAACGTGGAAGTTTCTCTCCTCAAGAAGCAGCCCTCAT
Basic information
species | Glycine max |
transcript | GLYMA08G20440.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA08G20440.1 (Glycine max), 3'ss of exon 1
lower sequence: AT3G13890.1 (Arabidopsis thaliana), 3'ss of exon 1
gtatatacacacacatatatagacatatataattaacaactctacactactattaatgtttttttcagcaccctctatatatgttattaatttctcagtttcttcattaagtaggtcttaaaactttctgagtttttttattaattatatgttcataatttca-tgatgtgtgcttagGCCTTCAGAGGTGTGGAAAGAGTTGCAGATTAAGATGGATAAATTATCTAAGACCTGATTTGAAACGTGGAAGTTTCTCTCCTCAAGAAGCAGCCCTCAT
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-----------------------------------------------------------------------------------------gtttcttgaattatctat--actaa---taagaagtctttgtatttaggttttaatt---tctttgtggttttgcttgtgtttaattagGTTTGCAGAGATGTGGAAAGAGTTGTAGATTAAGATGGATAAATTATCTAAGACCTGATCTTAAACGTGGAAGCTTCTCTCCTCAAGAAGCTGCTCTTAT
upper sequence: GLYMA08G20440.1 (Glycine max), 3'ss of exon 1
lower sequence: AT3G13890.2 (Arabidopsis thaliana), 3'ss of exon 1
gtatatacacacacatatatagacatatataattaacaactctacactactattaatgtttttttcagcaccctctatatatgttattaatttctcagtttcttcattaagtaggtcttaaaactttctgagtttttttattaattatatgttcataatttca-tgatgtgtgcttagGCCTTCAGAGGTGTGGAAAGAGTTGCAGATTAAGATGGATAAATTATCTAAGACCTGATTTGAAACGTGGAAGTTTCTCTCCTCAAGAAGCAGCCCTCAT
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---------------------------------------------------------gcacttatacaca-----tatacatgggttttgtttcttgaattatctat--actaa---taagaagtctttgtatttaggttttaatt---tctttgtggttttgcttgtgtttaattagGTTTGCAGAGATGTGGAAAGAGTTGTAGATTAAGATGGATAAATTATCTAAGACCTGATCTTAAACGTGGAAGCTTCTCTCCTCAAGAAGCTGCTCTTAT
upper sequence: GLYMA08G20440.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv09s0002g01670.t01 (Vitis vinifera), 3'ss of exon 1
gtatatacacacacatatatagacatatataattaacaactctacactactattaatgtttttttcagcaccctctatatatgttattaatttctcagtttcttcattaagtaggtcttaaaactttctga-gtttttttattaattatatgttcataatttcatgatgtgtgcttagGCCTTCAGAGGTGTGGAAAGAGTTGCAGATTAAGATGGATAAATTATCTAAGACCTGATTTGAAACGTGGAAGTTTCTCTCCTCAAGAAGCAGCCCTCAT
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----------------------------------------------------------------------------ctctttctctctctctctctaatcacttttgcaggctaaccccacaatattttcatggctttctctttgttttcttctggttaaatcttgatggtggc--agGTCTGCAGAGATGTGGAAAGAGCTGCAGACTGAGATGGATAAATTACCTGAGACCTGACTTAAAACGTGGGAGCTTCTCTCCCCAAGAAGCTGCTCTCAT
upper sequence: GLYMA08G20440.1 (Glycine max), 3'ss of exon 1
lower sequence: PP1S149_164V6.1 (Physcomitrella patens), 3'ss of exon 1
gtatatacacacacatatatagacatatataattaacaactctacactactattaatgtttttttcagcaccctctatatatgttattaatttctcagtttcttcattaagtaggtcttaaaactttctgagtttttttattaattatatgttcataatttcatgatgtgtgcttagGCCTTCAGAGGTGTGGAAAGAGTTGCAGATTAAGATGGATAAATTATCTAAGACCTGATTTGAAACGTGGAAGTTTCTCTCCTCAAGAAGCAGCCCTCAT
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---------------------------------------------------------------cagaaagttttcttgattgccaatcagtttacta---tttttatacattgaatttaaaaaaactaatgtctatttcgtcgatcaca----cacaattgc------tgtaac-agGTCTTCAACGGTGTGGAAAGAGCTGCAGACTGCGGTGGATAAATTATCTCCGACCGGATTTGAAACGAGGAGTGTTTTCAGCGGCAGAAGAGAATTTGAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.actttctgagtttttttattaattatatgttcataatttcatgatgtgtgcttagGCCTTCAGAGGTGTGGAAAGAGTTGCAGATTAAGATGGATAAATTATCTAAGACCTGATTTGAAACGTGGAAGTTTCTCTCCTCAAGAAGCAGCCCTCAT
tattaat putative branch site (score: 2)
agtttttttattaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatatacacacacatatatagacatatataattaacaactctacactactattaatgtttttttcagcaccctctatatatgttattaatttctcagtttcttcattaagtaggtcttaaaactttctgagtttttttattaattatatgttcataatttcatgatgtgtgcttagGCCTTCAGAGGTGTGGAAAGAGTTGCAGATTAAGATGGATAAATTATCTAAGACCTGATTTGAAACGTGGAAGTTTCTCTCCTCAAGAAGCAGCCCTCAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC