Sequence
atgc intronic sequence ATGC exonic sequence...gttaaaatatctctcatctgttccatatgtgttattgtaagtcacatatatgagaatctctagtgtaatttatttctcacttttctttggtgcggtgtagCCTTCTTTATGGAGCTGAAGACCCTTCTATTGCTGGAATGGTGTTGGATAGTGCCTTTTCAAACTTATATGATCTGATGATGGAGCTTGCTGATGTCTAT
Basic information
species | Glycine max |
transcript | GLYMA09G02050.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA09G02050.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os02g10440.1 (Oryza sativa), 3'ss of exon 5
gttaaaatatctctcatctgttccatatgtgttat-tgtaagtcacatatatgagaatctctagtgtaatttatttctcacttttct--ttggtgcggtgtagCCTTCTTTATGGAGCTGAAGACCCTTCTATTGCTGGAATGGTGTTGGATAGTGCCTTTTCAAACTTATATGATCTGATGATGGAGCTTGCTGATGTCTAT
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ctttgagttcatgtcatgtataagatgtcttaaatatgtgatctttgcgtaacgga---tccatcccaattcattcgttgttttgtgaactaatgtaatacagCCTACTCTATGGAGCAGAAGATTCCTCGATTGCTGGAATGGTATTGGATAGTGCTTTCACTAACTTATATGGCTTGATGATGGAGCTTGTGGATGTCTAC
upper sequence: GLYMA09G02050.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G092895_T01 (Zea mays), 3'ss of exon 5
gttaaaatatctctcatctgttccatatgtgttattgtaagtcacatat-atgagaatctctagtgtaatttatttctcacttttctttggtgcggtgtagCCTTCTTTATGGAGCTGAAGACCCTTCTATTGCTGGAATGGTGTTGGATAGTGCCTTTTCAAACTTATATGATCTGATGATGGAGCTTGCTGATGTCTAT
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-cggtacttgcatttaacgctgcaaaatatcttgatttaaattattcttgatatatgtgcattttgatatttcatgacaatttgtgttatgtctgctgcagTCTGCTATATGGAGCAGAAGACCCCTCAATTGCTGGCATGGTTCTGGATAGTGCTTTCGCTAACTTATATGACTTAATGATGGAGCTTGTAGAAGTTTAC
upper sequence: GLYMA09G02050.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G081642_T04 (Zea mays), 3'ss of exon 5
--gttaaaatatctctcatct-gttccatatgtgttattgtaagtcacatatatgagaatctctagtgtaatttatttctcacttttcttt---ggtgcgg-tgtagCCTTCTTTATGGAGCTGAAGACCCTTCTATTGCTGGAATGGTGTTGGATAGTGCCTTTTCAAACTTATATGATCTGATGATGGAGCTTGCTGATGTCTAT
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ccgctttaaaaaccatggtcaagcttgaaatatctcatcaccacttg-----atggctgtcccc--tttaattctttacaatattttgtatacaaatgtaaatacagCCTACTCTATGGAGCAGAGGACCCTTCTATTGGTGGCATGATATTGGATAGTGCCTTCACTAACCTGTATGACTTGATGATGGAACTTGTTGACGTTTAC
upper sequence: GLYMA09G02050.1 (Glycine max), 3'ss of exon 6
lower sequence: AT4G17150.2 (Arabidopsis thaliana), 3'ss of exon 5
-----------------------------------------------------gttaaaatatctctcatctgttccatatgtgt-tattgtaagtcacatatatgagaatctctagtgtaatttatttctcacttttctttggtgcgg-------------tgtagCCTTCTTTATGGAGCTGAAGACCCTTCTATTGCTGGAATGGTGTTGGATAGTGCCTTTTCAAACTTATATGATCTGATGATGGAGCTTGCTGATGTCTAT
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gttacttcttgagctacttttcagtcacacttaaaagtagtattagtagttgtgttgactatagattcaccagctttctaaaggtctatgatctgaaaagtgtgtcaactctccacatttcatcttgttctctccatcatttgatgaagcgggaatataatgtgcagCCTTCTCTATGGAGCAGAAGATCCTTCAATTGCTGGAATGGTCCTAGACAGTGCATTTTCAAACTTATTTGATCTGATGATGGAACTAGTGGATGTCTAC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atatatgagaatctctagtgtaatttatttctcacttttctttggtgcggtgtagCCTTCTTTATGGAGCTGAAGACCCTTCTATTGCTGGAATGGTGTTGGATAGTGCCTTTTCAAACTTATATGATCTGATGATGGAGCTTGCTGATGTCTAT
ttctcac putative branch site (score: 2)
tagtgtaatttattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttaaaatatctctcatctgttccatatgtgttattgtaagtcacatatatgagaatctctagtgtaatttatttctcacttttctttggtgcggtgtagCCTTCTTTATGGAGCTGAAGACCCTTCTATTGCTGGAATGGTGTTGGATAGTGCCTTTTCAAACTTATATGATCTGATGATGGAGCTTGCTGATGTCTAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - -ctgttcc
- - - - - - - - - - - - -tatgtgt