Sequence
atgc intronic sequence ATGC exonic sequence...caatgattattgtgaaattgtgctgttctgcttggaacagtagctcactttgcagatagacactgagaatttactcgtttcttgtttcatggagcagcagGAGGTGTCGCCGCTGACCTCCGGCCGCCTCTCACACAGCAGCGGCCCTCTCAACGGCGGCGGCTCGCTCTCCGACAGCCCACCGGTCTCGCCGGACGTCG
Basic information
species | Oryza sativa |
transcript | LOC_Os12g41140.3 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os12g41140.3 (Oryza sativa), 3'ss of exon 1
lower sequence: AT3G63300.1 (Arabidopsis thaliana), 3'ss of exon 1
caatgattattgtgaaattgtgctgttctgcttggaacagtagctcactttgcagatagacactgagaatttactcgtttcttgtttcatggagcagcagGAGGTGTCGCCGCTGACCTCCGGCCGCCTCTCACACAGCAGCGGCCCTCTCAACGGCGGCGGCTCGCTCTCCGA------CAGCCCACCGGTCTCGCCGGACGTCG
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-----------gtacggttacatagttatggaccgaccgaca---cactctgtttttgtatcttgatgatgagtttatt--ctgttttgaaaaat-gaagGAGGTGTCACCGTTAACGTCGGGGAGGCTATCACACAGCAGCGGCCCACTCAACGGCGGCGGTTCTTTTACGGAGACAGACAGTCCTCCTATCTCCCCTT------
upper sequence: LOC_Os12g41140.3 (Oryza sativa), 3'ss of exon 1
lower sequence: Vv05s0020g04020.t01 (Vitis vinifera), 3'ss of exon 1
--------caatgattattgtgaaattgtgctgttctgcttggaacagtagctcactttgcagatagacactgagaatttactcgtttcttgtttcatggagcagcagGAGGTGTCGCCGCTGACCTCCGGCCGCCTCTCACACAGCAGCGGCCCTCTCAACGGCG---------GCGGCTCGCTCTCCGACAGCCCACCGGTCTCGCCGGACGTCG
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ttcaagtaatatgattattat--aatcacactcacccac--aaatccttcgcgctaatcatcaccattccattccatcattaacactcttcatctc-tgttacagCAGGAGGTGTCCCCGCGCACTTCAGGCCGTCTCTCACACAGCAGTGGCCCCCTCAACGGAACTCAGAGTTGTGGCTCCTTAACGGACAGCCCCCCAGTCT------------ atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cactttgcagatagacactgagaatttactcgtttcttgtttcatggagcagcagGAGGTGTCGCCGCTGACCTCCGGCCGCCTCTCACACAGCAGCGGCCCTCTCAACGGCGGCGGCTCGCTCTCCGACAGCCCACCGGTCTCGCCGGACGTCG
agctcac putative branch site (score: 3)
agaattta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
caatgattattgtgaaattgtgctgttctgcttggaacagtagctcactttgcagatagacactgagaatttactcgtttcttgtttcatggagcagcagGAGGTGTCGCCGCTGACCTCCGGCCGCCTCTCACACAGCAGCGGCCCTCTCAACGGCGGCGGCTCGCTCTCCGACAGCCCACCGGTCTCGCCGGACGTCG
- - - - - - - - - - tgctgtt
- - - - - - - - - - - - - -ctgcttg
- - - - - - - - - - - - - - - - - - -cagtagc
- - - - - - - - - - - - - - - - - - - - - - - -ctttgca