Sequence
atgc intronic sequence ATGC exonic sequence...tctgatcactattagcaatatgtttatttttttctgtagtgctcataaatatgcgtcataattttattattactattattattttgtcaatcttcaacagCAGTGGCTTGCCAAGATCAAATGAGGGCATGAGGCTCCTATTCTCAGCAGTTATTGGTGTTATGCTAGGTTACTTGTTTGGGATTTCATTTCCTACTGTC
Basic information
species | Oryza sativa |
transcript | LOC_Os01g68260.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g68260.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM5G801369_T01 (Zea mays), 3'ss of exon 2
-tctgatcactattagcaatatgtttatt-tttttctgtagtgct-cataaatatgcgtcataattttattattactattattattttgtcaatcttcaacagCAGTGGCTTGCCAAGATCAAATGAGGGCATGAGGCTCCTATTCTCAGCAGTTATTGGTGTTATGCTAGGTTACTTGTTTGGGATTTCATTTCCTACTGTC---
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gtatgttcgatgcttagagtttatgtattgctcttctgtatagcaacaaaagaataccttttaggtg-atcattcacacaaatacgt-attcatctcaatcttcagCAGTGCACAGAGATCAAATGAGGGCATGCGAATCATATTCTCAGCAGTTATTGGTGTTATGCTAGGGTACTTGTTTGGCATTTCCTTCCCTACCGTTAAT
upper sequence: LOC_Os01g68260.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM5G801369_T02 (Zea mays), 3'ss of exon 2
-tctgatcactattagcaatatgtttatt-tttttctgtagtgct-cataaatatgcgtcataattttattattactattattattttgtcaatcttcaacagCAGTGGCTTGCCAAGATCAAATGAGGGCATGAGGCTCCTATTCTCAGCAGTTATTGGTGTTATGCTAGGTTACTTGTTTGGGATTTCATTTCCTACTGTC------
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gtatgttcgatgcttagagtttatgtattgctcttctgtatagcaacaaaagaataccttttaggtg-atcattcacacaaatacgt-attcatctcaatcttcagcagTGCACAGAGATCAAATGAGGGCATGCGAATCATATTCTCAGCAGTTATTGGTGTTATGCTAGGGTACTTGTTTGGCATTTCCTTCCCTACCGTTAATATA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.taaatatgcgtcataattttattattactattattattttgtcaatcttcaacagCAGTGGCTTGCCAAGATCAAATGAGGGCATGAGGCTCCTATTCTCAGCAGTTATTGGTGTTATGCTAGGTTACTTGTTTGGGATTTCATTTCCTACTGTC
tcttc CT-rich tract
tcataattttattatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tctgatcactattagcaatatgtttatttttttctgtagtgctcataaatatgcgtcataattttattattactattattattttgtcaatcttcaacagCAGTGGCTTGCCAAGATCAAATGAGGGCATGAGGCTCCTATTCTCAGCAGTTATTGGTGTTATGCTAGGTTACTTGTTTGGGATTTCATTTCCTACTGTC
- - - - - - -agcaata
- - - - - - - - - - - - - - -ttttctg
- - - - - - - - - - - - - - - - - - tagtgct