Sequence
atgc intronic sequence ATGC exonic sequence...gtaataaactgaccgtaaaatttattgcagaactgcctatgatgtgagcattaatgatgatacttggccaaaggaggcatttgagcttgtctctggagagATGTCAAAGACATTGGAAAGGCTTGACCC
Basic information
species | Oryza sativa |
transcript | LOC_Os01g01307.2 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g01307.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G376727_T05 (Zea mays), 3'ss of exon 1
-----------------------------------------------------------------------gtaataaactgaccgtaaaatttattgcagaactgcctatgatgtgagcattaatgatgatacttggccaaaggaggcatttgagcttgtctctggagagATGTCAAAGACATTGGAAAGGCTTGACCC
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ttgcatgaagtatacgtgttactttctgtttcatatgatggctaaccaatccgatatgttcccatagcatctgcatggacttat-gtaaagcctattgcagGACTGCCTATGATGTGTCACTTAATGACGACTCTTGGCCAACACAAGCATTTGAGCTTGTCACTGGAGAGAAATCGAAGACATTGGAAAGGCTTGACCC
upper sequence: LOC_Os01g01307.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G067476_T03 (Zea mays), 3'ss of exon 1
----------------------------------------------------------------------gtaataaactgaccgtaaaatttattgcagaactgcctatgatgtgagcattaatgatgatacttggccaaaggaggcatttgagcttgtctctggagagATGTCAAAGACATTGGAAAGGCTTGACCC
|| ||| | |||||| |||||||| ||||||||||||||| ||||||||| || ||||||||| || | |||||||||||| ||||||||| || |||||||||||||||||||||||
tgcatcatgtatatgtgctcccttccgtttcatatgacggcaaatcaatcccatatgttctcatagcatctgcatggacttattgtaaaacctattgcagGACTGCCTATGATGTGTCCATTAATGACGACTCTTGGCCAACAGAAGTGTTTGAGCTTGTCACTGGAGAGAAATCGAAGACATTGGAAAGGCTTGACCC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gagcattaatgatgatacttggccaaaggaggcatttgagcttgtctctggagagATGTCAAAGACATTGGAAAGGCTTGACCC
cattaat putative branch site (score: 3)
cttgtctct putative PPT
ttaatgat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaataaactgaccgtaaaatttattgcagaactgcctatgatgtgagcattaatgatgatacttggccaaaggaggcatttgagcttgtctctggagagATGTCAAAGACATTGGAAAGGCTTGACCC
- aataaac
- - - - - - - - - - - tattgca
- - - - - - - - - - - - - - - -actgcct
- - - - - - - - - - - - - - - - - - - atgatgt
- - - - - - - - - - - - - - - - - - - - - - - - - - -atgatga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gcatttg