Sequence
atgc intronic sequence ATGC exonic sequencegtaggtcatttcaattgtactatgatttgagctggaattttttttaatctcgtagatgccatcaatgcaatgcttttcaaaagtatgcctattctgttcaagttctttatgtaagggttttttttttgcagGCACTTCTTTTTCACAGCAATGTTGTTTACTTATGGGCGTTTTCTTAGTCGACAGCTTGTTAACACAGTAACTTCAGATCACTTATTGTATAAGGTTGTC
Basic information
species | Oryza sativa |
transcript | LOC_Os01g55360.3 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g55360.4 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G031052_T01 (Zea mays), 3'ss of exon 2
-------gtaggtcatttcaattgtactatgatttgagctggaattttttttaatctcgtagatgccatcaatgcaatgcttttcaaaagtatgcctattctgttcaagttctttatgtaagggttttttttt--tgcagGCACTTCTTTTTCACAGCAATGTTGTTTACTTATGGGCGTTTTCTTAGTCGACAGCTTGTTAACACAGTAACTTCAGATCACTTATTGTATAAGGTTGTC
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gtaagcaatggttcattttgattctaccaag-tttaaacaaaaatttgtc--aatttcatagctgacatg----------ctttcagcagtattttttcccgttgtgacgtttatacccaagtattatttcctattgtagGCACTT-TTTTTCACGGAAATGTTGTACACTTATGGGCGCTTTCTTAGTCGTCAGCTGGTGAATATAGTGACTTCAGATCACTTGCTTTATAAGTGA---
upper sequence: LOC_Os01g55360.4 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM5G825110_T01 (Zea mays), 3'ss of exon 3
gtaggtcatttcaattgtactatgatttgagctg-gaattttttttaatctcgtagatgccatc--aatgcaatgcttttcaaaagtatgcctattctgttcaagttctttatgtaagggt----tttttttttgcagGCACTTCTTTTTCACAGCAATGTTGTTTACTTATGGGCGTTTTCTTAGTCGACAGCTTGTTAACACAGTAACTTCAGATCACTTATTGTATAAGGTTGTC
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--------------------------gtaagttatgggtcattttgattctactaagtttaaactgaaattcacacttttcaacagta--ctttttttccttgtgtcatttatgcacaagtgtcatttcctattgtagGCACTTCTTTTTCACGGCAATGCTGTACACTTATGGGCGCTTTCTTAGTCGGCAGCTTGTGAATACAGTAACTTCA------------------------
upper sequence: LOC_Os01g55360.4 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM5G825110_T02 (Zea mays), 3'ss of exon 3
gtaggtcatttcaattgtactatgatttgagctg-gaattttttttaatctcgtagatgccatc--aatgcaatgcttttcaaaagtatgcctattctgttcaagttctttatgtaagggt----tttttttttgcagGCACTTCTTTTTCACAGCAATGTTGTTTACTTATGGGCGTTTTCTTAGTCGACAGCTTGTTAACACAGTAACTTCAGATCACTTATTGTATAAGGTTGTC
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--------------------------gtaagttatgggtcattttgattctactaagtttaaactgaaattcacacttttcaacagta--ctttttttccttgtgtcatttatgcacaagtgtcatttcctattgtagGCACTTCTTTTTCACGGCAATGCTGTACACTTATGGGCGCTTTCTTAGTCGGCAGCTTGTGAATACAGTAACTTCAGATCACTTGCTTTATAAGGTCGTT
upper sequence: LOC_Os01g55360.4 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G452529_T02 (Zea mays), 3'ss of exon 3
-------gtaggtcatttcaattgtactatgatttgagctggaattttttttaatctcgtagatgccatcaatgcaatgcttttcaaaagtatgcctattctgt-tcaagttctttatgtaagggtttttttt----ttgcagGCACTTCTTTTTCACAGCAATGTTGTTTACTTATGGGCGTTTTCTTAGTCGACAGCTTGTTAACACAGTAACTTCAGATCACTTATTGTATAAGGTTGTC
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gtaagcaatggttcattttgatcctaccaag-tttaaacagaaatttgtc--aatttcacagctgccat---------gcttttcaacagtattttttttttctgttgtgacgtttatgcccaagtattatttcctattgtagGCACTTCTTTTTCACGGCAATGCTGTACACTTATGGGCGCTTTCTTAGTCGTCAGCTGGTGAATACAGTGACTTCAGATCACTTGCTTTATAAGGTCGTCMapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|58689936|gb|CK078623.1|CK078623EST: AGAAAATCCAGTGAAGAAAAACAACTACCAGGTTTCAGGCTACTGAATTG GCACTTCTTTTTCACAGCAATGTTGTTTACTTATGGGCGTTTTCTTAGTCG
genomic: AGAAAATCCAGTGAAGAAAAACAACTACCAGGTTTCAGGCTACTGAATTGgtaggtcatt ... ttttttgcagGCACTTCTTTTTCACAGCAATGTTGTTTACTTATGGGCGTTTTCTTAGTCG
EST:
gi|29681974|gb|CB678249.1|CB678249EST: AGAAAATCCAGTGAAGAAAAACAACTACCAGGTTTCAGGCTACTGAATTG GCACTTCTTTTTCACAGCAATGTTGTTTACTTATGGGCGTTTTCTTAGTCG
genomic: AGAAAATCCAGTGAAGAAAAACAACTACCAGGTTTCAGGCTACTGAATTGgtaggtcatt ... ttttttgcagGCACTTCTTTTTCACAGCAATGTTGTTTACTTATGGGCGTTTTCTTAGTCG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcaaaagtatgcctattctgttcaagttctttatgtaagggttttttttttgcagGCACTTCTTTTTCACAGCAATGTTGTTTACTTATGGGCGTTTTCTTAGTCGACAGCTTGTTAACACAGTAACTTCAGATCACTTATTGTATAAGGTTGTC
ttttttttttgc CT-rich tract
tttttttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaggtcatttcaattgtactatgatttgagctggaattttttttaatctcgtagatgccatcaatgcaatgcttttcaaaagtatgcctattctgttcaagttctttatgtaagggttttttttttgcagGCACTTCTTTTTCACAGCAATGTTGTTTACTTATGGGCGTTTTCTTAGTCGACAGCTTGTTAACACAGTAACTTCAGATCACTTATTGTATAAGGTTGTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA