Sequence
atgc intronic sequence ATGC exonic sequence...tacctctgttgtctctggtacctctttcactatgcttgtaaggttttgtgtactgatagttgatattatcaatctggatctcatggttttctatgtttagGTATTGTGAATGCTTTGCATCGGGTGTTTACTGTGATGGATGCAACTGTTCCAACTGTTTTAATAATGTTAAGAACGAGACTGCTAGGCGTGAAGCTATT
Basic information
species | Oryza sativa |
transcript | LOC_Os01g55580.2 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g55580.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G104246_T02 (Zea mays), 3'ss of exon 2
--------tacctctgttgtctctggtacctctttc--actatgcttgtaaggttttgtgtactgatagttgatattatcaatctggatctcatggttttctatgtttagGTATTGTGAATGCTTTGCATCGGGTGTTTACTGTGATGGATGCAACTGTTCCAACTGTTTTAATAATGTTAAGAACGAGACTGCTAGGCGTGAAGCTATT
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agtaaaagaatgtactgtggttttgatatttttttccagctggacatcttgtgtacagtgtatacata-tccatctga--aatct---ttttatggttccttac----agATACTGTGAATGCTTCGCTTCTGGTACTCACTGTGATGGTTGCAACTGCACCAACTGTTTTAATAATCCTGAGAATGAGGTTGCCAGACGTGAAGCTATT
upper sequence: LOC_Os01g55580.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G059678_T01 (Zea mays), 3'ss of exon 2
tacctctgttgtctctggtacctctttcactatgcttgtaaggtttt----gtgtactgatagttgatat-tatcaatctgga----tctcatggttttctatgtttagGTATTGTGAATGCTTTGCATCGGGTGTTTACTGTGATGGATGCAACTGTTCCAACTGTTTTAATAATGTTAAGAACGAGACTGCTAGGCGTGAAGCTATT
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-----caggacctaaatacaaagaatgtactgtggttttggtatttttccagtagacatcttgtgtatatgtatccatttgaaaactttttatggttctttac----agGTACTGTGAATGCTTTGCTTCTGGTACTTACTGTGATGGTTGCAACTGCACCAACTGTTTTAATAATCCTGATAATGAGGTTGCCAGGCGTGAAGCTGTT
upper sequence: LOC_Os01g55580.2 (Oryza sativa), 3'ss of exon 2
lower sequence: AT2G20110.2 (Arabidopsis thaliana), 3'ss of exon 2
-tacctctgttgtctctggtacctctt--tcactatgcttgtaaggt-tttgtgtactgatagttgatattatcaatctggatctcatggttttctatgtttagGTATTGTGAATGCTTTGCATCGGGTGTTTACTGTGATGGATGCAACTGTTCCAACTGTTTTAATAATGTTAAGAACGAGACTGCTAGGCGTGAAGCTATT
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gtaagtctctcatc----ataccatttgatgacaaaactctttgtttctttgtggacttgttcattgtga-attgaacactgtacaatgtctttttttgatcagGTATTGTGAATGTTTTGCATCTGGCACTTACTGTGATGGTTGCAACTGTGTAAATTGTTTCAACAACGTTGAAAATGAACCTGCGAGACGACAAGCGGTTMapped 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|29621005|gb|CB626016.1|CB626016EST: CCGACAAAGAAGAAGTGCTGCAACTGCAAGCACTCCAAATGTTTGAAGTT GTATTGTGAATGCTTTGCATCGGGTGTTTACTGTGATGGATGCAACTGTTC
genomic: CCGACAAAGAAGAAGTGCTGCAACTGCAAGCACTCCAAATGTTTGAAGTTgtaagtcaga ... ctatgtttagGTATTGTGAATGCTTTGCATCGGGTGTTTACTGTGATGGATGCAACTGTTC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttgtgtactgatagttgatattatcaatctggatctcatggttttctatgtttagGTATTGTGAATGCTTTGCATCGGGTGTTTACTGTGATGGATGCAACTGTTCCAACTGTTTTAATAATGTTAAGAACGAGACTGCTAGGCGTGAAGCTATT
ttttctat CT-rich tract
atagttgatattat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tacctctgttgtctctggtacctctttcactatgcttgtaaggttttgtgtactgatagttgatattatcaatctggatctcatggttttctatgtttagGTATTGTGAATGCTTTGCATCGGGTGTTTACTGTGATGGATGCAACTGTTCCAACTGTTTTAATAATGTTAAGAACGAGACTGCTAGGCGTGAAGCTATT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC