Sequence
atgc intronic sequence ATGC exonic sequence...cgattttagcttagagtgagtttgcttgttcttactgtagacactgataatgtatcgattcaacgctctcatcaggtgtgcaccattcctctcgacacagCCAAAGTGCGGCTTCAGCTGCAAAAGAAAGCAGCCCTAGCTACAGGCGGAGGAGGAGGGACCACTGGAGGAATGCTGGGCACAATAATGTGCATCGCAAG
Basic information
species | Oryza sativa |
transcript | LOC_Os01g74640.3 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g74640.3 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G165629_T02 (Zea mays), 3'ss of exon 1
----------------------cgattttagcttagagtgagtttgcttgttcttactgtagacactgataatgtatcgatt---caacgctctcatcaggtgtgcaccattcctctcgacacagCCAAAGTGCGGCTTCAGCTGCAAAAGAAAGCAGCCCTAGCTACAGGCGGAGGAGGAGGGACCACTGGAGGAATGCTGGGCACAATAATGTGCATCGCAAG
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ttaaaaataggagtatgattatttgatctaaaaaagaatggatctcactgtcaacgatttgggtttggagccagctttgatttaccaatgatataatcagGTGTGCACCATTCCTTTGGACACAGCCAAAGTGCGGCTCCAGCTGCAAAGGAAGGCGCCACTA-CCGCTGCCACCGGCGGCTGCAGCAGCC-ACAGCTGCTG-----------------------
upper sequence: LOC_Os01g74640.3 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM5G852877_T02 (Zea mays), 3'ss of exon 1
---------------------cgattttagcttagagtgagtt-tgcttgttcttactgtagacactgataatgtatcgatt---caacgctctcatcaggtgtgcaccattcctctcgacacagCCAAAGTGCGGCTTCAGCTGCAAAAGAAAGCAGCCCTA--GCTACAGGCGGAGGAGG-AGGGACCACTGGAGGAATGCTGGGCACAATAATGTGCATCGCAAG
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gcttcttcaaagaaagtaggacgatgtttatttgatctcagacacaagtgtcaacgattttggcttggagtcagctttgatttaccagtgatataatcagGTGTGCACCATTCCTTTGGACACAGCCAAAGTGCGGCTCCAGCTGCAAAGGAAGGCACCACTACCGTCGCCACCAGTGGCTGCAGCAGCTGCTGCTGGAG----------------------------
upper sequence: LOC_Os01g74640.3 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM5G852877_T01 (Zea mays), 3'ss of exon 1
--cgattttagcttaga-gtgagtttgcttgttcttactgtagacactgataatgtatcgattcaacgctctcatcaggtgtgcaccattcctctcgacacagCCAAAGTGCGGCTTCAGCTGCAAAAGAAAGCAGCCCTA-----GCTACAGGCGGAGG-AGGAGGGACCACTGGAGGAATGCTGGGCACAATAATGTGCATCGCAAG
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gtttatttgatctcagacacaagtgtcaacgattttggcttggagtcagct--ttgatttac-cagtgatataatcaggtgtgcaccattcctttggacacagCCAAAGTGCGGCTCCAGCTGCAAAGGAAGGCACCACTACCGTCGCCACCAGTGGCTGCAGCAGCTGCTGCTGGAGGCACGCTAGCCACAATCATGTGCAT------Mapped 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|88329968|gb|CI652356.1|CI652356EST: CCTTCGCCGCCGTCTTCTTCAGCAGCGCCTTCGCTGCCTGCTTCGCTGAG CCAAAGTGCGGCTTCAGCTGCAAAAGAAAGCAGCCCTAGCTACAGGCGGAG
genomic: CCTTCGCCGCCGTCTTCTTCAGCAGCGCCTTCGCTGCCTGCTTCGCTGAGgtaagcacgc ... ctcgacacagCCAAAGTGCGGCTTCAGCTGCAAAAGAAAGCAGCCCTAGCTACAGGCGGAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gataatgtatcgattcaacgctctcatcaggtgtgcaccattcctctcgacacagCCAAAGTGCGGCTTCAGCTGCAAAAGAAAGCAGCCCTAGCTACAGGCGGAGGAGGAGGGACCACTGGAGGAATGCTGGGCACAATAATGTGCATCGCAAG
cactgat putative branch site (score: 3)
ccattcctctc putative PPT
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
cgattttagcttagagtgagtttgcttgttcttactgtagacactgataatgtatcgattcaacgctctcatcaggtgtgcaccattcctctcgacacagCCAAAGTGCGGCTTCAGCTGCAAAAGAAAGCAGCCCTAGCTACAGGCGGAGGAGGAGGGACCACTGGAGGAATGCTGGGCACAATAATGTGCATCGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - -ttgcttg
- - - - - - - - - - - - - - - cttactg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccattcc