Sequence
atgc intronic sequence ATGC exonic sequence...tcagtttagataaacagctactttgcaaattacaactccagatggcattcgacactgatatcctcaaaattatttaagcgacgctacctactgttttcagGCAGCAGCAATACGATTGGAGATCAAAGGTGGGCAATGGAGGGATGCATACATGCAAATGGATGGGGAGCCATGGAAGCAACCATTGGACCACGAGTACT
Basic information
species | Oryza sativa |
transcript | LOC_Os08g15090.1 |
intron # | 13 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os08g15090.1 (Oryza sativa), 3'ss of exon 13
lower sequence: GRMZM2G073380_T01 (Zea mays), 3'ss of exon 5
-----------------tcagtttagataaacagctactttgcaaattacaactccagatggcattcgacactgatatcctcaaaattatttaagc-gacgctacctactgttttcagGCAGCAGCAATACGATTGGAGATCAAAGGTGGGCAATGGAGGGATGCATACATGCAAATGGATGGGGAGCCATGGAAGCAACCATTGGACCACGAGTACT
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gtaacttgctcccccaaacaaaaacaaaaaaaaagtattctataaactatag----aaagaatatttattacttcattcagaagcaccgcataatttggtgcta------atgttcagGCAGCGGCAATACGGATAGAGATCAAAGGTGGGTATTGGCACGACGCGTTCATGCAAATGGACGGGGAGCCATGGAAGCAACCACTTAGCTCCGAGTATT
upper sequence: LOC_Os08g15090.1 (Oryza sativa), 3'ss of exon 13
lower sequence: GLYMA17G07480.1 (Glycine max), 3'ss of exon 11
tcagtttagataaacagctactttgcaaattacaactccagatggcattcgacactgatatcctcaa-aattatttaagc--gacgctacctactgttttcagGCAGCAGCAATACGATTGGAGATCAAAGGTGGGCAATGGAGGGATGCATACATGCAAATGGATGGGGAGCCATGGAAGCAACCATTGGACCACGAGTACT
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---gtcttggtctccattgtttctttatattgccattatttacattgtgaaaatttgtctttctcaatgaccagccccactggtttctatttatatctttcagGCATCAGCTATTCGATTGGAAGTCAGAGGTGGACAGTGGAAAAATGCATATATGCAAATGGATGGAGAACCTTGGAAACAACCATTGAGCAAGGACTTCT
upper sequence: LOC_Os08g15090.1 (Oryza sativa), 3'ss of exon 13
lower sequence: AT2G18730.1 (Arabidopsis thaliana), 3'ss of exon 11
tcagtttagataaacagctactttgcaaattacaactccagatggcattcgacactgatatcctcaaaattatttaagcgacgctacctactgttttcagGCAGCAGCAATACGATTGGAGATCAAAGGTGGGCAATGGAGGGATGCATACATGCAAATGGATGGGGAGCCATGGAAGCAACCATTGGACCACGAGTACT
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----------------gtaacttcaaaag-----acactggtcaatgtataatctttttagccatgtgtttgactgtttcattttggtgatcattt-cagGCTGCTGCGGTAAGATTTGAGCTAAGAGGAGGTGACTGGAGAGACGCATTCTTGCAAATGGATGGTGAGCCATGGAAGCAACCAATGAGCACTGAGTACT
upper sequence: LOC_Os08g15090.1 (Oryza sativa), 3'ss of exon 13
lower sequence: Vv11s0052g01840.t01 (Vitis vinifera), 3'ss of exon 11
tcagtttagataaa-cagctactttgcaaattacaactccagatggcattcgacactgatatcctcaaaatt--atttaagcgacgctacctactgttttcagGCAGCAGCAATACGATTGGAGATCAAAGGTGGGCAATGGAGGGATGCATACATGCAAATGGATGGGGAGCCATGGAAGCAACCATTGGACCACGAGTACT
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--gatttaagtgtttccatcatagtgtta-ttgatgctgatgttggattctgaaatctatgcttttataattccattgaataagttttatgggtatctttcagGCTGCAGCAATCCGATTGGAAATCAGAGGTGGAGAGTGGAAGCAAGCATATATGCAGATGGATGGGGAGCCATGGAAACAGCCAATAAACAATGAGTTTTMapped 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|88484940|gb|CI422211.1|CI422211EST: ATGCATCCCTTGTGATGGTTGAACTAATATCTNCAAAGCACATAGCTCAG GCAGCAGCAATACGATTGGAGATCAAAGGTGGGCAATGGAGGGATGCATAC
genomic: ATGCATCCCTTGTGATGGTTGAACTAATATCTGCAAAGCACATAGCTCAGgtacttttgc ... ctgttttcagGCAGCAGCAATACGATTGGAGATCAAAGGTGGGCAATGGAGGGATGCATAC
EST:
gi|29676335|gb|CB672610.1|CB672610EST: ATGCATCCCTTGTGATGGTTGAACTAATATCTGCAAAGCACATAGCTCAG GCAGCAGCAATACGATTGGAGATCAAAGGTGGGCAATGGAGGGATGCATAC
genomic: ATGCATCCCTTGTGATGGTTGAACTAATATCTGCAAAGCACATAGCTCAGgtacttttgc ... ctgttttcagGCAGCAGCAATACGATTGGAGATCAAAGGTGGGCAATGGAGGGATGCATAC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cattcgacactgatatcctcaaaattatttaagcgacgctacctactgttttcagGCAGCAGCAATACGATTGGAGATCAAAGGTGGGCAATGGAGGGATGCATACATGCAAATGGATGGGGAGCCATGGAAGCAACCATTGGACCACGAGTACT
cactgat putative branch site (score: 3)
ctgttttc putative PPT
tcaaaattatttaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tcagtttagataaacagctactttgcaaattacaactccagatggcattcgacactgatatcctcaaaattatttaagcgacgctacctactgttttcagGCAGCAGCAATACGATTGGAGATCAAAGGTGGGCAATGGAGGGATGCATACATGCAAATGGATGGGGAGCCATGGAAGCAACCATTGGACCACGAGTACT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - -ataaaca
- - - - - - - - - - ctttgca
- - - - - - - - - - - - - - - - - - - - - -ggcattc