Sequence
atgc intronic sequence ATGC exonic sequence...ctggcaaagaatagctgctatttctgtaggacacacttatcttgattaactgaattatctaactgatatgggtcattcttctattcctaatgcaattcagATTGGAGATGAGCTTGGTGATATCTATGACTATGTTGCACCATGTTTTCCTCCTAG
Basic information
species | Oryza sativa |
transcript | LOC_Os02g51430.2 |
intron # | 10 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os02g51430.2 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G070045_T01 (Zea mays), 3'ss of exon 6
ctggcaaagaatagctgctatttctgtaggacac--acttatcttgattaactgaatta-tctaactga--tatgggtcattcttctattcctaatgcaattcagATTGGAGATGAGCTTGGTGATATCTATGACTATGTTGCACCATGTTTTCCTCCTAG
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-----aagaagtacctgatgtttttttagaaaatgtacttaccttggtttaccttatcaatctttttggcttatagcttgctactttgcttctattgcaacacagATTGGAGATGAGCTTGGCGATATATATGATTATGTTGCACCATGCTTTCCTCCTAG
upper sequence: LOC_Os02g51430.2 (Oryza sativa), 3'ss of exon 10
lower sequence: AT1G71820.2 (Arabidopsis thaliana), 3'ss of exon 12
ctggca-aagaatagctgctatttctgtaggacacacttatcttgattaactgaattatc--taactgatatgggtcattcttctattcctaatgca-attcagATTGGAGATGAGCTTGGTGATATCTATGACTATGTTGCACCATGTTTTCCTCCTAG
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----cataatgattgatgtcaacctcgttttcttctgttatctttcacaaatatatatttatcaactgggttttcactttctttttatggtgttccacaactagATTGGAGAGGAACTTGGAGATATTTATGACTATGTGGCTCCTTGTTTTCCTCCAAG
upper sequence: LOC_Os02g51430.2 (Oryza sativa), 3'ss of exon 10
lower sequence: Vv03s0097g00670.t01 (Vitis vinifera), 3'ss of exon 11
--ctggcaaagaatagctgctatttctgtaggacacacttatcttgattaactgaattatctaactgatatgggtcattcttctattcctaatgcaattcagATTGGAGATGAGCTTGGTGATATCTATGACTATGTTGCACCATGTTTTCCTCCTAG
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ttcttaatgctgctagttttaaactttaataggtcctctc-tattcataagcccttttttcctgcaaatg-atgcctctggtttgattgttttgacttttagATTGGAGAAGAGCTTGGAGATATTTATGACTATGTGGCTCCTTGTTTTCCCCCAAG
upper sequence: LOC_Os02g51430.2 (Oryza sativa), 3'ss of exon 10
lower sequence: Vv12s0034g02360.t01 (Vitis vinifera), 3'ss of exon 11
ctggcaaagaatagctgctattt--ctgtaggacacacttatcttgattaactgaattatctaactgatatgggtcattcttctattcctaatgcaattcagATTGGAGATGAGCTTGGTGATATCTATGACTATGTTGCACCATGTTTTCCTCCTAG
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-tttcttaatgctgctagttttaaactttaatagtcctttctattcataagccactttttcctgcaaatg-atgcctctggtttggtttttttgacttttagATTGGAGAAGAGCTTGGAGATATTTATGACTATGTGGCTCCTTGTTTTCCCCCAAGMapped 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|58665364|gb|CK054050.1|CK054050EST: CTTGTTTTCTCAGAAGATTTGATGGAAGCTTTGGAGGAAGCTAAGGCA ATTGGAGATGAGCTTGGTGATATCTATGACTATGTTGCACCATGTTTTCCT
genomic: CTTGTTTTCTCAGAAGATTTGATGGAAGCTTTGGAGGAAGCTAAGGCAgtaagtactc ... tgcaattcagATTGGAGATGAGCTTGGTGATATCTATGACTATGTTGCACCATGTTTTCCT
EST:
gi|29666539|gb|CB662814.1|CB662814EST: CTTGTTTTCTCAGAAGATTTGATGGAAGCTTTGGAGGAAGCTAAGGCA ATTGGAGATGAGCTTGGTGATATCTATGACTATGTTGCACCATGTTTTCCT
genomic: CTTGTTTTCTCAGAAGATTTGATGGAAGCTTTGGAGGAAGCTAAGGCAgtaagtactc ... tgcaattcagATTGGAGATGAGCTTGGTGATATCTATGACTATGTTGCACCATGTTTTCCT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttaactgaattatctaactgatatgggtcattcttctattcctaatgcaattcagATTGGAGATGAGCTTGGTGATATCTATGACTATGTTGCACCATGTTTTCCTCCTAG
tcctaat putative branch site (score: 2)
aattatctaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ctggcaaagaatagctgctatttctgtaggacacacttatcttgattaactgaattatctaactgatatgggtcattcttctattcctaatgcaattcagATTGGAGATGAGCTTGGTGATATCTATGACTATGTTGCACCATGTTTTCCTCCTAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- -gcaaagaa
- - - - - - -gctgcta
- - - - - - - - - - -ttctgta