Sequence
atgc intronic sequence ATGC exonic sequenceTTCTTGCTGGATAGAAAATCCTAACTCAGAGGCATTCAGATTTCATATTCCAAGGGTTCATGATTACTTGTGGGTCGCTGAAGATGGCATGAAGATGCAAgtgcttatttcatatttgggactaatggctatcttttgaatccattttatttgctttcagttgaggtggttgtgtcaacagtaagcttatccacatattt...
Basic information
species | Oryza sativa |
transcript | LOC_Os02g04690.2 |
intron # | 10 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os02g04690.1 (Oryza sativa), 5'ss of exon 10
lower sequence: Vv09s0054g01550.t01 (Vitis vinifera), 5'ss of exon 8
TTCTTGCTGGATAGAAAATCCTAACTCAGAGGCATTCAGATTTCATATTCCAAGGGTTCATGATTACTTGTGGGTCGCTGAAGATGGCATGAAGATGCAAgtgcttatttcatatttgggactaatggctatcttttgaatccattttatttgctttcagttgagg-tggttg--tgtcaacagtaagcttatccacatattt--
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TTGCTGCTGGATTGAAGATCCAAACTCAGAGGCCTTTAAGTTGCATATTCCAAGAATTTTTGATTATTTGTGGATTGCTGAAGACGGCATGAAAATGCAGgtccataaatagtattagg---tggtgttttttttttt--tttttttttttggctttttgctgaaaataatttatttttagaatttaggttgtttgtttttatat
upper sequence: LOC_Os02g04690.1 (Oryza sativa), 5'ss of exon 10
lower sequence: Vv09s0054g01180.t01 (Vitis vinifera), 5'ss of exon 7
TTCTTGCTGGATAGAAAATCCTAACTCAGAGGCATTCAGATTTCATATTCCAAGGGTTCATGATTACTTGTGGGTCGCTGAAGATGGCATGAAGATGCAAgtgcttatttcatatttgggactaatggctatcttttgaatccattttatttgctttcagttgaggtggt-tgtgtcaacagtaagcttatccacatattt--------------------------------------------------------
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TTGCTGCTGGATTGAAGATCCAAACTCAGAGGCCTTTAAGTTGCATATTCCAAGAATTATTGATTATTTGTGGATTGCTGAAGACGGCATGAAAATGCAGgtccataaatagtattactctctttctattttatctcaga---gtgccatatgtagccatttatagtggcgtgttgtaaaggcagattttgtattttattccttggaaattattgaattttattatctgtctgtcatacataataagttcactgcag
upper sequence: LOC_Os02g04690.1 (Oryza sativa), 5'ss of exon 10
lower sequence: Vv09s0054g01110.t01 (Vitis vinifera), 5'ss of exon 10
TTCTTGCTGGATAGAAAATCCTAACTCAGAGGCATTCAGATTTCATATTCCAAGGGTTCATGATTACTTGTGGGTCGCTGAAGATGGCATGAAGATGCAAgtgcttatttcatatttgggactaat--ggctatcttttgaatccattttatttgctttcagttgaggtggttgtgtcaacagtaagcttatccacatattt-
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TTGCTGCTGGATTGAAGATCCAAACTCAGAGGCCTTTAAGTTGCATATTCCAAGAATTTTTGATTATTTGTGGATTGCTGAAGACGGCATGAAAATGCAGgtctgtaagtagtattagtctctttctagtttatctcagcgtgccatttccattttatatgttacagagaattgtg---atattactttttctggtggatgta
upper sequence: LOC_Os02g04690.1 (Oryza sativa), 5'ss of exon 10
lower sequence: Vv09s0054g01120.t01 (Vitis vinifera), 5'ss of exon 7
TTCTTGCTGGATAGAAAATCCTAACTCAGAGGCATTCAGATTTCATATTCCAAGGGTTCATGATTACTTGTGGGTCGCTGAAGATGGCATGAAGATGCAAgtgcttatttcatatttgggactaat--ggctatctt------ttgaatccattttatttgctttc---agttgaggtggttgtgtcaacagtaagcttatccacatattt-----------------------------------------------------------------------------
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TTGCTGCTGGATTGAAGATCCAAACTCAGAGGCCTTTAAGTTGCATATTCCAAGAATTTTTGATTATTTGTGGATTGCTGAAGACGGCATGAAAATGCAGgtccgtaagtagtattagtctctttctagtttatctcagcgtgccatttccattttatatgttacggagaattgtgatattactttttctggtggatgtagccattcatagtggcgtgttgtaaaggcagattttgtattttattccttggaaattattgaattttattatccatctgtttaccgcag
upper sequence: LOC_Os02g04690.1 (Oryza sativa), 5'ss of exon 10
lower sequence: PP1S33_211V6.1 (Physcomitrella patens), 5'ss of exon 8
TTCTTGCTGGATAGAAAATCCTAACTCAGAGGCATTCAGATTTCATATTCCAAGGGTTCATGATTACTTGTGGGTCGCTGAAGATGGCATGAAGATGCAAgtgcttatttcat---atttgggacta-atggctatcttttgaatccattttatttgctttcagttgaggtggttgtgtcaacagtaagcttatccacatattt
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GTCCTGCTGGATAGAGGACCCTAACTCAGAAGCCTTCAAGCTGCATTTGGCACGGGTTGTCGATTACCTATGGGTGGCTGAAGATGGCATGAAGATGCAGgtatctttttcattgtacttttacttgcacattcaacttagagataaatattcagaacttattgcttcataaatcttgg----atcaagtttaccagtatgatgMapped 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|58682913|gb|CK071600.1|CK071600EST: GGTTCATGATTACTTGTGGGTCGCTGAAGATGGCATGAAGATGCAG GGTTACAATGGCAGCCAGCTCTGGGACACAGCTTTCACAGTTCAAGCTATA
genomic: GGTTCATGATTACTTGTGGGTCGCTGAAGATGGCATGAAGATGCAAgtgcttattt ... cttactgtagGGTTACAATGGCAGCCAGCTCTGGGACACAGCTTTCACAGTTCAAGCTATA
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
TTCTTGCTGGATAGAAAATCCTAACTCAGAGGCATTCAGATTTCATATTCCAAGGGTTCATGATTACTTGTGGGTCGCTGAAGATGGCATGAAGATGCAAgtgcttatttcatatttgggactaatggctatcttttgaatccattttatttgctttcagttgaggtggttgtgtcaacagtaagcttatccacatattt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG