Sequence
atgc intronic sequence ATGC exonic sequencegcatgccatttctctgcttcggaagcctgttggctgtacccatttctcccccttaactagtaacgcccttcactgctttgcacttcagGTTGGTGATGCTAGTGGAATCCAGTCACCTGTTTCTTTTGGAGGTTTTGGAAGCTTGACAAGGCATCTTGGTCGTTTGTCAAATG
Basic information
species | Oryza sativa |
transcript | LOC_Os08g32630.1 |
intron # | 11 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os08g32630.5 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM5G851815_T02 (Zea mays), 3'ss of exon 11
gcatgccatttctctgcttcggaagcctgttggctgtacccatttctcccccttaactagtaacgcccttcactgct-ttgcacttcagGTTGGTGATGCTAGTGGAATCCAGTCACCTGTTTCTTTTGGAGGTTTTGGAAGCTTGACAAGGCATCTTGGTCGTTTGTCAAATG
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gcatgtgattttctcttaacagaagcct--------tattactcctgcacctgcaagtattctcaatcactgatgctcttgcatttcagGTTGGCGATGCTAGTGGAATACAGTCACCTGTTTCTTTTGGAGGTTTTGGAAGCTTGACGAGACATCTTGGCCGTTTGTCTAGTG
upper sequence: LOC_Os08g32630.5 (Oryza sativa), 3'ss of exon 10
lower sequence: GLYMA14G05100.1 (Glycine max), 3'ss of exon 12
gcatgccat-ttctctgcttcggaagcct--gttggctgtacccatttctccccc-ttaactagta---acgcccttcactgctttgcacttcagGTTGGTGATGCTAGTGGAATCCAGTCACCTGTTTCTTTTGGAGGTTTTGGAAGCTTGACAAGGCATCTTGGTCGTTTGTCAAATG
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gtaaattgcgttttacacttctgaagcctctataaaattaagccatctatgatctatcaactaatattaaagtaatgaagcttcattctctgtagTTTGGTGATGCTAGTGGCATACAATCACCTGTTTCATTTGGTGGATTTGGAAGCTTGACCAGGCACCTGGGGAGACTGTCAGCTG
upper sequence: LOC_Os08g32630.5 (Oryza sativa), 3'ss of exon 10
lower sequence: AT2G32640.1 (Arabidopsis thaliana), 3'ss of exon 11
-----------gcatgccatttctctgcttcggaagcctgttggctg--tacccatttctcccccttaactagtaacgcccttcactgctttgcacttcagGTTGGTGATGCTAGTGGAATCCAGTCACCTGTTTCTTTTGGAGGTTTTGGAAGCTTGACAAGGCATCTTGGTCGTTTGTCAAATG
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gttggtttggttcat-ttatatataagcttccaagataagtttgcggattgataatttgataaactaaataatcaaagttacttacaaattttttactcagTTTGGTGATGCTAGCGGTATTCAATCACCTGTTTCATTTGGGGGTTTTGGAAGTTTGACCAGACACCTTGGAAGATTGTCCAATG
upper sequence: LOC_Os08g32630.5 (Oryza sativa), 3'ss of exon 10
lower sequence: Vv12s0059g01150.t01 (Vitis vinifera), 3'ss of exon 11
gcatgccat-ttctctgcttcggaagcctgttggctgtacccatttctcccccttaactagtaacgcccttcactgctttgcacttcagGTTGGTGATGCTAGTGGAATCCAGTCACCTGTTTCTTTTGGAGGTTTTGGAAGCTTGACAAGGCATCTTGGTCGTTTGTCAAATG
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gtgttttacattatatacttctaaagcctccaatagataatggtcacatatcaaatggaatggaagtgttacaaaatcattctctgcagTTTGGTGATGCTAGCGGCATACAGTCACCAGTTTCATTTGGTGGTTTTGGGAGCTTGACCAGGCACCTTGAGAGGTTGTCAACTGMapped 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|29670150|gb|CB666425.1|CB666425EST: CCCCTTGCCAGCTGCATTTGACCGTGTCTTGCAG GTTGGTGATGCTAGTGGAATCCAGTCACCTGTTTCTTTTGGAGGTTTTGGA
genomic: CCCCTTGCCAGCTGCATTTGACCGTGTCTTGCAGgcatgccatt ... tgcacttcagGTTGGTGATGCTAGTGGAATCCAGTCACCTGTTTCTTTTGGAGGTTTTGGA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctgtacccatttctcccccttaactagtaacgcccttcactgctttgcacttcagGTTGGTGATGCTAGTGGAATCCAGTCACCTGTTTCTTTTGGAGGTTTTGGAAGCTTGACAAGGCATCTTGGTCGTTTGTCAAATG
tagtaac putative branch site (score: 1)
cccttcactgcttt CT-rich tract
ttaacta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gcatgccatttctctgcttcggaagcctgttggctgtacccatttctcccccttaactagtaacgcccttcactgctttgcacttcagGTTGGTGATGCTAGTGGAATCCAGTCACCTGTTTCTTTTGGAGGTTTTGGAAGCTTGACAAGGCATCTTGGTCGTTTGTCAAATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG