Sequence
atgc intronic sequence ATGC exonic sequencegtgggtacttttccctatccgtttctctttgctgcactttctcaataatttgtcacatattaaattgcttttgctaattaaatgcagccaaccagtttacatccaaatttcatgtgttaaggacttaaggtaggtgcactatgcacaagtaaatatactcttatattaattaccgttctatatattcatagGTGTCATAGCAATTGTTGTGGCAAATCCAACTGATCTTGTCAAAGTGAGATTGCAAGCTGATGGAAAGGCCACCACTGTCAAGAGGCACTATTCTGGAGC
Basic information
species | Oryza sativa |
transcript | LOC_Os01g74640.1 |
intron # | 3 |
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 3
lower sequence: GRMZM2G165629_T02 (Zea mays), 3'ss of exon 3
gtgggtacttttccctatccgtttctctttgctgcactttctcaataatttgtcacatattaaattgcttttgctaattaaatgcagccaaccagtttacatccaaatttcatgtgttaaggacttaaggtaggtgcactatgcacaagtaaatatactcttatattaattaccgttctatatattcatagGTGTCATAGCAATTGTTGTGGCAAATCCAACTGATCTTGTCAAAGTGAGATTGCAAGCTGATGGAAAGGCCACCACTGTCAAGAGGCACTATTCTGGAGC
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---------------------------------------------------------------------------------tcatagataataaaatcaggtcgg---ttcac-tttaaaggtgccacgctcg--gcaatgtggagaacca--tacattgttaaatga--tctttttttgtctattttcagGTGTGATAGCAATTGTTGTGGCAAATCCAACTGATCTTGTTAAAGTTAGGTTGCAAGCTGATGGAAAGGCTAACACTGTCAAGAGGAGTTATTCTGGAGC
upper sequence: LOC_Os01g74640.3 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM5G852877_T01 (Zea mays), 3'ss of exon 3
gtgggtacttttccctatccgtttctctttgctgcactttctcaataatttgtcacatattaaattgcttttgctaattaaatgcagccaaccagtttacatccaaatttcatgtgttaaggacttaaggtaggtgcactatgcacaagtaaatatactcttatattaattaccgttctatatattcatagGTGTCATAGCAATTGTTGTGGCAAATCCAACTGATCTTGTCAAAGTGAGATTGCAAGCTGATGGAAAGGCCACCACTGTCAAGAGGCACTATTCTGGAGC
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----------------------------------------------------------------------------atcgcagttaataaatcaggtcg-gttcactttaaaggtgcca--cactca--------gcaatgtggagaacca--tacattgttaaatga--tctttttttgtctattctcagGTGTGATAGCGATTGTTGTGGCAAATCCAACTGATCTTGTCAAAGTTAGGTTGCAAGCTGATGGAAAAGCTAACACTATCAAGAGGAGTTATTCTGGAGC
upper sequence: LOC_Os01g74640.3 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA07G17380.1 (Glycine max), 3'ss of exon 2
gtgggtacttttccctatccgtttctctttgctgcactttctcaataatttgtcacatattaaattgcttt------tgctaattaaatgcagccaaccagtttacatccaaatttcatgtgttaaggacttaaggtaggtgcactatgcacaagtaaatatactcttatattaattaccgttctatatattcatagGTGTCATAGCAATTGTTGTGGCAAATCCAACTGATCTTGTCAAAGTGAGATTGCAAGCTGATGGAAAGGCCACCACTGTCAAG---AGGCACTATTCTGGAGC
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gtaaa-gcccaattctggacattgtattgtagtgatggttttttctatatgccaatatgtgaatttgtttcctaatgtgcggagtgtgaacttcttgctagctggagcatacgttatttttgtcaagaattc----ttgatacattatgcaaaactctgcattgagccacttgaacttgtgtt------atcaacagGTGCTATGGCAATTGCAGTGGCAAATCCAACTGATCTTGTGAAAGTTAGACTTCAAGCAGAAGGAAAATTGCCTCCTGGCGTGCCCAAGCGCTACTCTGG---
upper sequence: LOC_Os01g74640.3 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA03G14780.1 (Glycine max), 3'ss of exon 3
gtgggtacttttccctatccgtttctctttgctgcactttctcaataatttgtcacatattaaattgcttttgctaattaaatgcagccaaccagtttacatccaaatttcatgtgttaaggacttaaggtaggtgcactatgcacaagtaaatatactcttatattaattaccgttctatatattcatagGTGTCATAGCAATTGTTGTGGCAAATCCAACTGATCTTGTCAAAGTGAGATTGCAAGCTGATGGAAAGG---CCACCACTGTCAAGAGGCACTATTCTGGAGC
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----gtaaatctcaatg-ctggaaattgtgggaataatttgtatatg-tgtgctattatatgagtttcttttctaatctatggattatttact--ttttcttaggggcatcttgtgttat---tcctatctaaatactcatcgca---ataact-caatcacgaactcgtt-caatttgtcttgtcaacagGTGCTTTTGCAATTGCAGTGGCAAATCCAACCGATCTTGTCAAAGTTAGACTTCAAGCTGAAGGAAAATTACCTCCTGGTGTTCCCAGGCGCTACTCTGG---
upper sequence: LOC_Os01g74640.3 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA01G27120.1 (Glycine max), 3'ss of exon 2
gtgggtacttttccctatccgtttctctttgctgcactttctcaataatttgtcacatattaaattgcttttgctaattaaatgcagccaaccagtttacatccaaatttcatgtgttaaggacttaaggtaggtgcactatgcacaagtaaatatactcttatattaattaccgttctatatattcatagGTGTCATAGCAATTGTTGTGGCAAATCCAACTGATCTTGTCAAAGTGAGATTGCAAGCTGATGGAAAGG---CCACCACTGTCAAGAGGCACTATTCTGGAGC
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----gtaaatctcaatgctggaaactgtggga-atattttgtatatatattctattctat-gagtttcttttctcatctatggattatttact--ttttcttaggaggatcttgtattat---tcccatctaaatactcattgca---ataact-caatcataaactcctcgaatttgtct-tgtcaacagGTGCTTTTGCAATTGCAGTGGCAAATCCAACTGATCTTGTCAAAGTTAGACTTCAAGCAGAAGGAAAATTACCTCCTGGTGTTCCCAGGCGGTACTCTGG---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|33684429|gb|CF312668.1|CF312668EST: TGCTGGTGGTGTCAGTTTATTTGCTAAGATCCTTGCTGCTCTTATGACAG GTGTCATAGCAATTGTTGTGGCAAATCCAACTGATCTTGTCAAAGTGAGAT
genomic: TGCTGGTGGTGTCAGTTTATTTGCTAAGATCCTTGCTGCTCTTATGACAGgtgggtactt ... atattcatagGTGTCATAGCAATTGTTGTGGCAAATCCAACTGATCTTGTCAAAGTGAGAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cactatgcacaagtaaatatactcttatattaattaccgttctatatattcatagGTGTCATAGCAATTGTTGTGGCAAATCCAACTGATCTTGTCAAAGTGAGATTGCAAGCTGATGGAAAGGCCACCACTGTCAAGAGGCACTATTCTGGAGC
tattaat putative branch site (score: 2)
acaagtaaatatactc 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgggtacttttccctatccgtttctctttgctgcactttctcaataatttgtcacatattaaattgcttttgctaattaaatgcagccaaccagtttacatccaaatttcatgtgttaaggacttaaggtaggtgcactatgcacaagtaaatatactcttatattaattaccgttctatatattcatagGTGTCATAGCAATTGTTGTGGCAAATCCAACTGATCTTGTCAAAGTGAGATTGCAAGCTGATGGAAAGGCCACCACTGTCAAGAGGCACTATTCTGGAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG