Sequence
atgc intronic sequence ATGC exonic sequence...ctaattacttcctaccgcattacttgaactgatttggtgattgatgaattaacagttgaatatgttttgcataataatgttgaagaaacttttcttgtagCATGCAGGTCATGCTTCTCGGATTTGTGCTTCTTGGACGATCTCTTGAAGAAAGTGCCAGGCTTAAGGCTTCTAGCGATATGAATGAGCTCGTT
Basic information
species | Oryza sativa |
transcript | LOC_Os03g08070.3 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os03g08070.3 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA04G05900.2 (Glycine max), 3'ss of exon 3
ctaattacttcctaccgcattacttgaactgatttggtgattgatgaattaacagttgaatatgttttgcataataatgttgaagaaacttttcttgtagCATGCAGGTCATGCTTCTCGGATTTGTGCTTCTTGGACGATCTCTTGAAGAAAGTGCCAGGCTTAAGGCTTCTAGCGATATGAATGAGCTCGTT
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---------------------------------------------------------gtataagctcctcatgtgagtattgaa--------tcttttagCATGCAGGTCATGCTTCTTGGTTTTGTGCTTCTGGGACGTTCTCTGGAAGAAAAGGCAAGGATTCAGGCATCTAGCGATATGAATGAACTGCTT
upper sequence: LOC_Os03g08070.3 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA06G05890.1 (Glycine max), 3'ss of exon 4
ctaattacttcctaccgcattacttgaactgatttggtgattgatgaattaaca-----gttgaatat--gttttgcataataatgttgaagaaacttttcttgtagCATGCAGGTCATGCTTCTCGGATTTGTGCTTCTTGGACGATCTCTTGAAGAAAGTGCCAGGCTTAAGGCTTCTAGCGATATGAATGAGCTCGTT
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------acctcttgcctttgtaaaagatgctatttattgtcttaacttcttacattcttgttgagtataagctcctcatgtgagtattgaa--------tcttttagcatgcagGTCATGCTTCTTGGTTTCGTGCTTCTGGGACGTTCTCTGGAGGAAAAGGCAAGGATTCAGGCATCTAGCGATATGAATGAACTGCTT
upper sequence: LOC_Os03g08070.3 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA04G05900.1 (Glycine max), 3'ss of exon 2
--ctaattacttcctaccgcattacttgaactgatttggtgattgatgaattaacagttgaatat--gttttgcataataatgttgaagaaacttttcttgtagCATGCAGGTCATGCTTCTCGGATTTGTGCTTCTTGGACGATCTCTTGAAGAAAGTGCCAGGCTTAAGGCTTCTAGCGATATGAATGAGCTCGTT
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ttgtcttcgtaaaagatgctatttcttgtctta--ttgacaattcttacattc-ttgttgagtataagctcctcatgtgagtattgaa--------tcttttagcatgcagGTCATGCTTCTTGGTTTTGTGCTTCTGGGACGTTCTCTGGAAGAAAAGGCAAGGATTCAGGCATCTAGCGATATGAATGAACTGCTT
upper sequence: LOC_Os03g08070.3 (Oryza sativa), 3'ss of exon 4
lower sequence: AT5G21930.1 (Arabidopsis thaliana), 3'ss of exon 4
ctaattacttcctaccgcattact------tgaactgatttggtgattgatgaattaaca-gttgaatatgttttgcataataat------gttgaagaaacttttcttgtagCATGCAGGTCATGCTTCTCGGATTTGTGCTTCTTGGACGATCTCTTGAAGAAAGTGCCAGGCTTAAGGCTTCTAGCGATATGAATGAGCTCGTT
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gtgagtttctctagcagatccacaagaggatgaaagctttttattattacttccactacatgcaaaatacagtttcaatagtaaatttctgattgatagctcttgtcatttagtatgcagGTCATGCTGCTTGGCTTTGTGCTCCTTGGTCGTTCTTTGGAAGAAAGAGCAAAGCTTCAAGCATCTACCGATATGAATGAACTATTG
upper sequence: LOC_Os03g08070.3 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv04s0008g01960.t01 (Vitis vinifera), 3'ss of exon 4
ctaattacttcctaccgcattacttgaactgatttggtgattgatgaattaacagttgaatatgttttgcataataatgttgaagaaacttttcttgtagCATGCAGGTCATGCTTCTCGGATTTGTGCTTCTTGGACGATCTCTTGAAGAAAGTGCCAGGCTTAAGGCTTCTAGCGATATGAATGAGCTCGTT
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--cattactcttccttgtattcattggtggcaatttctg-----tagatttgaaattctttcttgatgctaaatttttcaagcaggccattgttttttagtatgcagGTCATGCTTCTTGGTTTTGTGCTCCTTGGACGTTCTCTTGAAGAGAAGGCGAGGATCAGGGCATCTAGCGATATGAATAAACTTTTAMapped 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|29662865|gb|CB659140.1|CB659140EST: CCTTGCTGAACCCTGAACTGGAATGGAATTCAACCTTTTTTGATGAACCG CATGCAGGTCATGCTTCTCGGATTTGTGCTTCTTGGACGATCTCTTGAAGA
genomic: CCTTGCTGAACCCTGAACTGGAATGGAATTCAACCTTTTTTGATGAACCGgtgagtgatc ... tttcttgtagCATGCAGGTCATGCTTCTCGGATTTGTGCTTCTTGGACGATCTCTTGAAGA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gaattaacagttgaatatgttttgcataataatgttgaagaaacttttcttgtagCATGCAGGTCATGCTTCTCGGATTTGTGCTTCTTGGACGATCTCTTGAAGAAAGTGCCAGGCTTAAGGCTTCTAGCGATATGAATGAGCTCGTT
aattaac putative branch site (score: 2)
cttttcttgt putative PPT
ttttgcataataat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ctaattacttcctaccgcattacttgaactgatttggtgattgatgaattaacagttgaatatgttttgcataataatgttgaagaaacttttcttgtagCATGCAGGTCATGCTTCTCGGATTTGTGCTTCTTGGACGATCTCTTGAAGAAAGTGCCAGGCTTAAGGCTTCTAGCGATATGAATGAGCTCGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - tgaactg
- - - - - - - - - - - - - - - - - tggtgat
- - - - - - - - - - - - - - - - - - - - -tgatgaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ttttgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgttgaa