Sequence
atgc intronic sequence ATGC exonic sequence...cttcctaccgcattacttgaactgatttggtgattgatgaattaacagttgaatatgttttgcataataatgttgaagaaacttttcttgtagcatgcagGTCATGCTTCTCGGATTTGTGCTTCTTGGACGATCTCTTGAAGAAAGTGCCAGGCTTAAGGCTTCTAGCGATATGAATGAGCTCGTT
Basic information
species | Oryza sativa |
transcript | LOC_Os03g08070.2 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os03g08070.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA04G05900.2 (Glycine max), 3'ss of exon 3
cttcctaccgcattacttgaactgatttggtgattgatgaattaacagttgaatatgttttgcataataatgttgaagaaacttttcttgtagcatgcagGTCATGCTTCTCGGATTTGTGCTTCTTGGACGATCTCTTGAAGAAAGTGCCAGGCTTAAGGCTTCTAGCGATATGAATGAGCTCGTT
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--------------------------------------------------gtataagctcctcatgtgagtattgaa--------tcttttagCATGCAGGTCATGCTTCTTGGTTTTGTGCTTCTGGGACGTTCTCTGGAAGAAAAGGCAAGGATTCAGGCATCTAGCGATATGAATGAACTGCTT
upper sequence: LOC_Os03g08070.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA06G05890.1 (Glycine max), 3'ss of exon 4
-cttcctaccgcattacttgaactgatttggtgattgatgaattaaca-----gttgaatat--gttttgcataataatgttgaagaaacttttcttgtagcatgcagGTCATGCTTCTCGGATTTGTGCTTCTTGGACGATCTCTTGAAGAAAGTGCCAGGCTTAAGGCTTCTAGCGATATGAATGAGCTCGTT
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acctcttgcctttgtaaaagatgctatttattgtcttaacttcttacattcttgttgagtataagctcctcatgtgagtattgaa--------tcttttagcatgcagGTCATGCTTCTTGGTTTCGTGCTTCTGGGACGTTCTCTGGAGGAAAAGGCAAGGATTCAGGCATCTAGCGATATGAATGAACTGCTT
upper sequence: LOC_Os03g08070.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA04G05900.1 (Glycine max), 3'ss of exon 2
----cttcctaccgcat--tacttgaactgat-ttggtgattgatgaattaacagttgaatat--gttttgcataataatgttgaagaaacttttcttgtagcatgcagGTCATGCTTCTCGGATTTGTGCTTCTTGGACGATCTCTTGAAGAAAGTGCCAGGCTTAAGGCTTCTAGCGATATGAATGAGCTCGTT
|||| || || || || | | ||| ||| | ||| ||||| ||| | | ||| | | ||||| |||| ||||||||||||||||||||| || ||||||||||| ||||| ||||| ||||||| || ||| || |||| ||||||||||||||||| || ||
ttgtcttcgtaaaagatgctatttcttgtcttattgacaattcttacattctt-gttgagtataagctcctcatgtgagtattgaa--------tcttttagcatgcagGTCATGCTTCTTGGTTTTGTGCTTCTGGGACGTTCTCTGGAAGAAAAGGCAAGGATTCAGGCATCTAGCGATATGAATGAACTGCTT
upper sequence: LOC_Os03g08070.1 (Oryza sativa), 3'ss of exon 3
lower sequence: AT5G21930.1 (Arabidopsis thaliana), 3'ss of exon 4
------cttcctaccgcattact-------tgaactgatttggtgattgatgaattaaca-gttgaatatgttttgcataataat------gttgaagaaacttttcttgtagcatgcagGTCATGCTTCTCGGATTTGTGCTTCTTGGACGATCTCTTGAAGAAAGTGCCAGGCTTAAGGCTTCTAGCGATATGAATGAGCTCGTT
| ||| | || |||| ||| | ||| | ||| | |||| ||| ||| ||| |||| ||| || | ||| |||||||||||||| || || |||||||| ||||| || ||| | |||||||| || | |||| | || |||| |||||||||||| || |
gtgagtttctctagcagatccacaagaggatgaaagctttttattattacttccactacatgcaaaatacagtttcaatagtaaatttctgattgatagctcttgtcatttagtatgcagGTCATGCTGCTTGGCTTTGTGCTCCTTGGTCGTTCTTTGGAAGAAAGAGCAAAGCTTCAAGCATCTACCGATATGAATGAACTATTG
upper sequence: LOC_Os03g08070.1 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv04s0008g01960.t01 (Vitis vinifera), 3'ss of exon 4
cttcctaccgcattacttgaactgatttggtgattgatgaattaacagttgaatatgttttgcataataa--tgttgaagaaac---ttttcttgtagcatgcagGTCATGCTTCTCGGATTTGTGCTTCTTGGACGATCTCTTGAAGAAAGTGCCAGGCTTAAGGCTTCTAGCGATATGAATGAGCTCGTT
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--cattact--cttccttgtattcatt-ggtggcaatttctgtagatttgaaattctttcttgatgctaaatttttcaagcaggccattgttttttagtatgcagGTCATGCTTCTTGGTTTTGTGCTCCTTGGACGTTCTCTTGAAGAGAAGGCGAGGATCAGGGCATCTAGCGATATGAATAAACTTTTAMapped 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|29622946|gb|CB627957.1|CB627957EST: TTGATGGTCTTCGAGCATTCAAGCAAGGATCCCCCAACATGAACTCTCTT GTCATGCTTCTCGGATTTGTGCTTCTTGGACGATCTCTTGAAGAAAGTGCC
genomic: TTGATGGTCTTCGAGCATTCAAGCAAGGATCCCCCAACATGAACTCTCTTgtagggtttg ... tagcatgcagGTCATGCTTCTCGGATTTGTGCTTCTTGGACGATCTCTTGAAGAAAGTGCC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cagttgaatatgttttgcataataatgttgaagaaacttttcttgtagcatgcagGTCATGCTTCTCGGATTTGTGCTTCTTGGACGATCTCTTGAAGAAAGTGCCAGGCTTAAGGCTTCTAGCGATATGAATGAGCTCGTT
cttttcttgt CT-rich tract
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
cttcctaccgcattacttgaactgatttggtgattgatgaattaacagttgaatatgttttgcataataatgttgaagaaacttttcttgtagcatgcagGTCATGCTTCTCGGATTTGTGCTTCTTGGACGATCTCTTGAAGAAAGTGCCAGGCTTAAGGCTTCTAGCGATATGAATGAGCTCGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - -tgaactg
- - - - - - - - - - - - - -tggtgat
- - - - - - - - - - - - - - - - - tgatgaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttttgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgttgaa