Sequence
atgc intronic sequence ATGC exonic sequence...gaaataccaatctaggtaaatgttgatataaagatcttgatataaaaatgtgcttatatattcttgtgacttatggctgttcttgttgattatcaaccagCTTAACAGTGCTTCCTACAAAGATGCTTTACCAGAGATACTAGAAGTCCTGAGAGCAGCCTGCATCACCCACAAGCTACCATTAGCTCAGACCTGGGTCA
Basic information
species | Oryza sativa |
transcript | LOC_Os09g37710.2 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os09g37710.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G143566_T01 (Zea mays), 3'ss of exon 2
-gaaataccaatctaggtaaatgttgatataaagatcttgatataaaaatgtgcttatatattcttgtgactt-atggctgttcttgttgattatcaaccagCTTAACAGTGCTTCCTACAAAGATGCTTTACCAGAGATACTAGAAGTCCTGAGAGCAGCCTGCATCACCCACAAGCTACCATTAGCTCAGACCTGGGTCA
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gagaatataaagc-aagtgtgtaa-gatattgagacacgaacaccaatgcttatatcttctcacttatgacttcatggcaactcctattgattatccaccagTTCAGCACTGCTTCCTACAAAGATGCTTTACCAGAGATACTGGAGGTCCTGAGAGCAGCCTGCTTGACCCACAAGTTGCCATTAGCTCAGACATGGGTCA
upper sequence: LOC_Os09g37710.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G053298_T01 (Zea mays), 3'ss of exon 3
-gaaataccaatctaggtaaatgttgatataaagatcttgatataaaaatgtgcttatatattcttgtgactt-atggctgttcttgttgattatcaaccagCTTAACAGTGCTTCCTACAAAGATGCTTTACCAGAGATACTAGAAGTCCTGAGAGCAGCCTGCATCACCCACAAGCTACCATTAGCTCAGACCTGGGTCA
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gagaatataaagc-aagtgtgtaa-gatattgagacacgaacaccaatgcttatatcttctcacttatgacttcatggcaactcctattgattatccaccagTTCAGCACTGCTTCCTACAAAGATGCTTTACCAGAGATACTGGAGGTCCTGAGAGCAGCTTGCTTGACCCACAAGCTGCCATTAGCTCAGACATGGGTCA
upper sequence: LOC_Os09g37710.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G048582_T01 (Zea mays), 3'ss of exon 2
--gaaataccaatctaggtaaatgttgatataaagatcttgatataaaaatgtgcttatatattcttgtgactt-atggctgttcttgttgattatcaaccagCTTAACAGTGCTTCCTACAAAGATGCTTTACCAGAGATACTAGAAGTCCTGAGAGCAGCCTGCATCACCCACAAGCTACCATTAGCTCAGACCTGGGTCA
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ctcaaatataaagc-aagtgtataa-gatattgaga-catgaaacggcgatgcttatatatgctcacatgacttcatggccactcttattgattgtccaccagTTTAGCACTGCTTCCTACAAAGATGCTTTACCAGAGATACTGGAGGTCCTGAGGGCAGCCTGCTTGACCCACAAGCTGCCATTAGCTCAGACATGGGTCA
upper sequence: LOC_Os09g37710.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G346037_T01 (Zea mays), 3'ss of exon 5
-gaaataccaatctaggtaaatgttgatataaagatcttgatataaaaatgtgcttatatattcttgtgactt-atggctgttcttgttgattatcaaccagCTTAACAGTGCTTCCTACAAAGATGCTTTACCAGAGATACTAGAAGTCCTGAGAGCAGCCTGCATCACCCACAAGCTACCATTAGCTCAGACCTGGGTCA
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gagaatataaagc-aagtgtgtaa-gatattgagacacgaacaccaatgcttatatattctcacttatgacttcatggcaactcctattaattatccaccagTTCAGCACTGCTTCCTACAAAGATGCTTTACCAGAGATACTGGAGGTCCTAAGAGCAGCCTGCTTGACCCACAAGCTGCCATTAGCTCAGACATGGGTCA
upper sequence: LOC_Os09g37710.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G466549_T02 (Zea mays), 3'ss of exon 2
-gaaataccaatctaggtaaatgttgatataaagatcttgatataaaaatgtgcttatatattcttgtgactt-atggctgttcttgttgattatcaaccagCTTAACAGTGCTTCCTACAAAGATGCTTTACCAGAGATACTAGAAGTCCTGAGAGCAGCCTGCATCACCCACAAGCTACCATTAGCTCAGACCTGGGTCA
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gagaatataaagc-aagtgtgtaa-gatattgagacacgaacaccaatgcttatatcttctcacttatgacttcatggcaactcctattgattatccaccagTTCAGCACTGCTTCCTACAAAGATGCTTTACCAGAGATACTGGAGGTCCTGAGAGCAGCCTGCTTGACCCACAAGCTGCCATTAGCTCAGACATGGGTCAMapped 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|58606417|gb|CK034450.1|CK034450EST: GCAGTTAACCTGACAAGCACAGAAGTTTCAAGCATTCCGCGCACAAAG CTTAACAGTGCTTCCTACAAAGATGCTTTACCAGAGATACTAGAAGTCCTG
genomic: GCAGTTAACCTGACAAGCACAGAAGTTTCAAGCATTCCGCGCGCAAAGgtaagcagca ... tatcaaccagCTTAACAGTGCTTCCTACAAAGATGCTTTACCAGAGATACTAGAAGTCCTG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aaatgtgcttatatattcttgtgacttatggctgttcttgttgattatcaaccagCTTAACAGTGCTTCCTACAAAGATGCTTTACCAGAGATACTAGAAGTCCTGAGAGCAGCCTGCATCACCCACAAGCTACCATTAGCTCAGACCTGGGTCA
tgttgat putative branch site (score: 4)
ttatatattcttgt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gaaataccaatctaggtaaatgttgatataaagatcttgatataaaaatgtgcttatatattcttgtgacttatggctgttcttgttgattatcaaccagCTTAACAGTGCTTCCTACAAAGATGCTTTACCAGAGATACTAGAAGTCCTGAGAGCAGCCTGCATCACCCACAAGCTACCATTAGCTCAGACCTGGGTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- -ataccaa
- - - - - - - - - -atgttga
- - - - - - - - - - - - - - - - - - - - - - - aatgtgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -attcttg