Sequence
atgc intronic sequence ATGC exonic sequence...gacatatcgatgtacatattatgtttatttttttatagagtatatattatgttattgatatgctttactactttactcaatattaatgttgctattatagGTTGTCACTTGCCTCCGTCAACCATCACAAGGGCCTACTTTTGGAATCAAGGGGGGTGCTGCTGGAGGTGGCTACAGCCAAGTCATACCCATGGATGAGT
Basic information
species | Oryza sativa |
transcript | LOC_Os09g27420.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os09g27420.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM5G824944_T01 (Zea mays), 3'ss of exon 2
gacatatcgatgtacatattatgtttatttttttatagagtatatatt--atgttattgatatgctttactactttactcaatat-taatgttgctattatagGTTGTCACTTGCCTCCGTCAACCATCACAAGGGCCTACTTTTGGAATCAAGGGGGGTGCTGCTGGAGGTGGCTACAGCCAAGTCATACCCATGGATGAGT
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--catatgtgtgataaaataacttcagactgtcttgtaagtatctgctccagatcatgcggaagttgtttca-tgtattaatgatgtattgttttttatgtagGTTGTCACTTGCCTCCGTCAACCATCACAAGGGCCTACCTTTGGAATCAAGGGAGGTGCAGCTGGAGGTGGGTACAGCCAAGTTATACCCATGGATGAGT
upper sequence: LOC_Os09g27420.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA20G38740.1 (Glycine max), 3'ss of exon 2
-gacatatcgatgtacatattatgtttatttttttatagagtata-tattatgttattgatatgctttactactttactcaatattaatgttgctattatagGTTGTCACTTGCCTCCGTCAACCATCACAAGGGCCTACTTTTGGAATCAAGGGGGGTGCTGCTGGAGGTGGCTACAGCCAAGTCATACCCATGGATGAGT
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ctggttatttgggttcaagatattattgaaaaactacaatctttaatcgcatgtcaaagttatgctgga-tacataatcccatctta-tctctttttgttagGTAGTCACCTGCCTTCGTCAACCATCGCAAGGACCTACTTTTGGAATTAAAGGAGGTGCAGCTGGTGGTGGCTATAGCCAAGTTATTCCCATGGATGAAT
upper sequence: LOC_Os09g27420.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA10G44010.1 (Glycine max), 3'ss of exon 2
-gacatatcgatgtacatattatgtttatttttttatagagtata-tattatgttattgatatgctttactactttactcaatattaatgttgctattatagGTTGTCACTTGCCTCCGTCAACCATCACAAGGGCCTACTTTTGGAATCAAGGGGGGTGCTGCTGGAGGTGGCTACAGCCAAGTCATACCCATGGATGAGT
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caggttatttgggttcaagatattaatggaaaactataactttcaatcgcttgtcaaagttatgctgga-tacataatcccatctta-tctctttttgttagGTAGTTACCTGCCTTCGTCAACCATCGCAAGGACCTACTTTTGGAATTAAAGGAGGCGCAGCTGGTGGTGGCTATAGCCAAGTTATTCCCATGGATGAAT
upper sequence: LOC_Os09g27420.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA10G13840.1 (Glycine max), 3'ss of exon 3
-gacatatcgatgtacatattatgtttatttttttatagagtata-tattatgttattgatatgctttactactttactcaatattaatgttgctattatagGTTGTCACTTGCCTCCGTCAACCATCACAAGGGCCTACTTTTGGAATCAAGGGGGGTGCTGCTGGAGGTGGCTACAGCCAAGTCATACCCATGGATGAGT
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ctggttatttgggttcaagatattattgaaaaactacaatctttaatcgtatgtcaaagttatgctgga-tacataatcccatctta-tctctttttgttagGTAGTCACCTGCCTTCGTCAACCATCGCAAGGACCTACTTTTGGAATTAAAGGAGGTGCAGCTGGTGGTGGCTATAGCCAAGTTATTCCCATGGATGAAT
upper sequence: LOC_Os09g27420.2 (Oryza sativa), 3'ss of exon 2
lower sequence: AT1G50480.1 (Arabidopsis thaliana), 3'ss of exon 2
gacatatcgatgtacatattatgtttattttttta--tagagtatatattatgttattgatatgctttactactttactcaatatt---aatgttgctattatagGTTGTCACTTGCCTCCGTCAACCATCACAAGGGCCTACTTTTGGAATCAAGGGGGGTGCTGCTGGAGGTGGCTACAGCCAAGTCATACCCATGGATGAGT
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----------gttctctcttgctttcatttattagcttatgccttatgcttgcttttggacaaacttctctctttgtattgatttgtgaagtgttgttgct-tagGTTGTTACTTGTCTTCGCCAACCGTCACAAGGACCCACCTTTGGAATCAAAGGAGGTGCAGCTGGTGGTGGGTATAGTCAGGTGATTCCTATGGATGAGT
upper sequence: LOC_Os09g27420.2 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv06s0004g01160.t01 (Vitis vinifera), 3'ss of exon 2
gacatatcgatgtacatattatgtttatttttttatagagtatatattatgttattgatatgctttactactttactcaatattaatgttgct----attatagGTTGTCACTTGCCTCCGTCAACCATCACAAGGGCCTACTTTTGGAATCAAGGGGGGTGCTGCTGGAGGTGGCTACAGCCAAGTCATACCCATGGATGAGT
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---gcatggatgcattttttaatttgacgaacgca-attgtggtgattatgccccaagtaaaactgttaattaatgtcaatattctgtctgcttatgatgttagGTTGTCACCTGCCTTCGTCAACCATCACAAGGACCAACTTTTGGAATTAAAGGAGGTGCAGCAGGTGGTGGTTACAGTCAAGTGATTCCCATGGACGAGTMapped 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|1631916|gb|C19645.1|C19645EST: GCCAGGCGCTGGGTGCGTTTCTTGATAAAAAG GTTGTCACTTGCCTCCGTCAACCATCACAAGGGCCTACTTTTGGAATCAAG
genomic: GCCAGGCGCTGGGTGCGTTTCTTGATAAAAAGgtgagaggct ... gctattatagGTTGTCACTTGCCTCCGTCAACCATCACAAGGGCCTACTTTTGGAATCAAG
EST:
gi|29657308|gb|CB653583.1|CB653583EST: CCACCACCGTTGGGCTGTGCCAGGCGCTGGGTGCGTTTCTTGATAAAAAG GTTGTCACTTGCCTCCGTCAACCATCACAAGGGCCTACTTTTGGAATCAAG
genomic: CCACCACCGTTGGGCTGTGCCAGGCGCTGGGTGCGTTTCTTGATAAAAAGgtgagaggct ... gctattatagGTTGTCACTTGCCTCCGTCAACCATCACAAGGGCCTACTTTTGGAATCAAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.attatgttattgatatgctttactactttactcaatattaatgttgctattatagGTTGTCACTTGCCTCCGTCAACCATCACAAGGGCCTACTTTTGGAATCAAGGGGGGTGCTGCTGGAGGTGGCTACAGCCAAGTCATACCCATGGATGAGT
tattaat putative branch site (score: 2)
aatattaatgttgcta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gacatatcgatgtacatattatgtttatttttttatagagtatatattatgttattgatatgctttactactttactcaatattaatgttgctattatagGTTGTCACTTGCCTCCGTCAACCATCACAAGGGCCTACTTTTGGAATCAAGGGGGGTGCTGCTGGAGGTGGCTACAGCCAAGTCATACCCATGGATGAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - gatgtac
- - - - - - - - - ttatgtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - tatgctt