Sequence
atgc intronic sequence ATGC exonic sequence...tttatttcttgtctgctacgtcttctataattatagcaaaaatggctctgctacatatataaccgttccaggatttttctgtttgtacactatggaacagATTATGGCTGTCAAGAAGATCATTGAAGAGATACAAGGAAAGGATAGCTACCCATGGGGCCAACAGTTGCTGATTCACAATGGCAAGGTTTTGAAAGATG
Basic information
species | Oryza sativa |
transcript | LOC_Os02g08300.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os02g08300.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G143462_T06 (Zea mays), 3'ss of exon 1
tttatttcttgtctgctacgtcttctataattatagcaaaaatggctctgcta-catatataaccgttccaggatttttctgtttgtacactatggaacagATTATGGCTGTCAAGAAGATCATTGAAGAGATACAAGGAAAGGATAGCTACCCATGGGGCCAACAGTTGCTGATTCACAATGGCAAGGTTTTGAAAGATG
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-ataatgcttgtcagctaactgttttgtgatcgtagttgaatgagttttattggcattcaatattttgtcaaggttctactaaaggttccttatttaccagATTATGGCTGTGAAGAAGAATATAGAAGAGATACAAGGGAAAGACAGCTATCCATGGGGCCAACAACTGCTGATTTTCAATGGAAAGGTCTTGAAAGATG
upper sequence: LOC_Os02g08300.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA08G23930.2 (Glycine max), 3'ss of exon 1
tttatttcttgtctgctacgtctt-----ctataatta--tagcaaaaatggctctgctacatatataaccgttccaggatttttctgtttgtacactatggaacagATTATGGCTGTCAAGAAGATCATTGAAGAGATACAAGGAAAGGATAGCTACCCATGGGGCCAACAGTTGCTGATTCACAATGGCAAGGTTTTGAAAGATG
|| || | ||||| | || |||| || ||| |||| | || | | | ||| | | ||| | ||| | | || ||| |||||||||||||||||| |||||||| |||||||||| |||| |||||||| || || || ||| ||||||||||||||||||||||||||||||
--taattttgaagtgctattttttgaaatctattgtttatcagctgaaattg-tcaatttgttgtttaattagctgaagttttctgcttttttgtcccat----cagGTTATGGCTGTCAAGAAGAATATTGAAGATGTACAAGGAAAAGATAATTACCCATGTGGACAGCAATTGTTGATTCACAATGGCAAGGTTTTGAAAGATG
upper sequence: LOC_Os02g08300.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA13G44910.1 (Glycine max), 3'ss of exon 1
----tttatttcttgtctgctacgtcttctataattatagcaaaaatggctctgctacatatataaccgttccaggatttttctgtttgtacactatggaacagATTATGGCTGTCAAGAAGATCATTGAAGAGATACAAGGAAAGGATAGCTACCCATGGGGCCAACAGTTGCTGATTCACAATGGCAAGGTTTTGAAAGATG
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gtcagtcatatgatctc-attcccaacccaattctgctttttaatttcattcttccaaat-cctatgcatttcttaattgtgatgttt-tat-cttcacctcagATTATGGCAGTCAAGAAGAATATCGAAGATGTACAAGGCAAAGACAATTACCCATGTGGACAGCAATTGCTCATTCACAATGGTAAGGTTTTGAAAGATG
upper sequence: LOC_Os02g08300.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA07G00490.1 (Glycine max), 3'ss of exon 1
------tttatttcttgtctgctacgtcttctataatta--tagcaaaaatggctctgctacatatataaccgttccaggatttttctgtttgtacactatggaacagATTATGGCTGTCAAGAAGATCATTGAAGAGATACAAGGAAAGGATAGCTACCCATGGGGCCAACAGTTGCTGATTCACAATGGCAAGGTTTTGAAAGATG
||| | | || | | |||||| || ||| |||| || | | | || | | || || |||| ||||| || ||| |||||||||||||||||| |||||||| |||||||||| |||| |||||||| || || || ||||||||||||||||| ||||||||||||||||
ggaaaattttgaagtgctatgtttcaaattctattgtttatcagccgaaatta-tcaatttgttgtttattagctg-agtgttcttctttttgtcacct------cagGTTATGGCTGTCAAGAAGAATATTGAAGATGTACAAGGAAAAGATAATTACCCATGTGGACAGCAATTGCTGATTCACAATGGTAAGGTTTTGAAAGATG
upper sequence: LOC_Os02g08300.2 (Oryza sativa), 3'ss of exon 1
lower sequence: AT1G16190.1 (Arabidopsis thaliana), 3'ss of exon 1
----tttatttcttgtctgctacgtcttctataattatagcaaaaatggctctgc-tacatatataaccgt--tccaggatttttctgtttgtacactatggaacagATTATGGCTGTCAAGAAGATCATTGAAGAGATACAAGGAAAGGATAGCTACCCATGGGGCCAACAGTTGCTGATTCACAATGGCAAGGTTTTGAAAGATG
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agtttttttttttccgatgaaatggatgggttgagtg-agtgtatttgtctatgagttcttacatggttatatcctggaatttttctactt---tgctttgaa---gATAATGGCGGTGAAGAAGAATATTGAAGATTCACAAAGCAAAGACAACTATCCTTGTGGGCAGCAATTACTGATTCACAATGGAAAGGTTTTGAAAGATGMapped 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|88351863|gb|CI624668.1|CI624668EST: GTTCGAGATCCGGGTGCAGCCCAACGACACC ATTATGGCTGTCAAGAAGATCATTGAAGAGATACAAGGAAAGGATAGCTAC
genomic: GTTCGAGATCCGGGTGCAGCCCAACGACACCgtgagaaatt ... tatggaacagATTATGGCTGTCAAGAAGATCATTGAAGAGATACAAGGAAAGGATAGCTAC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctctgctacatatataaccgttccaggatttttctgtttgtacactatggaacagATTATGGCTGTCAAGAAGATCATTGAAGAGATACAAGGAAAGGATAGCTACCCATGGGGCCAACAGTTGCTGATTCACAATGGCAAGGTTTTGAAAGATG
atataac putative branch site (score: 3)
tacatatataa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tttatttcttgtctgctacgtcttctataattatagcaaaaatggctctgctacatatataaccgttccaggatttttctgtttgtacactatggaacagATTATGGCTGTCAAGAAGATCATTGAAGAGATACAAGGAAAGGATAGCTACCCATGGGGCCAACAGTTGCTGATTCACAATGGCAAGGTTTTGAAAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG