Sequence
atgc intronic sequence ATGC exonic sequencegtaaaacctcaaatatccataaacataaccatttgcttgatagtattgcactcaatatgcaacacattaatttagtgatgttccatctttttttttcttttttcattagaaacattgatttttccaaacaaatatttctctttgaaatctgagtgccatgacctgttcactgttaacccatcaataatgcagAATTCATCAACTCCTGGACTTGTCTTGGAGGATTTTGATTCCCAATTTTCTAATAGATTTTACCACAGCACTTTGGATGGCCCTG
Basic information
species | Oryza sativa |
transcript | LOC_Os02g50360.1 |
intron # | 13 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os02g50360.1 (Oryza sativa), 3'ss of exon 13
lower sequence: GRMZM2G168337_T01 (Zea mays), 3'ss of exon 13
gtaaaacctcaaatatccataaacataaccattt--gcttgatagtattgcactcaatatgcaacacattaatttagtgatgttccatctttttttttcttttttcattagaaacattgatttttccaaacaaatatttctctttgaaatctgagtgccatgacctgttcactgttaacccatcaataatgcagAATTCATCAACTCCTGGACTTGTCTTGGAGGATTTTGATTCCCAATTTTCTAATAGATTTTACCACAGCACTTTGGATGGCCCTG
| ||||| || |||| || | | | || | || || | | | |||| || | || | ||| |||||| |||||||| | | | | | ||||| || ||||| || |||| ||| || ||| | |||| |||||| ||||| |||| |||||||||||||||||||| || || ||||||||||| || ||| | ||||| | |||
----------------------gtaaaaccacttatgcttacta--aatatatatgattcatagttgcttccttcacctgggg---aactttcttctcacttgtacatccataacatt-atttttcccactatgt---tttatttgaggacttctgctcatgatgtg----ctgtcaactaatgaat---gtagAACATGTCAACTTCTGGAGTTGTGTTGGAGGATTTTGATTCCCACTTCTCCAATAGATTTTATCATAGCTATCTGGATAACTCTGMapped 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|58675494|gb|CK064181.1|CK064181EST: CATCAAATCCTGGTGTTCCACCATCTTCATTAATGTCGTTCCTAGGAAAG AATTCATCAACTCCTGGACTTGTCTTGGAGGATTTTGATTCCCAATTTTCT
genomic: CATCAAATCCTGGTGTTCCACCATCTTCATTAATGTCGTTCCTAGGAAAGgtaaaacctc ... aataatgcagAATTCATCAACTCCTGGACTTGTCTTGGAGGATTTTGATTCCCAATTTTCT
EST:
gi|58595832|gb|CK006360.1|CK006360EST: CATCAAATCCTGGTGTTCCACCATCTTCATTAATGTCGTTCCTAGGAAAG AATTCATCAACTCCTGGACTTGTCTTGGAGGATTTTGATTCCCAATTTTCT
genomic: CATCAAATCCTGGTGTTCCACCATCTTCATTAATGTCGTTCCTAGGAAAGgtaaaacctc ... aataatgcagAATTCATCAACTCCTGGACTTGTCTTGGAGGATTTTGATTCCCAATTTTCT
EST:
gi|58673433|gb|CK062119.1|CK062119EST: CATCAAATCCTGGTGTTCCACCATCTTCATTAATGTCGTTCCTAGGAAAG AATTCATCAACTCCTGGACTTGTCTTGGAGGATTTTGA
genomic: CATCAAATCCTGGTGTTCCACCATCTTCATTAATGTCGTTCCTAGGAAAGgtaaaacctc ... aataatgcagAATTCATCAACTCCTGGACTTGTCTTGGAGGATTTTGA
RNA-Seq data
ATGC Supported by RNA-Seq exonic block that spans over the splice site
atgs Truncated intron sequence
Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.
Found data for 1 RNA-Seqlibrary.
Block sizes:
74 (upstream exon),
67 (downstream exon)
Score:
11TGCCAGTGAATCACTTGGTTCTGATAATGTTAAAGTAAAACCAGCAGCTTCATCAAATCCTGGTGTTCCACCATCTTCATTAATGTCGTTCCTAGGAAAGgtaaaacctc ... aataatgcagAATTCATCAACTCCTGGACTTGTCTTGGAGGATTTTGATTCCCAATTTTCTAATAGATTTTACCACAGCACTTTGGATGGCCCTG
<
<
<
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctctttgaaatctgagtgccatgacctgttcactgttaacccatcaataatgcagAATTCATCAACTCCTGGACTTGTCTTGGAGGATTTTGATTCCCAATTTTCTAATAGATTTTACCACAGCACTTTGGATGGCCCTG
tgttaac putative branch site (score: 11)
atcaataat TA-rich tract