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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtgtgataaatttggtccaagaagtataatattattcgtgcattatgcttactgttggtgttcctctttccatgaccaacttgcagATCGAGGGACCTCAACTATTGCAGCATGGTTTTAACGATGCAATTGCAAAAGTAGGCTTGACAAAGTTCGTTTCTGACCTTTTCTTCGTGGGACTGTTCT

Basic information

species Oryza sativa
transcript LOC_Os01g13770.2
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g13770.2 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G070605_T01 (Zea mays), 3'ss of exon 8
gtaagtgtgataaatttggtccaagaagtat-----aatattattcgtgcattatgcttactgttggtgttcctctttccatgaccaacttgcagATCGAGGGACCTCAACTATTGCAGCATGGTTTTAACGATGCAATTGCAAAAGTAGGCTTGACAAAGTTCGTTTCTGACCTTTTCTTCGTGGGACTGTTCT
|||||||||    |        ||| ||||      ||||  |||||||    || | |||  ||  |  |  ||  |  ||||      ||||| | || || || |  ||| |||||||||| || |  ||||| |||||||||||||||||||||||||| |||  |||||| ||||| || ||||||||||
gtaagtgtggattaccacagttaagtagtagtaagaaataggattcgtgggccatacatacaattt-taatggtccatatatgattg---tgcagTTTGAAGGGCCCCGGCTAATGCAGCATGGATTCAGTGATGCCATTGCAAAAGTAGGCTTGACAAAGTTTGTTAGTGACCTATTCTTGGTTGGACTGTTCT

upper sequence: LOC_Os01g13770.2 (Oryza sativa), 3'ss of exon 8
lower sequence: Vv10s0003g00300.t01 (Vitis vinifera), 3'ss of exon 8
gtaagtgtgataaatttggtccaagaagtataatattattcgtgcattatgcttac-tgttggtgttcctctttccatgaccaactt-gcagATCGAGGGACCTCAACTATTGCAGCATGGTTTTAACGATGCAATTGCAAAAGTAGGCTTGACAAAGTTCGTTTCTGACCTTTTCTTCGTGGGACTGTTCT
|||||||  | |    || |   |||    | |   | ||  | | | |  || |  |    || | | |  || |||| |  | ||  ||| | ||||||||||||||  || ||||||| ||||| ||||||||||| ||||| ||  |||| |||||| | || || || || |  |||||| |||| |
gtaagtgcaaca----tgatttgagatccttgagggttttgattcctaaaactaaaataacagtttccatactttcatgtctgattttacagGTGGAGGGACCTCAACTGATGAAGCATGGCTTTAATGATGCAATTGCTAAAGTGGGTCTGACCAAGTTCCTCTCAGATCTCTTTTGGGTGGGAATGTTTT
















Mapped 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|29640948|gb|CB645955.1|CB645955
EST:     CTTATATCTCAATAATTGCCCTTATTGTGTGCATTCCACCAGCAGTGATC                         ATCGAGGGACCTCAACTATTGCAGCATGGTTTTAACGATGCAATTGCAAAA
genomic: CTTATATCTCAATAATTGCCCTTATTGTGTGCATTCCACCAGCAGTGATCgtaagtgtga ... caacttgcagATCGAGGGACCTCAACTATTGCAGCATGGTTTTAACGATGCAATTGCAAAA
EST: gi|29661884|gb|CB658159.1|CB658159
EST:     CTTATATCTCAATAATTGCCCTTATTGTGTGCATTCCACCAGCAGTGATC                         ATCGAGGGACCTCAACTATTGCAGCATGGTTTTAACGATGCAATTGCAAAA
genomic: CTTATATCTCAATAATTGCCCTTATTGTGTGCATTCCACCAGCAGTGATCgtaagtgtga ... caacttgcagATCGAGGGACCTCAACTATTGCAGCATGGTTTTAACGATGCAATTGCAAAA
EST: gi|325493498|gb|JG458022.1|JG458022
EST:     CTTATATCTCAATAATTGCCCTTATTGTGTGCATTCCACCAGCAGTGATC                         ATCGAGGGACCTCAACTATTGCAGCATGGTTTTAACGATGCAATTGCAAAA
genomic: CTTATATCTCAATAATTGCCCTTATTGTGTGCATTCCACCAGCAGTGATCgtaagtgtga ... caacttgcagATCGAGGGACCTCAACTATTGCAGCATGGTTTTAACGATGCAATTGCAAAA
EST: gi|29657881|gb|CB654156.1|CB654156
EST:     CTTATATCTCAATAATTGCCCTTATTGTGTGCATTCCACCAGCAGTGATC                         ATCGAGGGACCTCAACTATTGCAGCATGGT
genomic: CTTATATCTCAATAATTGCCCTTATTGTGTGCATTCCACCAGCAGTGATCgtaagtgtga ... caacttgcagATCGAGGGACCTCAACTATTGCAGCATGGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttattcgtgcattatgcttactgttggtgttcctctttccatgaccaacttgcagATCGAGGGACCTCAACTATTGCAGCATGGTTTTAACGATGCAATTGCAAAAGTAGGCTTGACAAAGTTCGTTTCTGACCTTTTCTTCGTGGGACTGTTCT
              tgcttac  putative branch site (score: 2)
          attat  TA-rich tract