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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaggatttttctcttatctactgtatggtgcaacatgcctctggtgacaccttttgctttaaacagGTTAAACTTCTTTTTGCCGCGGAACGTCAGCTTTGTGACCAGGTTTTTGAGTGCAGTCAATCTTTGAGGGATAAGTGCTTTGCTCAAATAACTAGGAATA

Basic information

species Oryza sativa
transcript LOC_Os04g58880.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g58880.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G046590_T01 (Zea mays), 3'ss of exon 5
gtaaggatttt-------tctctta--tctactgt-atggtgcaacatgcctctggtgacacct---tttgctttaaacagGTTAAACTTCTTTTTGCCGCGGAACGTCAGCTTTGTGACCAGGTTTTTGAGTGCAGTCAATCTTTGAGGGATAAGTGCTTTGCTCAAATAACTAGGAATA
||||| | |||       || || |  ||| |||| |||||  | |||  |||||||||||  |   | ||||| | ||||||||||||||||||||| | ||| || || ||||| ||||| |||||||||||||||||||| |||||||||||||||||||||  |||||| | ||| |
gtaagtaatttccctccctccctcaggtcttctgttatggtatagcattgctctggtgacatttgcctctgcttgagacagGTTAAACTTCTTTTTGCTGGGGAGCGCCAACTTTGCGACCAAGTTTTTGAGTGCAGTCAATCGTTGAGGGATAAGTGCTTTGCTGCAATAACAAAGAACA
















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|29669620|gb|CB665895.1|CB665895
EST:     AAATTTTGGAGTCTAAAATAGGGAATTGGATTCACTTCATGCGAATTGCT                         GTTAAACTTCTTTTTGCCGCGGAACGTCAGCTTTGTGACCAGGTTTTTGAG
genomic: AAATTTTGGAGTCTAAAATAGGGAATTGGATTCACTTCATGCGAATTGCTgtaaggattt ... ctttaaacagGTTAAACTTCTTTTTGCCGCGGAACGTCAGCTTTGTGACCAGGTTTTTGAG
EST: gi|29630823|gb|CB635832.1|CB635832
EST:     AAATTTTGGAGTCTAAAATAGGGAATTGGATTCACTTCATGCGAATTGCT                         GTTAAACTTCTTTTTGCCGCGGAACGTCAGCTTTGTGACCAGGTTTTTGAG
genomic: AAATTTTGGAGTCTAAAATAGGGAATTGGATTCACTTCATGCGAATTGCTgtaaggattt ... ctttaaacagGTTAAACTTCTTTTTGCCGCGGAACGTCAGCTTTGTGACCAGGTTTTTGAG
EST: gi|86821957|gb|CI309340.1|CI309340
EST:     AAATTTTGGAGTCTAAAATAGGGAATTGGATTCACTTCATGCGAATTGCT                         GTTAAACTTCTTTTTGCCGCGGAACGTCAGTTTTGTGACCAGGTTTTTGAG
genomic: AAATTTTGGAGTCTAAAATAGGGAATTGGATTCACTTCATGCGAATTGCTgtaaggattt ... ctttaaacagGTTAAACTTCTTTTTGCCGCGGAACGTCAGCTTTGTGACCAGGTTTTTGAG
EST: gi|58663378|gb|CK052064.1|CK052064
EST:     AAATTTTGGAGTCTAAAATAGGGAATTGGATTCACTTCATGCGAATTGCT                         GTTAAACTTCTTTTTGCCGCGGAACGTCAGCTTTGTGACCAGGTTTTTGAG
genomic: AAATTTTGGAGTCTAAAATAGGGAATTGGATTCACTTCATGCGAATTGCTgtaaggattt ... ctttaaacagGTTAAACTTCTTTTTGCCGCGGAACGTCAGCTTTGTGACCAGGTTTTTGAG
EST: gi|66922614|gb|CX119142.1|CX119142
EST:     AAATTTTGGAGTCTAAAATAGGGAATTGGATTCACTTCATGCGAATTGCT                         GTTAAACTTCTTTTTGCCGCGGAACGTCAGCTTTGTGACCAGGTTTTTGAG
genomic: AAATTTTGGAGTCTAAAATAGGGAATTGGATTCACTTCATGCGAATTGCTgtaaggattt ... ctttaaacagGTTAAACTTCTTTTTGCCGCGGAACGTCAGCTTTGTGACCAGGTTTTTGAG

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: 71 (upstream exon), 75 (downstream exon)
Score: 25

CTTGGGTGTTGAAAAACTGAGCAAAGATGAAGTGCAGAAAATGCCATGGGAAATTTTGGAGTCTAAAATAGGGAATTGGATTCACTTCATGCGAATTGCTgtaaggattt ... ctttaaacagGTTAAACTTCTTTTTGCCGCGGAACGTCAGCTTTGTGACCAGGTTTTTGAGTGCAGTCAATCTTTGAGGGATAAGTGCTTTGCTCAAATAACTAGGAATA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcttatctactgtatggtgcaacatgcctctggtgacaccttttgctttaaacagGTTAAACTTCTTTTTGCCGCGGAACGTCAGCTTTGTGACCAGGTTTTTGAGTGCAGTCAATCTTTGAGGGATAAGTGCTTTGCTCAAATAACTAGGAATA
                                      ccttttgcttt  CT-rich tract
                                              tttaaaca  TA-rich tract