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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaacctgttgttacaacttacaagtgtcatctactctgttttggaggttagacatctggtgaaaactttctaatttttttcttcttgttgttattgttagTTGGCTGCATGGAAAGAAATCGGAGTGGCAAACTTACCCGGTGTGATCAGCTTGGCAGCCGGCCTGCTAATGTGGGTGACATCACTCCACCCAGTGAGGA

Basic information

species Oryza sativa
transcript 13113.m00231
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g36720.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G068557_T01 (Zea mays), 3'ss of exon 4
aaacctgttgtt-acaacttacaagtgtcatctactctgttttggaggttagacatctggtgaaaactttctaatttttttcttc-ttgttgttattgt-tagTTGGCTGCATGGAAAGAAATCGGAGTGGCAAACTTACCCGGTGTGATCAGCTTGGCAGCCGGCCTGCTAATGTGGGTGACATCACTCCACCCAGTGAGGA
  |  | | ||| ||  | || |    | || |    || |      ||    |||||   ||| |||    | |     | ||   | ||||| |||| ||| ||      ||||| ||||| ||||| |||||| | || |||||||||||||||||||||||||| || ||||||||||||||||| |||||||||||||
--atttttggttgacggcatatagtaattatatttcttgctacacttgtcctgcatctca-gaacactagtaactagccatattggcttttgtttttgtatagCTGAGACAGTGGAAGGAAATTGGAGTAGCAAACCTGCCTGGTGTGATCAGCTTGGCAGCCGGCCTACTTATGTGGGTGACATCACTTCACCCAGTGAGGA
















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|29645909|gb|CB650916.1|CB650916
EST:     TCGAGGGGAATCTACTCGTATAA                         TTGGCTGCATGGAAAGAAATCGGAGTGGCAAACCCACCCGGTGTGATCAGC
genomic: TCGAGGGGAATCTACTTGGAGAAgtaagaatga ... ttattgttagTTGGCTGCATGGAAAGAAATCGGAGTGGCAAACTTACCCGGTGTGATCAGC
EST: gi|29663836|gb|CB660111.1|CB660111
EST:     GCCTATGCTATGTGATCGCATGGTCTCTCGAGGGGAATCTACTTGGAGAA                         TTGGCTGCATGGAAAGAAATCGGAGTGGCAAACTTACCCGGTGTGATCAGC
genomic: GCCTATGCTATGTGATCGCATGGTCTCTCGAGGGGAATCTACTTGGAGAAgtaagaatga ... ttattgttagTTGGCTGCATGGAAAGAAATCGGAGTGGCAAACTTACCCGGTGTGATCAGC

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: 73 (upstream exon), 72 (downstream exon)
Score: 97

ATACCACGTCTGGCTCGGCCATCTCACAATGGCTCTCTTCACATTACATGGCCTATGCTATGTGATCGCATGGTCTCTCGAGGGGAATCTACTTGGAGAAgtaagaatga ... ttattgttagTTGGCTGCATGGAAAGAAATCGGAGTGGCAAACTTACCCGGTGTGATCAGCTTGGCAGCCGGCCTGCTAATGTGGGTGACATCACTCCACCCAGTGAGGA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggttagacatctggtgaaaactttctaatttttttcttcttgttgttattgttagTTGGCTGCATGGAAAGAAATCGGAGTGGCAAACTTACCCGGTGTGATCAGCTTGGCAGCCGGCCTGCTAATGTGGGTGACATCACTCCACCCAGTGAGGA
                      ttctaat  putative branch site (score: 97)
                    ctttctaatttttttc  CT-rich tract
                aaaactttctaatttt  TA-rich tract