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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgttgttagattctatgtaactatacattcagcaaataggtatccccagaagatctcattaacattcatgtaaatttcagGGAAAGCTTAACCTAAGTGGTGGTGGTGTTTCTCTGGGCCATCCTATTGGTTGCAGTGGTGCGAGAATCATAGTCACTTTGCTCGGG

Basic information

species Oryza sativa
transcript LOC_Os01g02020.2
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g02020.2 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM5G860137_T02 (Zea mays), 3'ss of exon 10
gtatgttgttagattctatgtaactatacattcagcaaatag-----gtat---ccccagaagatctcattaa-cattcatgtaaatttcagGGAAAGCTTAACCTAAGTGGTGGTGGTGTTTCTCTGGGCCATCCTATTGGTTGCAGTGGTGCGAGAATCATAGTCACTTTGCTCGGG
||  ||   |  ||| | | |   | || ||||||||  |||     ||||   || | | | |||| || ||  ||   |||| ||| ||||||||||| ||| |||||||||||| |||||| |||||||||||||| ||||||||||||||  | || || ||||||||||| |||
gtgagtcactt-attttttatttgtctatattcagcagttagtatttgtatttgcctccggatatctaataaaatatctctgtacatt-cagGGAAAGCTAAACTTAAGTGGTGGTGCTGTTTCCCTGGGCCATCCTATCGGTTGCAGTGGTGCACGGATAATTGTCACTTTGCTTGGG
















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|66915792|gb|CX102640.1|CX102640
EST:     GTCGTTGCTTTAGCCAACCAGAAGCTTCTTGGTATTCCTTCG                         GGAAAGCTTAACCTAAGTGGTGGTGGTGTTTCTCTGGGCCATCCTATTGGT
genomic: GTCGTTGCTTTAGCCAACCAGAAGCTTCTTGGTATTCCTTCGgtatgttgtt ... taaatttcagGGAAAGCTTAACCTAAGTGGTGGTGGTGTTTCTCTGGGCCATCCTATTGGT
EST: gi|58609247|gb|CK037280.1|CK037280
EST:     GTCGTTGCTTTAGCCAACCAGAAGCTTCTTGGTATTCCTTCG                         GGAAAGCTTAACCTAAGTGGTGGTGGTGTTTCTCTGGGCCATCCTATTGGT
genomic: GTCGTTGCTTTAGCCAACCAGAAGCTTCTTGGTATTCCTTCGgtatgttgtt ... taaatttcagGGAAAGCTTAACCTAAGTGGTGGTGGTGTTTCTCTGGGCCATCCTATTGGT
EST: gi|125863427|gb|EL586709.1|EL586709
EST:     TTGCTTTAGCCAACCAGAAGCTTCTTGGTATTCCTTCG                         GGAAAGCTTAACCTAAGTGGTGGTGGTGTTTCTCTGGGCCATCCTATTGGT
genomic: TTGCTTTAGCCAACCAGAAGCTTCTTGGTATTCCTTCGgtatgttgtt ... taaatttcagGGAAAGCTTAACCTAAGTGGTGGTGGTGTTTCTCTGGGCCATCCTATTGGT
EST: gi|218504789|gb|FG958555.1|FG958555
EST:     GTCGTTGCTTTAGCCAACCAGAAGCTTCTTGGTATTCCTTCG                         GGAAAGCTTAACCTAAGTGGTGGTGGTGTTTCTCTGGGCCATCCTATTGGT
genomic: GTCGTTGCTTTAGCCAACCAGAAGCTTCTTGGTATTCCTTCGgtatgttgtt ... taaatttcagGGAAAGCTTAACCTAAGTGGTGGTGGTGTTTCTCTGGGCCATCCTATTGGT

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: 42 (upstream exon), 66 (downstream exon)
Score: 13

GTCGTTGCTTTAGCCAACCAGAAGCTTCTTGGTATTCCTTCGgtatgttgtt ... taaatttcagGGAAAGCTTAACCTAAGTGGTGGTGGTGTTTCTCTGGGCCATCCTATTGGTTGCAGTGGTGCGAGAATCATAGTCACTTTGCTCGGG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cattcagcaaataggtatccccagaagatctcattaacattcatgtaaatttcagGGAAAGCTTAACCTAAGTGGTGGTGGTGTTTCTCTGGGCCATCCTATTGGTTGCAGTGGTGCGAGAATCATAGTCACTTTGCTCGGG
                               cattaac  putative branch site (score: 13)
                                      attcatgtaaattt  TA-rich tract