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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttttgtgtttgtgaagcatgttccacttttatgttggactttatcttactgtaatgcgatattgtgaatatgcaattaatgtactcttcatctgtgctagCTGGCTCGGAAAGATTACCTTAGAAACGTACATATCACAGTTCCATATTTGGCTCAG

Basic information

species Oryza sativa
transcript LOC_Os03g19970.1
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g19970.1 (Oryza sativa), 3'ss of exon 12
lower sequence: GRMZM2G020721_T01 (Zea mays), 3'ss of exon 12
gtaagttttgtgtttgtgaagcatgttccacttttatgttggactttatcttactgtaatgcgatattgtgaatatgcaattaatgtactcttcatctgtgctagCTGGCTCGGAAAGATTACCTTAGAAACGTACATATCACAGTTCCATATTTGGCTCAG
||||||||||  | |||   |||   | |  |||    ||   |||  | | | |||  |||||   ||||| |     |||  |  |   ||    ||| | |||||||| |||||||||||  ||||||| |||||||| ||||||||||| ||||||||
gtaagttttggttgtgtattgcactgtaccttttatctttaaccttcctgtcattgttgtgcgaatatgtgactcctgtatttgttca---tttggttgttccagCTGGCTTGGAAAGATTACACTAGAAACATACATATCTCAGTTCCATATCTGGCTCAG
















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|38475137|gb|CF959270.1|CF959270
EST:     TTACGCAACTTCACTCAAGAATTCCGGTGCTGCTCTCTCACACTATTTGC                         CTGGCTCGGAAAGATTACCTTAGAAACGTACATATCACAGTTCCATATTTG
genomic: TTACGCAACTTCACTCAAGAATTCCGGTGCTGCTCTCTCACACTATTTGCgtaagttttg ... tctgtgctagCTGGCTCGGAAAGATTACCTTAGAAACGTACATATCACAGTTCCATATTTG
EST: gi|27577031|gb|CA999725.1|CA999725
EST:     TTACGCAACTTCACTCAAGAATTCCGGTGCTGCTCTCTCACACTATTTGC                         CTGGCTCGGAAAGATTACCTTAGAAACGTACATATCACAGTTCCATATTTG
genomic: TTACGCAACTTCACTCAAGAATTCCGGTGCTGCTCTCTCACACTATTTGCgtaagttttg ... tctgtgctagCTGGCTCGGAAAGATTACCTTAGAAACGTACATATCACAGTTCCATATTTG
EST: gi|58594781|gb|CF993089.1|CF993089
EST:     TTACGCAACTTCACTCAAGAATTCCGGTGCTGCTCTCTCAGGCTATTTGC                         CTGGCTCGGAAAGATTACCTTAGAAACGTACATATCACAGTTCCATATTTG
genomic: TTACGCAACTTCACTCAAGAATTCCGGTGCTGCTCTCTCACACTATTTGCgtaagttttg ... tctgtgctagCTGGCTCGGAAAGATTACCTTAGAAACGTACATATCACAGTTCCATATTTG

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: 57 (upstream exon), 69 (downstream exon)
Score: 36

TGTGTACATCTGCTTACGCAACTTCACTCAAGAATTCCGGTGCTGCTCTCTCACACTATTTGCgtaagttttg ... tctgtgctagCTGGCTCGGAAAGATTACCTTAGAAACGTACATATCACAGTTCCATATTTGGCTCAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttactgtaatgcgatattgtgaatatgcaattaatgtactcttcatctgtgctagCTGGCTCGGAAAGATTACCTTAGAAACGTACATATCACAGTTCCATATTTGGCTCAG
                            aattaat  putative branch site (score: 36)
                                      ctcttcatct  putative PPT
                     aatatgcaattaat  TA-rich tract