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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaggacaccagcattttcctgtttgccaacattttattcagctttcactgatgtagctaatatatttgttgtcacttcctgtagATGAAAGAAACTGTATCTGCTGATGCTAAAAAAGAAAAG

Basic information

species Oryza sativa
transcript LOC_Os02g27594.1
intron # 2
splice site 3'
intron type U2

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|13896996|gb|AU183332.1|AU183332
EST:     AGCTCATTCTGCCTCACACTTCTTCCATGGCCACAGAAACAGCTAGCCAG                         ATGAAAGAAACTGTATCTGCTGATGCTAAAAAAGAAAAG
genomic: AGCTCATTCTGCCTCACACTTCTTCCATGGCCACAGAAACAGCTAGCCAGgtaggacacc ... cttcctgtagATGAAAGAAACTGTATCTGCTGATGCTAAAAAAGAAAAG
EST: gi|27577231|gb|CA999925.1|CA999925
EST:     AGCTCATTCTGCCTCACACTTCTTCCATGGCCACAGAAACAGCTAGCCAG                         ATGAAAGAAACTGTATCTGCTGATGCTAAAAAAGAAAAG
genomic: AGCTCATTCTGCCTCACACTTCTTCCATGGCCACAGAAACAGCTAGCCAGgtaggacacc ... cttcctgtagATGAAAGAAACTGTATCTGCTGATGCTAAAAAAGAAAAG
EST: gi|38480502|gb|CF964591.1|CF964591
EST:     CTTCTTCCATGGTCACAGAAACAGCTAGCCAG                         ATGAAAGAAACTGTATCTGCGTGGTGCTAAAAAAGAAAAG
genomic: CTTCTTCCATGGCCACAGAAACAGCTAGCCAGgtaggacacc ... cttcctgtagATGAAAGAAACTGTATCTGC-TGATGCTAAAAAAGAAAAG
EST: gi|88465588|gb|CI522339.1|CI522339
EST:     AGCTCATTCTGCCTCACACTTCTTCCATGGCCACAGAAACAGCTAGCCAG                         ATGAAAGAAACTGTATCTGCTGATGCT
genomic: AGCTCATTCTGCCTCACACTTCTTCCATGGCCACAGAAACAGCTAGCCAGgtaggacacc ... cttcctgtagATGAAAGAAACTGTATCTGCTGATGCT
EST: gi|58693295|gb|CK081982.1|CK081982
EST:     AGCTCATTCTGCCTCACACTTCTTCCATGGTCACAGAAACAGCTAGCCAG                         ATGAAAGAAACTGTATCTGCTGATGCTAAAAAAGAAAAG
genomic: AGCTCATTCTGCCTCACACTTCTTCCATGGCCACAGAAACAGCTAGCCAGgtaggacacc ... cttcctgtagATGAAAGAAACTGTATCTGCTGATGCTAAAAAAGAAAAG
EST: gi|88374682|gb|CI518549.1|CI518549
EST:     AGCTCATTCTGCCTCACACTTCTTCCATGGCCACAGAAACAGCTAGCCAG                         ATGAAAGAAACTGTATCTGCTGATGCTAAAAAAGAAAAG
genomic: AGCTCATTCTGCCTCACACTTCTTCCATGGCCACAGAAACAGCTAGCCAGgtaggacacc ... cttcctgtagATGAAAGAAACTGTATCTGCTGATGCTAAAAAAGAAAAG
EST: gi|86496213|gb|CI138846.1|CI138846
EST:     AGCTCATTCTGCCTCACACTTCTTCCATGGCCACAGAAACAGCTAGCCAG                         ATGAAAGAAACTGTATCTGCTGATGCTAAAAAAGAAAAG
genomic: AGCTCATTCTGCCTCACACTTCTTCCATGGCCACAGAAACAGCTAGCCAGgtaggacacc ... cttcctgtagATGAAAGAAACTGTATCTGCTGATGCTAAAAAAGAAAAG

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: 74 (upstream exon), 39 (downstream exon)
Score: 69

GTGAGCAACCCACATAGGCTGATAAGCTCATTCTGCCTCACACTTCTTCCATGGCCACAGAAACAGCTAGCCAGgtaggacacc ... cttcctgtagATGAAAGAAACTGTATCTGCTGATGCTAAAAAAGAAAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cattttattcagctttcactgatgtagctaatatatttgttgtcacttcctgtagATGAAAGAAACTGTATCTGCTGATGCTAAAAAAGAAAAG
                         agctaat  putative branch site (score: 69)
                                          tcacttcct  putative PPT
                            taatatatttgttgt  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaggacaccagcattttcctgtttgccaacattttattcagctttcactgatgtagctaatatatttgttgtcacttcctgtagATGAAAGAAACTGTATCTGCTGATGCTAAAAAAGAAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA