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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agaaagagcattacagcgccaaattttgagccatgcgccaaaaaacatcccctgtggatttctttgttcccaatatcattgcaacttgtgaatcaaacagGCAGCAGCTGCTATCTTCCATCGTATGATCTCTCATACTACCATATCATTCTCCAACATGATCGGCCCAGTTGAACAGGTGGAGTTTTGTGGGCATCCAG

Basic information

species Oryza sativa
transcript LOC_Os01g56360.1
intron # 5
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|29672385|gb|CB668660.1|CB668660
EST:     TATTCACTCATTTAGCTGCAGAAGTGATCCTCAAACTTTTTGGGCTCAAG                         GCAGCAGCTGCTATCTTCCATCGTATGATCTCTCATACTACCATATCATTC
genomic: TATTCACTCATTTAGCTGCAGAAGTGATCCTCAAACTTTTTGGGCTCAAGgtaaatttgt ... aatcaaacagGCAGCAGCTGCTATCTTCCATCGTATGATCTCTCATACTACCATATCATTC
EST: gi|29633484|gb|CB638493.1|CB638493
EST:     TATTCACTCATTTAGCTGCAGAAGTGATCCTCAAACTTTTTGGGCTCAAG                         GCAGCAGCTGCTATCTTCCATCGTATGATCTCTCATACTACCATATCATTC
genomic: TATTCACTCATTTAGCTGCAGAAGTGATCCTCAAACTTTTTGGGCTCAAGgtaaatttgt ... aatcaaacagGCAGCAGCTGCTATCTTCCATCGTATGATCTCTCATACTACCATATCATTC
EST: gi|58690336|gb|CK079023.1|CK079023
EST:     TATTCACTCATTTAGCTGCAGAAGTGATCCTCAAACTTTTTGGGCTCAAG                         GCAGCGGCCGCAATCTTCCATCGTATGATCTCTCATACTACCATATCATTC
genomic: TATTCACTCATTTAGCTGCAGAAGTGATCCTCAAACTTTTTGGGCTCAAGgtaaatttgt ... aatcaaacagGCAGCAGCTGCTATCTTCCATCGTATGATCTCTCATACTACCATATCATTC
EST: gi|58608842|gb|CK036875.1|CK036875
EST:     TATTCACTCATTTAGCTGCAGAAGTGATCCTCAAACTTTTTGGGCTCAAG                         GCAGCGGCCGCAATCTTCCATCGTATGATCTCTCATACTACCATATCATTC
genomic: TATTCACTCATTTAGCTGCAGAAGTGATCCTCAAACTTTTTGGGCTCAAGgtaaatttgt ... aatcaaacagGCAGCAGCTGCTATCTTCCATCGTATGATCTCTCATACTACCATATCATTC
EST: gi|29680740|gb|CB677015.1|CB677015
EST:     TATTCACTCATTTAGCTGCAGAAGTGATCCTCAAACTTTTTGGGCTCAAG                         GCAGCAGCTGCTATCTTCCATCGTATGATCTCTCATACTACCATATCATTC
genomic: TATTCACTCATTTAGCTGCAGAAGTGATCCTCAAACTTTTTGGGCTCAAGgtaaatttgt ... aatcaaacagGCAGCAGCTGCTATCTTCCATCGTATGATCTCTCATACTACCATATCATTC
EST: gi|29678634|gb|CB674909.1|CB674909
EST:     TATTCACTCATTTAGCTGCAGAAGTGATCCTCAAACTTTTTGGGCTCAAG                         GCAGCAGCTGCTATCTTCCATCGTATGATCTCTCATACTACCATATCATTC
genomic: TATTCACTCATTTAGCTGCAGAAGTGATCCTCAAACTTTTTGGGCTCAAGgtaaatttgt ... aatcaaacagGCAGCAGCTGCTATCTTCCATCGTATGATCTCTCATACTACCATATCATTC
EST: gi|29664303|gb|CB660578.1|CB660578
EST:     TATTCACTCATTTAGCTGCAGAAGTGATCCTCAAACTTTTTGGGCTCAAG                         GCAGCAGCTGCTATCTTCCATCGTATGATCTCTCATACTACCATATCATTC
genomic: TATTCACTCATTTAGCTGCAGAAGTGATCCTCAAACTTTTTGGGCTCAAGgtaaatttgt ... aatcaaacagGCAGCAGCTGCTATCTTCCATCGTATGATCTCTCATACTACCATATCATTC
EST: gi|38468635|gb|CF952766.1|CF952766
EST:     TATTCACTCATTTAGCTGCAGAAGTGATCCTCAAACTTTTTGGGCTCAAG                         GCAGCGGCCGCAATCTTCCATCGTATGATCTCTCATACTACCATATCATTC
genomic: TATTCACTCATTTAGCTGCAGAAGTGATCCTCAAACTTTTTGGGCTCAAGgtaaatttgt ... aatcaaacagGCAGCAGCTGCTATCTTCCATCGTATGATCTCTCATACTACCATATCATTC

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), 73 (downstream exon)
Score: 11

TCGGAAAGCAAAGAAGGTTGTTGATAGGAAGAAGAGCTCATTAGAAGTGGTATTCACTCATTTAGCTGCAGAAGTGATCCTCAAACTTTTTGGGCTCAAGgtaaatttgt ... aatcaaacagGCAGCAGCTGCTATCTTCCATCGTATGATCTCTCATACTACCATATCATTCTCCAACATGATCGGCCCAGTTGAACAGGTGGAGTTTTGTGGGCATCCAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catcccctgtggatttctttgttcccaatatcattgcaacttgtgaatcaaacagGCAGCAGCTGCTATCTTCCATCGTATGATCTCTCATACTACCATATCATTCTCCAACATGATCGGCCCAGTTGAACAGGTGGAGTTTTGTGGGCATCCAG
                          aatatcatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agaaagagcattacagcgccaaattttgagccatgcgccaaaaaacatcccctgtggatttctttgttcccaatatcattgcaacttgtgaatcaaacagGCAGCAGCTGCTATCTTCCATCGTATGATCTCTCATACTACCATATCATTCTCCAACATGATCGGCCCAGTTGAACAGGTGGAGTTTTGTGGGCATCCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
agaaagag
- - - - - - - - - - - - - - - -catgcgc
- - - - - - - - - - - - - - - - - - - caaaaaa
- - - - - - - - - - - - - - - - - - - - - - -catcccc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cattgca