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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgttcattgtgctattaaatgatagaatcacttgtcagtaacactttttgctactcctttcatgatatataattgacacagctttatgtcttgcaatcagAGCCCAAATTTTGCTTCCAAGGCTGTGGATTTGGCAGCAGGAGAGCTTCTTGAGGTTGCAACTCCTGGAAAAG

Basic information

species Oryza sativa
transcript LOC_Os01g53700.1
intron # 8
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|27577068|gb|CA999762.1|CA999762
EST:     TCAACAGTATCTACAACCATTCTGGTCTTTTTGGAATTCATGCAACAACT                         AGCCCAAATTTTGCTTCCAAGGCTGTGGATTTGGCAGCAGGAGAGCTTCTT
genomic: TCAACAGTATCTACAACCATTCTGGTCTTTTTGGAATTCATGCAACAACTgtgagcccct ... ttgcaatcagAGCCCAAATTTTGCTTCCAAGGCTGTGGATTTGGCAGCAGGAGAGCTTCTT
EST: gi|86593940|gb|CI260169.1|CI260169
EST:     TCAACAGTATCTACAACCATTCTGGTCTTTTTGGAATTCATGCAACAACT                         AGCCCAAATTTTGCTTCCAAGGCTGTGGATTTGGCAGCAGGAGAGCTTCTT
genomic: TCAACAGTATCTACAACCATTCTGGTCTTTTTGGAATTCATGCAACAACTgtgagcccct ... ttgcaatcagAGCCCAAATTTTGCTTCCAAGGCTGTGGATTTGGCAGCAGGAGAGCTTCTT
EST: gi|38475250|gb|CF959383.1|CF959383
EST:     CAACAGTATACTACAACCATTCAGGTCTTTTTGGAATTCATGCAACAACT                         AGCCCAAATTTTGCTTCCAAGGCTGTGGATTTGGCAGCAGGAGAGCTTCTT
genomic: CAACAGTAT-CTACAACCATTCTGGTCTTTTTGGAATTCATGCAACAACTgtgagcccct ... ttgcaatcagAGCCCAAATTTTGCTTCCAAGGCTGTGGATTTGGCAGCAGGAGAGCTTCTT
EST: gi|9864980|gb|AU100730.1|AU100730
EST:     TCAACAGTATCTACAACCATTCTGGTCTTTTTGGAATTCATGCAACAACT                         AGCCCAAATTTTGCTTCCCAAGGCTGTGGATTTGGCAGCAGGAGAGCTTCT
genomic: TCAACAGTATCTACAACCATTCTGGTCTTTTTGGAATTCATGCAACAACTgtgagcccct ... ttgcaatcagAGCCCAAATTTTGCTT-CCAAGGCTGTGGATTTGGCAGCAGGAGAGCTTCT
EST: gi|58690219|gb|CK078906.1|CK078906
EST:     TCAACAGTATCTACAACCATTCAGGTCTTTTTGGAATTCATGCAACAACT                         AGCCCAAATTTTGCTTCCAAGGCTGTGGATTTGGCAGCAGGAGAGCTTCTT
genomic: TCAACAGTATCTACAACCATTCTGGTCTTTTTGGAATTCATGCAACAACTgtgagcccct ... ttgcaatcagAGCCCAAATTTTGCTTCCAAGGCTGTGGATTTGGCAGCAGGAGAGCTTCTT
EST: gi|2311057|gb|C27212.1|C27212
EST:     TCAACAGTATCTACAACCATTCTGGNCTTTTTGGAATTCATGCAACAACT                         AGCCCAA-TTTTGGTTNCA-GGTTTGTGGATTTGG
genomic: TCAACAGTATCTACAACCATTCTGGTCTTTTTGGAATTCATGCAACAACTgtgagcccct ... ttgcaatcagAGCCCAAATTTTGCTTCCAAGGCT-GTGGATTTGG
EST: gi|87021256|gb|CI295315.1|CI295315
EST:     CAGTATCTACAACCATTCTGGTCTTTTTGGAATTCATGCAACAACT                         AGCCCAAATTTTGCTTCCAAGGCTGTGGATTTGGCAGCAGGAGAGCTTCTT
genomic: CAGTATCTACAACCATTCTGGTCTTTTTGGAATTCATGCAACAACTgtgagcccct ... ttgcaatcagAGCCCAAATTTTGCTTCCAAGGCTGTGGATTTGGCAGCAGGAGAGCTTCTT
EST: gi|163920798|gb|EG710061.1|EG710061
EST:     TCAACAGTATCTACAACCATTCTGGTCTTTTTGGAATTCATGCAACAACT                         AGCCCAAATTTTGCTTCCAAGGCTGTGGATTTGGCAGCAGGAGAGCTTCTT
genomic: TCAACAGTATCTACAACCATTCTGGTCTTTTTGGAATTCATGCAACAACTgtgagcccct ... ttgcaatcagAGCCCAAATTTTGCTTCCAAGGCTGTGGATTTGGCAGCAGGAGAGCTTCTT

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: 70 (upstream exon), 72 (downstream exon)
Score: 29

ATCTCCGGATATTAAACAACTACCATCAGATCGAGTCATTCTCTGCATTCAACAGTATCTACAACCATTCTGGTCTTTTTGGAATTCATGCAACAACTgtgagcccct ... ttgcaatcagAGCCCAAATTTTGCTTCCAAGGCTGTGGATTTGGCAGCAGGAGAGCTTCTTGAGGTTGCAACTCCTGGAAAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttgctactcctttcatgatatataattgacacagctttatgtcttgcaatcagAGCCCAAATTTTGCTTCCAAGGCTGTGGATTTGGCAGCAGGAGAGCTTCTTGAGGTTGCAACTCCTGGAAAAG
                         aattgac  putative branch site (score: 29)
            tttcatgatatataat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgttcattgtgctattaaatgatagaatcacttgtcagtaacactttttgctactcctttcatgatatataattgacacagctttatgtcttgcaatcagAGCCCAAATTTTGCTTCCAAGGCTGTGGATTTGGCAGCAGGAGAGCTTCTTGAGGTTGCAACTCCTGGAAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - -attgtgc