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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgcactcatcacataatgatcatctatctccttttcatttatctagcaacaagttttatgtattgtttatacagGTCCAGATGCAGTTCAGTTCATTGTTAACCATGCGACAGTACAAGCTATTTTCTGTGTGCCTCAAACACTAAGCACT

Basic information

species Oryza sativa
transcript LOC_Os12g04990.1
intron # 6
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|29667939|gb|CB664214.1|CB664214
EST:     TGCCTGTGCGGCATATTCATATGTATCCGTGCCACTTTATGATACTCTAG                         GTCCAGATGCAGTTCAGTTCATTGTTAACCATGCGACAGTAC
genomic: TGCCTGTGCGGCATATTCATATGTATCCGTGCCACTTTATGATACTCTAGgtatgcactc ... gtttatacagGTCCAGATGCAGTTCAGTTCATTGTTAACCATGCGACAGTAC
EST: gi|29626657|gb|CB631668.1|CB631668
EST:     TGCCTGTGCGGCATATTCATATGTATCCGTGCCACTTTATGATACTCTAC                         GTCCAGATGCAGTTCAGTTCATTGTTAACCATGCGACAGTACAAGCTATTG
genomic: TGCCTGTGCGGCATATTCATATGTATCCGTGCCACTTTATGATACTCTAGgtatgcactc ... gtttatacagGTCCAGATGCAGTTCAGTTCATTGTTAACCATGCGACAGTACAAGCTATTT
EST: gi|29627108|gb|CB632119.1|CB632119
EST:     TGCCTGTGCGGCATATTCATATGTATCCGTGCCACTTTATGATACTCTAG                         GTCCAGATGCAGTTCAGTTCATTGTTAACCATGCGACAGTACAAGCTATTT
genomic: TGCCTGTGCGGCATATTCATATGTATCCGTGCCACTTTATGATACTCTAGgtatgcactc ... gtttatacagGTCCAGATGCAGTTCAGTTCATTGTTAACCATGCGACAGTACAAGCTATTT
EST: gi|29630786|gb|CB635795.1|CB635795
EST:     TGCCTGTGCGGCATATTCATATGTATCCGTGCCACTTTATGATACTCTAG                         GTCCAGATGCAGTTCAGTTCATTGTTAACCATGCGACAGTACAAGCTATTT
genomic: TGCCTGTGCGGCATATTCATATGTATCCGTGCCACTTTATGATACTCTAGgtatgcactc ... gtttatacagGTCCAGATGCAGTTCAGTTCATTGTTAACCATGCGACAGTACAAGCTATTT
EST: gi|29627343|gb|CB632354.1|CB632354
EST:     TGCCTGTGCGGCATATTCATATGTATCCGTGCCACTTTATGATACTCTAG                         GTCCAGATGCAGTTCAGTTCATTGTTAACCATGCGACAGTACAAGCTATTT
genomic: TGCCTGTGCGGCATATTCATATGTATCCGTGCCACTTTATGATACTCTAGgtatgcactc ... gtttatacagGTCCAGATGCAGTTCAGTTCATTGTTAACCATGCGACAGTACAAGCTATTT
EST: gi|29674287|gb|CB670562.1|CB670562
EST:     TGCCTGTGCGGCATATTCATATGTATCCGTGCCACTTTATGATACTCTAG                         GTCCAGATGCAGTTCAGTTCATTGTTAACCATGCGACAGTACAAGCTATTT
genomic: TGCCTGTGCGGCATATTCATATGTATCCGTGCCACTTTATGATACTCTAGgtatgcactc ... gtttatacagGTCCAGATGCAGTTCAGTTCATTGTTAACCATGCGACAGTACAAGCTATTT
EST: gi|58689916|gb|CK078603.1|CK078603
EST:     TGCCTGTGCGGCATA-TCATATGTATCCGTGCCACTTTATGATACTCTAG                         GTCCAGATGCAGTTCAGTTCATTGTTAACCATGCGACAGTACAAGCTATTT
genomic: TGCCTGTGCGGCATATTCATATGTATCCGTGCCACTTTATGATACTCTAGgtatgcactc ... gtttatacagGTCCAGATGCAGTTCAGTTCATTGTTAACCATGCGACAGTACAAGCTATTT
EST: gi|58658513|gb|CK047193.1|CK047193
EST:     TGCCTGTGCGGCATATTCATATGTATCCGTGCCACTTTATGATACTCTAG                         GTCCAGATGCAGTTCAGTTCATTGTTAACCATGCGACAGTACAAGCTA
genomic: TGCCTGTGCGGCATATTCATATGTATCCGTGCCACTTTATGATACTCTAGgtatgcactc ... gtttatacagGTCCAGATGCAGTTCAGTTCATTGTTAACCATGCGACAGTACAAGCTA
EST: gi|117224882|gb|CT845959.1|CT845959
EST:     TGCCTGTGCGGCATATTCATATGTATCCGTGCCACTTTATGATACTCTAG                         GTCCAGATGCAGTTCAGTTCATTGTTAACCATGCGACAGTACAAGCTATTT
genomic: TGCCTGTGCGGCATATTCATATGTATCCGTGCCACTTTATGATACTCTAGgtatgcactc ... gtttatacagGTCCAGATGCAGTTCAGTTCATTGTTAACCATGCGACAGTACAAGCTATTT

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: 41 (upstream exon), 73 (downstream exon)
Score: 20

CGCATTGGTTTGTATTTTATAAACAGACCTGAGTGGACCATAGTTGATCATGCCTGTGCGGCATATTCATATGTATCCGTGCCACTTTATGATACTCTAGgtatgcactc ... gtttatacagGTCCAGATGCAGTTCAGTTCATTGTTAACCATGCGACAGTACAAGCTATTTTCTGTGTGCCTCAAACACTAAGCACT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcatctatctccttttcatttatctagcaacaagttttatgtattgtttatacagGTCCAGATGCAGTTCAGTTCATTGTTAACCATGCGACAGTACAAGCTATTTTCTGTGTGCCTCAAACACTAAGCACT
                               aagttttatgtattgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgcactcatcacataatgatcatctatctccttttcatttatctagcaacaagttttatgtattgtttatacagGTCCAGATGCAGTTCAGTTCATTGTTAACCATGCGACAGTACAAGCTATTTTCTGTGTGCCTCAAACACTAAGCACT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT