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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cagaaatttggtaacatactatttgattatatattttgatcttcacttattggtctagttaatggagacaatataatggaacatttaatttgatttgtagATATATTGGATATCATGGGCTGTGCTTGGTGGCCTTTTTGTCCTCTTACTG

Basic information

species Oryza sativa
transcript LOC_Os03g02756.1
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g02756.2 (Oryza sativa), 3'ss of exon 14
lower sequence: GRMZM2G453794_T01 (Zea mays), 3'ss of exon 13
cagaaatttggtaacatactatttgattatatattttgatcttcacttattggtctagttaatggagacaatataatggaacatttaatttgatttgtagATATATTGGATATCATGGGCTGTGCTTGGTGGCCTTTTTGTCCTCTTACTG
                   ||| | | | | |   ||    ||  ||| |||   ||| |  |    | ||||  |   ||    |  || |   || || | |||||||| || |||||||||||||||||||||||  ||||| |  ||
------------------gtatgttagtgtttcagttcccattttcttgttgacgtagatgttctgaataatagtagtaaattaatccttggccctgcagGTGTATTGGATTTCTTGGGCTGTGCTTGGTGGCCTTTTCATCCTCCTCTTG
















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|27921275|gb|CB097083.1|CB097083
EST:     ATGGAGTTGTTTACCATATGGATGCAAGCGAATCAAGTAAAGCACTATTG                         ATATATTGGATATCATGGGCTGTGCTTGGTGGCCTTTTTGTCCTCCTACTG
genomic: ATGGAGTTGTTTACCATATGGATGCAAGCGAATCAAGTAAAGCACTATTGgtatgttttc ... tgatttgtagATATATTGGATATCATGGGCTGTGCTTGGTGGCCTTTTTGTCCTCTTACTG
EST: gi|88331584|gb|CI675926.1|CI675926
EST:     ATGGAGTTGTTTACCATATGGATGCAAGCGAATCAAGTAAAGCACTATTG                         ATATATTGGATATCATGGGCTGTGCTTGGTGGCCTTTTTGTCCTCTTACTG
genomic: ATGGAGTTGTTTACCATATGGATGCAAGCGAATCAAGTAAAGCACTATTGgtatgttttc ... tgatttgtagATATATTGGATATCATGGGCTGTGCTTGGTGGCCTTTTTGTCCTCTTACTG
EST: gi|29670123|gb|CB666398.1|CB666398
EST:     GTTGTTTACCATATGGATGCAAGCGAATCAAGTAAAGCACTATTG                         ATATATTGGATATCATGGGCTGTGCTTGGTGGCCTTTTTGTCCTCTTACTG
genomic: GTTGTTTACCATATGGATGCAAGCGAATCAAGTAAAGCACTATTGgtatgttttc ... tgatttgtagATATATTGGATATCATGGGCTGTGCTTGGTGGCCTTTTTGTCCTCTTACTG
EST: gi|568436|gb|D39285.1|D39285
EST:     GTTGTTTACCATATGGATGCAAGCGAATCAAGTAAAGCACTATTG                         ATATATTGGATATCATGGGCTGTGCTTGGTGGCCTTTTTGTCCTCTTACTG
genomic: GTTGTTTACCATATGGATGCAAGCGAATCAAGTAAAGCACTATTGgtatgttttc ... tgatttgtagATATATTGGATATCATGGGCTGTGCTTGGTGGCCTTTTTGTCCTCTTACTG
EST: gi|29675247|gb|CB671522.1|CB671522
EST:     CATATGGATGCAAGCGAATCAAGTAAAGCACTATTG                         ATATATTGGATATCATGGGCTGTGCTTGGTGGCCTTTTTGTCCTCTTACTG
genomic: CATATGGATGCAAGCGAATCAAGTAAAGCACTATTGgtatgttttc ... tgatttgtagATATATTGGATATCATGGGCTGTGCTTGGTGGCCTTTTTGTCCTCTTACTG
EST: gi|29670124|gb|CB666399.1|CB666399
EST:     ATATGGATGCAAGCGAATCAAGTAAAGCACTATTG                         ATATATTGGATATCATGGGCTGTGCTTGGTGGCCTTTTTGTCCTCTTACTG
genomic: ATATGGATGCAAGCGAATCAAGTAAAGCACTATTGgtatgttttc ... tgatttgtagATATATTGGATATCATGGGCTGTGCTTGGTGGCCTTTTTGTCCTCTTACTG
EST: gi|29613903|gb|CB618916.1|CB618916
EST:     ATATGGATGCAAGCGAATCAAGTAAAGCACTATTG                         ATATATTGGATATCATGGGCTGTGCTTGGTGGCCTTTTTGTCCTCCTACTG
genomic: ATATGGATGCAAGCGAATCAAGTAAAGCACTATTGgtatgttttc ... tgatttgtagATATATTGGATATCATGGGCTGTGCTTGGTGGCCTTTTTGTCCTCTTACTG

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: 65 (upstream exon), 51 (downstream exon)
Score: 18

TGGGAGGATACTGGAAACTGTACTGAGTTTAAGATTTTTCATCTTCCAGTATGGAGTTGTTTACCATATGGATGCAAGCGAATCAAGTAAAGCACTATTGgtatgttttc ... tgatttgtagATATATTGGATATCATGGGCTGTGCTTGGTGGCCTTTTTGTCCTCTTACTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttattggtctagttaatggagacaatataatggaacatttaatttgatttgtagATATATTGGATATCATGGGCTGTGCTTGGTGGCCTTTTTGTCCTCTTACTG
                        aatataatggaacatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cagaaatttggtaacatactatttgattatatattttgatcttcacttattggtctagttaatggagacaatataatggaacatttaatttgatttgtagATATATTGGATATCATGGGCTGTGCTTGGTGGCCTTTTTGTCCTCTTACTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - aacatac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gagacaa