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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAAAAACTCCACCAGTGGATATTGAGAAAGCATGAGGAAGAGTCGAGGCTCACGGCGGCTGATATAATGTCTCATATCCAGgttcaaccttgaatttccttaccttatggttctgccttgttttctattaataacttgagtatgaactagcttagaaatgcagattgtatcatccatctca...

Basic information

species Oryza sativa
transcript LOC_Os01g40690.1
intron # 2
splice site 5'
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|568850|gb|D39699.1|D39699
EST:     ATGAGGAAGAGTCGAGGCTCACGGCGGCTGATATAATGTCTCATATCCAG                         CATGAGTTGGATTATGGAGGTAATGATCCACATGTTTCCCCCAGAGTACAT
genomic: ATGAGGAAGAGTCGAGGCTCACGGCGGCTGATATAATGTCTCATATCCAGgttcaacctt ... tctttgacagCATGAGTTGGATTATGGAGGTAATGATCCACATGTTTCCCCCAGAGTACAT
EST: gi|88421754|gb|CI621398.1|CI621398
EST:     ACGAGGAAGAGTCGAGGCTCACGGGGGCTGATATAATGTCTCATATCCAG                         CATGAGTTGGATTATGGAGGTAATGATCCACATGTTTCCCCCAGAGTACAT
genomic: ATGAGGAAGAGTCGAGGCTCACGGCGGCTGATATAATGTCTCATATCCAGgttcaacctt ... tctttgacagCATGAGTTGGATTATGGAGGTAATGATCCACATGTTTCCCCCAGAGTACAT
EST: gi|32948314|gb|BP184886.1|BP184886
EST:     ATGAGGAAGAGTCGAGGCTCACGGCGGCTGATATAATGTCTCATATCCAG                         CATGAGTTGGATTATGGAGGTAATGATCCACATGTTTCCCCCAGAGTACAT
genomic: ATGAGGAAGAGTCGAGGCTCACGGCGGCTGATATAATGTCTCATATCCAGgttcaacctt ... tctttgacagCATGAGTTGGATTATGGAGGTAATGATCCACATGTTTCCCCCAGAGTACAT
EST: gi|8860125|gb|AU097443.1|AU097443
EST:     CGAGGCTCACGGCGGCTGATATAATGTCTCATATCCAG                         CATGAGTTGGATTATGGGAGNTAATGATCCACATGTTTCCCCCAGAGTACA
genomic: CGAGGCTCACGGCGGCTGATATAATGTCTCATATCCAGgttcaacctt ... tctttgacagCATGAGTTGGATTAT-GGAGGTAATGATCCACATGTTTCCCCCAGAGTACA
EST: gi|218495366|gb|FG958231.1|FG958231
EST:     ATGAGGAAGAGTCGAGGCTCACGGCGGCTGATATAATGTCTCATATCCAG                         CATGAGTTGGATTATGGAGGTAATGATCCACATGTTTCCCCCAGAGTACAT
genomic: ATGAGGAAGAGTCGAGGCTCACGGCGGCTGATATAATGTCTCATATCCAGgttcaacctt ... tctttgacagCATGAGTTGGATTATGGAGGTAATGATCCACATGTTTCCCCCAGAGTACAT
EST: gi|8858461|gb|AU095779.1|AU095779
EST:     GGCTCACGGCGNCTGATATAATGTCTCATATCCAG                         CATGGAGTTGGATTATGGAGGTAATGATCCCACATGTTTCCCCCAGAGTAC
genomic: GGCTCACGGCGGCTGATATAATGTCTCATATCCAGgttcaacctt ... tctttgacagCAT-GAGTTGGATTATGGAGGTAATGAT-CCACATGTTTCCCCCAGAGTAC
EST: gi|8858452|gb|AU095770.1|AU095770
EST:     GCTCACGGCGGCTGATATAATGTCTCATATCCAG                         CATGAGTTGGATTATGGAGGTAATGATCCACATGTTTCCCCCAGAGTACAT
genomic: GCTCACGGCGGCTGATATAATGTCTCATATCCAGgttcaacctt ... tctttgacagCATGAGTTGGATTATGGAGGTAATGATCCACATGTTTCCCCCAGAGTACAT
EST: gi|218496837|gb|FG946813.1|FG946813
EST:     ATGAGGAAGAGTCGAGGCTCACGGCGGCTGATATAATGTCTCATATCCAG                         CATGAGTTGGATTATGGAGGTAATGATCCACATGTTTCCCCCAGAGTACAT
genomic: ATGAGGAAGAGTCGAGGCTCACGGCGGCTGATATAATGTCTCATATCCAGgttcaacctt ... tctttgacagCATGAGTTGGATTATGGAGGTAATGATCCACATGTTTCCCCCAGAGTACAT
EST: gi|218492762|gb|FG946015.1|FG946015
EST:     CTGATATAATGTCTCATATCCAG                         CATGAGTTGGATTATGGAGGTAATGATCCACATGTTTCCCCCAGAGTACAT
genomic: CTGATATAATGTCTCATATCCAGgttcaacctt ... tctttgacagCATGAGTTGGATTATGGAGGTAATGATCCACATGTTTCCCCCAGAGTACAT

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: 61 (upstream exon), 40 (downstream exon)
Score: 17

GAAAAACTCCACCAGTGGATATTGAGAAAGCATGAGGAAGAGTCGAGGCTCACGGCGGCTGATATAATGTCTCATATCCAGgttcaacctt ... tctttgacagCATGAGTTGGATTATGGAGGTAATGATCCACATGTTTCCCCCAGAGTACATCAGCATAGTGCAAATCCGTTTGCAAACTCAAGCATCCAACCCTCAGCTG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAAAAACTCCACCAGTGGATATTGAGAAAGCATGAGGAAGAGTCGAGGCTCACGGCGGCTGATATAATGTCTCATATCCAGgttcaaccttgaatttccttaccttatggttctgccttgttttctattaataacttgagtatgaactagcttagaaatgcagattgtatcatccatctca

- - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT