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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtatttacttccatactgtacgtggtggtgctattattgggcaattttatttgtttaagtgctaacttctgtttttttccccaagTAGCCTGGACATGTGTGTGTCACTTGTTTCTATACACATGAAATGCTGATGTTCTTCTCGGGAGCAAGCTGGTATTTGAGTCAGCAACTCGGCATTAATC

Basic information

species Oryza sativa
transcript LOC_Os09g36530.2
intron # 10
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|88261828|gb|CI365404.1|CI365404
EST:     GAAACGCCGGTGACTAATTTCTCTTTTATCGCATAGGTGTAACACTCAC-                         T--CCTGGACATGTGTGTGTCACTTGTTTCTATACACATGAAATGCTGATG
genomic: GAAACGCCGGTGACTAATTTCTCTTTTATCGCATAGGTGTAACACTCACTgtaagtattt ... tttccccaagTAGCCTGGACATGTGTGTGTCACTTGTTTCTATACACATGAAATGCTGATG
EST: gi|88488903|gb|CI426174.1|CI426174
EST:     GAAACGCCGGTGACTAATTTCTCTTTTATCGCATAGGTGTAACACTCAC-                         T--CCTGGACATGTGTGTGTCACTTGTTTCTATACACATGAAATGCTGATG
genomic: GAAACGCCGGTGACTAATTTCTCTTTTATCGCATAGGTGTAACACTCACTgtaagtattt ... tttccccaagTAGCCTGGACATGTGTGTGTCACTTGTTTCTATACACATGAAATGCTGATG
EST: gi|88254612|gb|CI353436.1|CI353436
EST:     GAAACGCCGGTGACTAATTTCTCTTTTATCGCATAGGTGTAACACTCAC-                         T--CCTGGACATGTGTGTGTCACTTGTTTCTATACACATGAAATGCTGATG
genomic: GAAACGCCGGTGACTAATTTCTCTTTTATCGCATAGGTGTAACACTCACTgtaagtattt ... tttccccaagTAGCCTGGACATGTGTGTGTCACTTGTTTCTATACACATGAAATGCTGATG
EST: gi|88969421|gb|CI382959.1|CI382959
EST:     GAAACGCCGGTGACTAATTTCTCTTTTATCGCATAGGTGTAACACTCACT                         TAGCCTGGACATGTGTTTGTCACTTGTTTCTATACACATGAAATGCTGATG
genomic: GAAACGCCGGTGACTAATTTCTCTTTTATCGCATAGGTGTAACACTCACTgtaagtattt ... tttccccaagTAGCCTGGACATGTGTGTGTCACTTGTTTCTATACACATGAAATGCTGATG
EST: gi|88271762|gb|CI387815.1|CI387815
EST:     GAAACGCCGGTGACTAATTTCTCTTTTATCGCATAGGTGTAACACTCAC-                         T--CCTGGACATGTGTGTGTCACTTGTTTCTATACACATGAAATGCTGATG
genomic: GAAACGCCGGTGACTAATTTCTCTTTTATCGCATAGGTGTAACACTCACTgtaagtattt ... tttccccaagTAGCCTGGACATGTGTGTGTCACTTGTTTCTATACACATGAAATGCTGATG
EST: gi|88262507|gb|CI366281.1|CI366281
EST:     CCGGTGACTAATTTCTCTTTTATCGCATA-GTCTAACACTCGCT                         TAGCCTGGACATGTGTGTGTCACTTGTTTCTATACACATGAAATGCTGATG
genomic: CCGGTGACTAATTTCTCTTTTATCGCATAGGTGTAACACTCACTgtaagtattt ... tttccccaagTAGCCTGGACATGTGTGTGTCACTTGTTTCTATACACATGAAATGCTGATG
EST: gi|86437027|gb|CI118749.1|CI118749
EST:     GAAACGCCGGTGACTAATTTCTCTTTTATCGCATAGGTGTAACACTCACT                         TAGCCTGGACATGTGTGTGTCACTTGTTTCTATACACATGAAATGCTGATG
genomic: GAAACGCCGGTGACTAATTTCTCTTTTATCGCATAGGTGTAACACTCACTgtaagtattt ... tttccccaagTAGCCTGGACATGTGTGTGTCACTTGTTTCTATACACATGAAATGCTGATG

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: 52 (upstream exon), 24 (downstream exon)
Score: 1

CAAGAAGCAAATTGTGGTCACTTTCAGTGGGCCACTGTTAAGTCTAAAGAGAAACGCCGGTGACTAATTTCTCTTTTATCGCATAGGTGTAACACTCACTgtaagtattt ... tttccccaagTAGCCTGGACATGTGTGTGTCACTTGTTTCTATACACATGAAATGCTGATGTTCTTCTCGGGAGCAAGCTGGTATTTGAGTCAGCAACTCGGCATTAATC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctattattgggcaattttatttgtttaagtgctaacttctgtttttttccccaagTAGCCTGGACATGTGTGTGTCACTTGTTTCTATACACATGAAATGCTGATGTTCTTCTCGGGAGCAAGCTGGTATTTGAGTCAGCAACTCGGCATTAATC
                             tgctaac  putative branch site (score: 1)
                               ctaacttctgtttttt  CT-rich tract
            aattttatttgtttaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtatttacttccatactgtacgtggtggtgctattattgggcaattttatttgtttaagtgctaacttctgtttttttccccaagTAGCCTGGACATGTGTGTGTCACTTGTTTCTATACACATGAAATGCTGATGTTCTTCTCGGGAGCAAGCTGGTATTTGAGTCAGCAACTCGGCATTAATC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG