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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGCATCAGCAGAAGCAGAAAATAAACCATTACCTCCCCCTCGTTCTAGCAGTGATGTTCGTTCCCTAAGAATGAACGATTTCAAACATGCACATGAGCAGgtaatgttactgccacttctttcctttttcaggaaaagaaaatgaggaaaagggaaaaacaaaaagagactcaggctactacaagatctgatgtctcaaa...

Basic information

species Oryza sativa
transcript LOC_Os07g47530.1
intron # 27
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|27546551|gb|CA764668.2|CA764668
EST:     GTGATGTTCGTTCCCTAAGAATGAACGATTTCAAACATGCACATGAGCAG                         GTATGTGCAAGTATAACATCTGATTCGAGAAATATGACTGAGCTTATTCAG
genomic: GTGATGTTCGTTCCCTAAGAATGAACGATTTCAAACATGCACATGAGCAGgtaatgttac ... ttatgtatagGTATGTGCAAGTATAACATCTGATTCGAGAAATATGACTGAGCTTATTCAG
EST: gi|58599941|gb|CK010469.1|CK010469
EST:     GAACGATTTCAAACATGCACAGTGAGCAG                         GTATGTGCAAGTATAACATCTGATTCGAGAAATATGACTGAGCTTATTCA
genomic: GAACGATTTCAAACATGCACA-TGAGCAGgtaatgttac ... ttatgtatagGTATGTGCAAGTATAACATCTGATTCGAGAAATATGACTGAGCTTATTCA
EST: gi|86524067|gb|CI164273.1|CI164273
EST:     GTGATGTTCGTTCCCTAAGAATGAACGATTTCAAACATGCACATGAGCAG                         GTATGTGCAAGTATAACATCTGATTCGAGAAATATGACTGAGCTTATTCAG
genomic: GTGATGTTCGTTCCCTAAGAATGAACGATTTCAAACATGCACATGAGCAGgtaatgttac ... ttatgtatagGTATGTGCAAGTATAACATCTGATTCGAGAAATATGACTGAGCTTATTCAG
EST: gi|66914068|gb|CX100916.1|CX100916
EST:     GTGATGTTCGTTCCCTAAGAATGAACGATTTCAAACATGCACATGAGCAG                         GTATGTGCAAGTATAACATCTGATTCGAGAAATATGACTGAGCTTATTCAG
genomic: GTGATGTTCGTTCCCTAAGAATGAACGATTTCAAACATGCACATGAGCAGgtaatgttac ... ttatgtatagGTATGTGCAAGTATAACATCTGATTCGAGAAATATGACTGAGCTTATTCAG
EST: gi|29669557|gb|CB665832.1|CB665832
EST:     GTGATGTTCGTTCCCTAAGAATGAACGATTTCAAACATGCACATGAGCAG                         GTATGTGCAAGTATAACATCTGATTCGAGAAATATGACTGAGCTTATTCAG
genomic: GTGATGTTCGTTCCCTAAGAATGAACGATTTCAAACATGCACATGAGCAGgtaatgttac ... ttatgtatagGTATGTGCAAGTATAACATCTGATTCGAGAAATATGACTGAGCTTATTCAG
EST: gi|29632466|gb|CB637475.1|CB637475
EST:     GTGATGTTCGTTCCCTAAGAATGAACGATTTCAAACATGCACATGAGCAG                         GTATGTGCAAGTATAACATCTGATTCGAGAAATATGACTGAGCTTATTCAG
genomic: GTGATGTTCGTTCCCTAAGAATGAACGATTTCAAACATGCACATGAGCAGgtaatgttac ... ttatgtatagGTATGTGCAAGTATAACATCTGATTCGAGAAATATGACTGAGCTTATTCAG
EST: gi|58676924|gb|CK065611.1|CK065611
EST:     GTGATGTTCGTTCCCTAAGAATGAACGATTTCAAACATGCACATGAGCAG                         GTATGTGCAAGTATAACATCTGATTCGAGAAATATGACTGAGCTTATTCAG
genomic: GTGATGTTCGTTCCCTAAGAATGAACGATTTCAAACATGCACATGAGCAGgtaatgttac ... ttatgtatagGTATGTGCAAGTATAACATCTGATTCGAGAAATATGACTGAGCTTATTCAG
EST: gi|88842684|gb|CI081940.1|CI081940
EST:     GTGATGTTCGTTCCCTAAGAATGAACGATTTCAAAAATGCACATGAGCAG                         GTATGTGCAAGTATAAAATCTGATTCGAGAAATATGACTGAGCTTATTCAG
genomic: GTGATGTTCGTTCCCTAAGAATGAACGATTTCAAACATGCACATGAGCAGgtaatgttac ... ttatgtatagGTATGTGCAAGTATAACATCTGATTCGAGAAATATGACTGAGCTTATTCAG
EST: gi|89190959|gb|CI392812.1|CI392812
EST:     GTTATGTTCGTTCCCTAAGAATGAACGATTTCAAACATGCACATGAGCAG                         GTATGTGCAAGTATAACATCTGATTCGAGAAATATGACTGAGCTTATTCAG
genomic: GTGATGTTCGTTCCCTAAGAATGAACGATTTCAAACATGCACATGAGCAGgtaatgttac ... ttatgtatagGTATGTGCAAGTATAACATCTGATTCGAGAAATATGACTGAGCTTATTCAG
EST: gi|88219604|gb|CI219164.1|CI219164
EST:     TTTCAAACATGCACATGAGCAG                         GTATGTGCAAGTATAACATCTGATTCGAGAAATATGACTGAGCTTATTCAG
genomic: TTTCAAACATGCACATGAGCAGgtaatgttac ... ttatgtatagGTATGTGCAAGTATAACATCTGATTCGAGAAATATGACTGAGCTTATTCAG
EST: gi|29685522|gb|CB681797.1|CB681797
EST:     GTGATGTTCGTTCCCTAAGAATGAACGATTTCAAACATGCACATGAGCAG                         GTATGTGCAAGTATAACATCTGATTCGAGAAATATGACTGAGCTTATTCAG
genomic: GTGATGTTCGTTCCCTAAGAATGAACGATTTCAAACATGCACATGAGCAGgtaatgttac ... ttatgtatagGTATGTGCAAGTATAACATCTGATTCGAGAAATATGACTGAGCTTATTCAG
EST: gi|29632742|gb|CB637751.1|CB637751
EST:     GTGATGTTCGTTCCCTAAGAATGAACGATTTCAAACATGCACATGAGCAG                         GTATGTGCAAGTATAACATCTGATTCGAGAAATATGACTGAGCTTATTCAG
genomic: GTGATGTTCGTTCCCTAAGAATGAACGATTTCAAACATGCACATGAGCAGgtaatgttac ... ttatgtatagGTATGTGCAAGTATAACATCTGATTCGAGAAATATGACTGAGCTTATTCAG
EST: gi|86906255|gb|CI320186.1|CI320186
EST:     GTGATGTTCGTTCCCTAAGAATGAACGATTTCAAACATGCACATGAGCAG                         GTATGTGCAAGTATAACATCTGATTCGAGAAATATGACTGAGCTTATTCAG
genomic: GTGATGTTCGTTCCCTAAGAATGAACGATTTCAAACATGCACATGAGCAGgtaatgttac ... ttatgtatagGTATGTGCAAGTATAACATCTGATTCGAGAAATATGACTGAGCTTATTCAG
EST: gi|88960303|gb|CI382181.1|CI382181
EST:     GTGATGTTCGTTCCCTAAGAATGAACGATTTCAAACATGCACATGAGCAG                         GTATGTGCAAGTATAACATCTGATTCGAGAAATATGACTGAGCTTATTCAG
genomic: GTGATGTTCGTTCCCTAAGAATGAACGATTTCAAACATGCACATGAGCAGgtaatgttac ... ttatgtatagGTATGTGCAAGTATAACATCTGATTCGAGAAATATGACTGAGCTTATTCAG

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: 74 (upstream exon), 75 (downstream exon)
Score: 65

AGCATCAGCAGAAGCAGAAAATAAACCATTACCTCCCCCTCGTTCTAGCAGTGATGTTCGTTCCCTAAGAATGAACGATTTCAAACATGCACATGAGCAGgtaatgttac ... ttatgtatagGTATGTGCAAGTATAACATCTGATTCGAGAAATATGACTGAGCTTATTCAGTGGAACGATCTATATGGAGAAGGCGGGTCCAGGAAGAAGACTTCTCTAA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGCATCAGCAGAAGCAGAAAATAAACCATTACCTCCCCCTCGTTCTAGCAGTGATGTTCGTTCCCTAAGAATGAACGATTTCAAACATGCACATGAGCAGgtaatgttactgccacttctttcctttttcaggaaaagaaaatgaggaaaagggaaaaacaaaaagagactcaggctactacaagatctgatgtctcaaa

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aagaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaaaga