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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tccttttttgtgtatgttagatggttagcgcatactgtgtgctattaaatgattctttgcaccatgagcgtggacactgaaattgaagtcttctctgcagCTTAAGTTCACTATGTCTGGAATGCCATCTGATGAGGCAACTGGTCAAGTGAGGCTCGAAGGAGATGTTTCTGACAAAAAGGAAGAAAAAACTCAAGAGC

Basic information

species Oryza sativa
transcript LOC_Os01g47490.2
intron # 1
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|88424671|gb|CI606470.1|CI606470
EST:     TCCCCGTTCCCGCGGATCCATCCGGGGCTCTGGGTTGATCTACCTCGCCG                         CTTAAGTTCACTATGTCTGGAATGCCATCTGATGAGGCAACTGGTCAAGTG
genomic: TCCCCGTTCCCGCGGATCCATCCGGGGCTCTGGGTTGATCTACCTCGCCGgtgacgtacc ... ttctctgcagCTTAAGTTCACTATGTCTGGAATGCCATCTGATGAGGCAACTGGTCAAGTG
EST: gi|33681993|gb|CF310232.1|CF310232
EST:     TCCCCGTTCCCGCGGATCCATCCGGGGCTCTGGGTTGATCTACCTCGCCG                         CTTAAGTTCACTATGTCTGGAATGCCATCTGATGAGGCAACTGGTCAAGTG
genomic: TCCCCGTTCCCGCGGATCCATCCGGGGCTCTGGGTTGATCTACCTCGCCGgtgacgtacc ... ttctctgcagCTTAAGTTCACTATGTCTGGAATGCCATCTGATGAGGCAACTGGTCAAGTG
EST: gi|66915652|gb|CX102500.1|CX102500
EST:     TCCCCGTTCCCGCGGATCCATCCGGGGCTCTGGGTTGATCTACCTCGCCG                         CTTAAGTTCACTATGTCTGGAATGCCATCTGATGAGGCAACTGGTCAAGTG
genomic: TCCCCGTTCCCGCGGATCCATCCGGGGCTCTGGGTTGATCTACCTCGCCGgtgacgtacc ... ttctctgcagCTTAAGTTCACTATGTCTGGAATGCCATCTGATGAGGCAACTGGTCAAGTG
EST: gi|286650|gb|D15457.1|D15457
EST:     TCCCCGTTCCCGCGGATCCATCCGGGGCTCTGGGTTGATCTACCTCGCCG                         CTTAAGTTCACTATGTCTGGAATGCCATCTGATGAGGCAACTGGTCAAGTG
genomic: TCCCCGTTCCCGCGGATCCATCCGGGGCTCTGGGTTGATCTACCTCGCCGgtgacgtacc ... ttctctgcagCTTAAGTTCACTATGTCTGGAATGCCATCTGATGAGGCAACTGGTCAAGTG
EST: gi|88744902|gb|CI768262.1|CI768262
EST:     TCCCCGTTCCCGCGGATCCATCCGGGGCTCTGGGTTGATCTACCTCGCCG                         CTTAAGTTCACTATGTCTGGAATGCCACCTGATGAGGCAACTGGTCAAGTG
genomic: TCCCCGTTCCCGCGGATCCATCCGGGGCTCTGGGTTGATCTACCTCGCCGgtgacgtacc ... ttctctgcagCTTAAGTTCACTATGTCTGGAATGCCATCTGATGAGGCAACTGGTCAAGTG
EST: gi|33693173|gb|CF321412.1|CF321412
EST:     TCCCCGTTCCCGCGGATCCATCCGGGGCTCTGGGTTGATCTACCTCGCCG                         CTTAAGTTCACTATGTCTGGAATGCCATCTGATGAGGCAACTGGTCAAGTG
genomic: TCCCCGTTCCCGCGGATCCATCCGGGGCTCTGGGTTGATCTACCTCGCCGgtgacgtacc ... ttctctgcagCTTAAGTTCACTATGTCTGGAATGCCATCTGATGAGGCAACTGGTCAAGTG
EST: gi|88585945|gb|CI703620.1|CI703620
EST:     TCCCCGTTCCCGCGGATCCATCCGGGGCTCTGGGTTGATCTACCTCGCCG                         CTTAAGTTCACTATGTCTGGAATGCCATCTGATGAGGCAACTGGTCAAGTG
genomic: TCCCCGTTCCCGCGGATCCATCCGGGGCTCTGGGTTGATCTACCTCGCCGgtgacgtacc ... ttctctgcagCTTAAGTTCACTATGTCTGGAATGCCATCTGATGAGGCAACTGGTCAAGTG
EST: gi|33683325|gb|CF311564.1|CF311564
EST:     TCCCCGTTCCCGCGGATCCATCCGGGGCTCTGGGTTGATCTACCTCGCCG                         CTTAAGTTCACTATGTCTGGAATGCCATCTGATGAGGCAACTGGTCAAGTT
genomic: TCCCCGTTCCCGCGGATCCATCCGGGGCTCTGGGTTGATCTACCTCGCCGgtgacgtacc ... ttctctgcagCTTAAGTTCACTATGTCTGGAATGCCATCTGATGAGGCAACTGGTCAAGTG
EST: gi|58688945|gb|CK077632.1|CK077632
EST:     TCCCCGTTCCCGCGGATCCATCCGGGGCTCTGGGTTGATCTACCTCGCCG                         CTTAAGTTCACTATGTCTGGAATGCCATCTGATGAGGCAACTGGTCAAGTG
genomic: TCCCCGTTCCCGCGGATCCATCCGGGGCTCTGGGTTGATCTACCTCGCCGgtgacgtacc ... ttctctgcagCTTAAGTTCACTATGTCTGGAATGCCATCTGATGAGGCAACTGGTCAAGTG
EST: gi|88410948|gb|CI581312.1|CI581312
EST:     TCCCCGTTCCCGCGGATCCATCCGGGGCTCTGGGTTGATCTACCTCGCCG                         CTTAAGTTCACTATGTCTGGAATGCCATCTGATGAGGCAACTGGTCAAGTG
genomic: TCCCCGTTCCCGCGGATCCATCCGGGGCTCTGGGTTGATCTACCTCGCCGgtgacgtacc ... ttctctgcagCTTAAGTTCACTATGTCTGGAATGCCATCTGATGAGGCAACTGGTCAAGTG
EST: gi|33691809|gb|CF320048.1|CF320048
EST:     TCCCCGTTCCCGCGGATCCATCCGGGGCTCTGGGTTGATCTACCTCGCCG                         CTTAAGTTCACTATGTCTGGAATGCCATCTGATGAGGCAACTGGTCAAGTG
genomic: TCCCCGTTCCCGCGGATCCATCCGGGGCTCTGGGTTGATCTACCTCGCCGgtgacgtacc ... ttctctgcagCTTAAGTTCACTATGTCTGGAATGCCATCTGATGAGGCAACTGGTCAAGTG
EST: gi|88335397|gb|CI650362.1|CI650362
EST:     TCCCCGTTCCCGCGGATCCATCCGGGGCTCTGGGTTGATCTACCTCGCCG                         CTTAAGTTCACTATGTCTGGAATGCCATCTGATGAGGCAACTGGTCAAGTG
genomic: TCCCCGTTCCCGCGGATCCATCCGGGGCTCTGGGTTGATCTACCTCGCCGgtgacgtacc ... ttctctgcagCTTAAGTTCACTATGTCTGGAATGCCATCTGATGAGGCAACTGGTCAAGTG
EST: gi|88736528|gb|CI760036.1|CI760036
EST:     TCCCCGTTCCCGCGGATCCATCCGGGGCTCTGGGTTGATCTACCTCGCCG                         CTTAAGTTCACTATGTCTGGAATGCCACCTGATGAGGCAACTGGTCAAGTG
genomic: TCCCCGTTCCCGCGGATCCATCCGGGGCTCTGGGTTGATCTACCTCGCCGgtgacgtacc ... ttctctgcagCTTAAGTTCACTATGTCTGGAATGCCATCTGATGAGGCAACTGGTCAAGTG

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), 73 (downstream exon)
Score: 17

TCCCTCCTTCCCACCCAAGGGGGAAAGCTCCGCCGCCATCGTCGTGCTGCTCCCCGTTCCCGCGGATCCATCCGGGGCTCTGGGTTGATCTACCTCGCCGgtgacgtacc ... ttctctgcagCTTAAGTTCACTATGTCTGGAATGCCATCTGATGAGGCAACTGGTCAAGTGAGGCTCGAAGGAGATGTTTCTGACAAAAAGGAAGAAAAAACTCAAGAGC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taaatgattctttgcaccatgagcgtggacactgaaattgaagtcttctctgcagCTTAAGTTCACTATGTCTGGAATGCCATCTGATGAGGCAACTGGTCAAGTGAGGCTCGAAGGAGATGTTTCTGACAAAAAGGAAGAAAAAACTCAAGAGC
                                           tcttctctgc  CT-rich tract
                                  aaattgaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tccttttttgtgtatgttagatggttagcgcatactgtgtgctattaaatgattctttgcaccatgagcgtggacactgaaattgaagtcttctctgcagCTTAAGTTCACTATGTCTGGAATGCCATCTGATGAGGCAACTGGTCAAGTGAGGCTCGAAGGAGATGTTTCTGACAAAAAGGAAGAAAAAACTCAAGAGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA