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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtgtacactgtggtaagcttttcatccaatgataacctgttccccgttagaaaactgtattctatactggtcattgttctctttaatgtcctttctctgtattagtacctggttcaggggagaatattattaattttgctaactttatttgccagGAAAATAGTCTAAATAGACCAGTGTGGTTATGATGCTTGTATCTGTAATAAATGTATCACTTGAAGAGGAAGGAGAGAAACCTCTTACTGGCTCATCTCA

Basic information

species Oryza sativa
transcript LOC_Os01g61320.1
intron # 4
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|88478049|gb|CI415320.1|CI415320
EST:     CAGTGCCTTAATTCTCAACTCTTG                         GAAAATAGTCTAAATAGACCAGTGTGGTTATGATGCTTGTATCTGTAATAA
genomic: CAGTGCCTTAATTCTCAACTCTTGgtgagtgtac ... tatttgccagGAAAATAGTCTAAATAGACCAGTGTGGTTATGATGCTTGTATCTGTAATAA
EST: gi|88226856|gb|CI224841.1|CI224841
EST:     TGCATTTCAGCGCTTATGTATTGAGACAGTGCCTTAATTCTCAACTCTTG                         GAAAATAGTCTAAATAGACCAGTGTGGTTATGATGCTTGTATCTGTAATAA
genomic: TGCATTTCAGCGCTTATGTATTGAGACAGTGCCTTAATTCTCAACTCTTGgtgagtgtac ... tatttgccagGAAAATAGTCTAAATAGACCAGTGTGGTTATGATGCTTGTATCTGTAATAA
EST: gi|88848205|gb|CI086727.1|CI086727
EST:     TGCATTTCAGCGCTTATGTATTGAGACAGTGCCTTAATTCTCAACTCTTG                         GAAAATAGTCTAAATAGACCAGTGTGGTTATGATGCTTGTATCTGTAATAA
genomic: TGCATTTCAGCGCTTATGTATTGAGACAGTGCCTTAATTCTCAACTCTTGgtgagtgtac ... tatttgccagGAAAATAGTCTAAATAGACCAGTGTGGTTATGATGCTTGTATCTGTAATAA
EST: gi|86522908|gb|CI163114.1|CI163114
EST:     TGCATTTCAGCGCTTATGTATTGAGACAGTGCCTTAATTCTCAACTCTTG                         GAAAATAGTCTAAATAGACCAGTGTGGTTATGATGCTTGTATCTGTAATAA
genomic: TGCATTTCAGCGCTTATGTATTGAGACAGTGCCTTAATTCTCAACTCTTGgtgagtgtac ... tatttgccagGAAAATAGTCTAAATAGACCAGTGTGGTTATGATGCTTGTATCTGTAATAA
EST: gi|8528092|gb|AU092907.1|AU092907
EST:     TGCATTTCAGCGCTTATGTATTGAGACAGTGCCTTAATTCTCAACTCTTG                         GAAAATNGTCTAAATAGACCAGTGTGGTTATGATGCTTGTATCTGTAATAA
genomic: TGCATTTCAGCGCTTATGTATTGAGACAGTGCCTTAATTCTCAACTCTTGgtgagtgtac ... tatttgccagGAAAATAGTCTAAATAGACCAGTGTGGTTATGATGCTTGTATCTGTAATAA
EST: gi|88993399|gb|CI257827.1|CI257827
EST:     TGCATTTCAGCGCTTATGTATTGAGACAGTGCCTTAATTCTCAACTCTTG                         GAAAATAGTCTAAATAGACCAGTGTGGTTATGATGCTTGTATCTGTAATAA
genomic: TGCATTTCAGCGCTTATGTATTGAGACAGTGCCTTAATTCTCAACTCTTGgtgagtgtac ... tatttgccagGAAAATAGTCTAAATAGACCAGTGTGGTTATGATGCTTGTATCTGTAATAA

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: 45 (upstream exon), 54 (downstream exon)
Score: 6

AGACCATCTTGTGTTAATCCTGAAGCTATTGCACCTCCGTGCTAATCTCCTGCATTTCAGCGCTTATGTATTGAGACAGTGCCTTAATTCTCAACTCTTGgtgagtgtac ... tatttgccagGAAAATAGTCTAAATAGACCAGTGTGGTTATGATGCTTGTATCTGTAATAAATGTATCACTTGAAGAGGAAGGAGAGAAACCTCTTACTGGCTCATCTCA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attagtacctggttcaggggagaatattattaattttgctaactttatttgccagGAAAATAGTCTAAATAGACCAGTGTGGTTATGATGCTTGTATCTGTAATAAATGTATCACTTGAAGAGGAAGGAGAGAAACCTCTTACTGGCTCATCTCA
                                    tgctaac  putative branch site (score: 6)
                                          ctttattt  CT-rich tract
                    agaatattattaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtgtacactgtggtaagcttttcatccaatgataacctgttccccgttagaaaactgtattctatactggtcattgttctctttaatgtcctttctctgtattagtacctggttcaggggagaatattattaattttgctaactttatttgccagGAAAATAGTCTAAATAGACCAGTGTGGTTATGATGCTTGTATCTGTAATAAATGTATCACTTGAAGAGGAAGGAGAGAAACCTCTTACTGGCTCATCTCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA