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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgtgatgcattgttaaattctatgtgcatttcacatatggttttcttacccttttcatttcttttataacacattgttgctattttcatcagCCTCTTTCAGTTGAATTGGGACCTGGTATCCTTGGAAATATCTTTGATGGAATCCAG

Basic information

species Oryza sativa
transcript LOC_Os06g45120.1
intron # 3
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|58692180|gb|CK080867.1|CK080867
EST:     AGGAAACAGCTGGGTTGATGGTCAATGATCCAGTGTTGAGAACAAGAAAG                         CCTCTTTCAGTTGAATTGGGACCTGGTATCCTTGGAAATATCTTTGATGGA
genomic: AGGAAACAGCTGGGTTGATGGTCAATGATCCAGTGTTGAGAACAAGAAAGgtgtgatgca ... ttttcatcagCCTCTTTCAGTTGAATTGGGACCTGGTATCCTTGGAAATATCTTTGATGGA
EST: gi|58597715|gb|CK008243.1|CK008243
EST:     AGGAAACAGATGGGTTGATGGTCAATGATCCAGTGTTGAGAACAAGAAAG                         CCTCTTTCAGTTGACTTGGGACCTGGTATCCTTGGAAATATCTTTGATGGA
genomic: AGGAAACAGCTGGGTTGATGGTCAATGATCCAGTGTTGAGAACAAGAAAGgtgtgatgca ... ttttcatcagCCTCTTTCAGTTGAATTGGGACCTGGTATCCTTGGAAATATCTTTGATGGA
EST: gi|29656411|gb|CB652686.1|CB652686
EST:     AGGAAACAGCTGGGTTGATGGTCAATGATCCAGTGTTGAGAACAAGAAAG                         CCTCTTTCAGTTGAATTGGGACCTGGTATCCTTGGAAATATCTTTGATGGA
genomic: AGGAAACAGCTGGGTTGATGGTCAATGATCCAGTGTTGAGAACAAGAAAGgtgtgatgca ... ttttcatcagCCTCTTTCAGTTGAATTGGGACCTGGTATCCTTGGAAATATCTTTGATGGA
EST: gi|29620942|gb|CB625953.1|CB625953
EST:     AGGAAACAGCTGGGTTGATGGTCAATGATCCAGTGTTGAGAACAAGAAAG                         CCTCTTTCAGTTGAATTGGGACCTGGTATCCTTGGAAATATCTTTGATGGA
genomic: AGGAAACAGCTGGGTTGATGGTCAATGATCCAGTGTTGAGAACAAGAAAGgtgtgatgca ... ttttcatcagCCTCTTTCAGTTGAATTGGGACCTGGTATCCTTGGAAATATCTTTGATGGA
EST: gi|29634503|gb|CB639512.1|CB639512
EST:     AGGAAACAGCTGGGTTGATGGTCAATGATCCAGTGTTGAGAACAAGAAAG                         CCTCTTTCAGTTGAATTGGGACCTGGTATCCTTGGAAATATCTTTGATGGA
genomic: AGGAAACAGCTGGGTTGATGGTCAATGATCCAGTGTTGAGAACAAGAAAGgtgtgatgca ... ttttcatcagCCTCTTTCAGTTGAATTGGGACCTGGTATCCTTGGAAATATCTTTGATGGA
EST: gi|88256210|gb|CI358598.1|CI358598
EST:     GAAACAGCTGGGTTGATGGTCAATGATCCAGTGTTGAGAACAAGAAAG                         CCTCTTTCAGTTGAATTGGGACCTGGTATCCTTGGAAATATCTTTGATGGA
genomic: GAAACAGCTGGGTTGATGGTCAATGATCCAGTGTTGAGAACAAGAAAGgtgtgatgca ... ttttcatcagCCTCTTTCAGTTGAATTGGGACCTGGTATCCTTGGAAATATCTTTGATGGA

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: 75 (upstream exon), 75 (downstream exon)
Score: 123

TTTATGAGGAAACAGCTGGGTTGATGGTCAATGATCCAGTGTTGAGAACAAGAAAGgtgtgatgca ... ttttcatcagCCTCTTTCAGTTGAATTGGGACCTGGTATCCTTGGAAATATCTTTGATGGAATCCAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggttttcttacccttttcatttcttttataacacattgttgctattttcatcagCCTCTTTCAGTTGAATTGGGACCTGGTATCCTTGGAAATATCTTTGATGGAATCCAG
                          ttataac  putative branch site (score: 123)
                                          ctattttc  putative PPT
              ttttcatttcttttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgtgatgcattgttaaattctatgtgcatttcacatatggttttcttacccttttcatttcttttataacacattgttgctattttcatcagCCTCTTTCAGTTGAATTGGGACCTGGTATCCTTGGAAATATCTTTGATGGAATCCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA