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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttagtcttcggtatatgatgcaagggatgttatacttgaactatttgggttaatgtcatcttacacctgctaatatcattgtaccccaaatgcaatgcagGCAGTACTACACATCTATTTTTGTGGGCAATCCACCCAGACCTTATTTTCTTGATGTTGATACTGGAAGCGATTTGACATGGATCCAGTGTGATGCACCA

Basic information

species Oryza sativa
transcript LOC_Os02g49800.1
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|29666292|gb|CB662567.1|CB662567
EST:     ACGAACTCGACGGCTCTGCTCCCGATCAAGGGGAATGTCTTCCCTGATGG                         GCAGTACTACACATCTATTTTTGTGGGCAATCCACCCAGACCTTATTTTCT
genomic: ACGAACTCGACGGCTCTGCTCCCGATCAAGGGGAATGTCTTCCCTGATGGgtgcgtataa ... tgcaatgcagGCAGTACTACACATCTATTTTTGTGGGCAATCCACCCAGACCTTATTTTCT
EST: gi|29658892|gb|CB655167.1|CB655167
EST:     ACGAACTCGACGGCTCTGCTCCCGATCAAGGGGAATGTCTTCCCTGATGG                         GCAGTACTACACATCTATTTTTGTGGGCAATCCACCCAGACCTTATTTTCT
genomic: ACGAACTCGACGGCTCTGCTCCCGATCAAGGGGAATGTCTTCCCTGATGGgtgcgtataa ... tgcaatgcagGCAGTACTACACATCTATTTTTGTGGGCAATCCACCCAGACCTTATTTTCT
EST: gi|29666293|gb|CB662568.1|CB662568
EST:     ACGAACTCGACGGCTCTGCTCCCGATCAAGGGGAATGTCTTCCCTGATGG                         GCAGTACTACACATCTATTTTTGTGGGCAATCCACCCAGACCTTATTTTCT
genomic: ACGAACTCGACGGCTCTGCTCCCGATCAAGGGGAATGTCTTCCCTGATGGgtgcgtataa ... tgcaatgcagGCAGTACTACACATCTATTTTTGTGGGCAATCCACCCAGACCTTATTTTCT
EST: gi|29633918|gb|CB638927.1|CB638927
EST:     ACGAACTCGACGGCTCTGCTCCCGATCAAGGGGAATGTCTTCCCTGATGG                         GCAGTACTACACATCTATTTTTGTGGGCAATCCACCCAGACCTTATTTTCT
genomic: ACGAACTCGACGGCTCTGCTCCCGATCAAGGGGAATGTCTTCCCTGATGGgtgcgtataa ... tgcaatgcagGCAGTACTACACATCTATTTTTGTGGGCAATCCACCCAGACCTTATTTTCT
EST: gi|29642625|gb|CB647632.1|CB647632
EST:     ACGAACTCGACGGCTCTGCTCCCGATCAAGGGGAATGTCTTCCCTGATGG                         GCAGTACTACACATCTATTTTTGTGGGCAATCCACCCAGACCTTATTTTCT
genomic: ACGAACTCGACGGCTCTGCTCCCGATCAAGGGGAATGTCTTCCCTGATGGgtgcgtataa ... tgcaatgcagGCAGTACTACACATCTATTTTTGTGGGCAATCCACCCAGACCTTATTTTCT
EST: gi|86903772|gb|CI302418.1|CI302418
EST:     ACGAACTCGACGGCTCTGCTCCCGATCAAGGGGAATGTCTTCCCTGATGG                         GCAGTACTACACATCTATTTTTGTGGGCAATCCACCCAGACCTTATTTTCT
genomic: ACGAACTCGACGGCTCTGCTCCCGATCAAGGGGAATGTCTTCCCTGATGGgtgcgtataa ... tgcaatgcagGCAGTACTACACATCTATTTTTGTGGGCAATCCACCCAGACCTTATTTTCT
EST: gi|29664921|gb|CB661196.1|CB661196
EST:     ACGAACTCGACGGCTCTGCTCCCGATCAAGGGGAATGTCTTCCCTGATGG                         GCAGTACTACACATCTATTTTTGTGGGCAATCCACCCAGACCTTATTTTCT
genomic: ACGAACTCGACGGCTCTGCTCCCGATCAAGGGGAATGTCTTCCCTGATGGgtgcgtataa ... tgcaatgcagGCAGTACTACACATCTATTTTTGTGGGCAATCCACCCAGACCTTATTTTCT

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: 72 (upstream exon), 72 (downstream exon)
Score: 101

GCAGGAAATCTAGGAACAAATTGGAGGTCAAGAAGGCAGCTGCGGCGGGGACGAACTCGACGGCTCTGCTCCCGATCAAGGGGAATGTCTTCCCTGATGGgtgcgtataa ... tgcaatgcagGCAGTACTACACATCTATTTTTGTGGGCAATCCACCCAGACCTTATTTTCTTGATGTTGATACTGGAAGCGATTTGACATGGATCCAGTGTGATGCACCA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgggttaatgtcatcttacacctgctaatatcattgtaccccaaatgcaatgcagGCAGTACTACACATCTATTTTTGTGGGCAATCCACCCAGACCTTATTTTCTTGATGTTGATACTGGAAGCGATTTGACATGGATCCAGTGTGATGCACCA
                      tgctaat  putative branch site (score: 101)
                         taatatcatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttagtcttcggtatatgatgcaagggatgttatacttgaactatttgggttaatgtcatcttacacctgctaatatcattgtaccccaaatgcaatgcagGCAGTACTACACATCTATTTTTGTGGGCAATCCACCCAGACCTTATTTTCTTGATGTTGATACTGGAAGCGATTTGACATGGATCCAGTGTGATGCACCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA
- - - - - - - -tgatgca
- - - - - - - - - - - - - - - -atacttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cctgcta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgtaccc