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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattgccacatatgtattctgtacaactgatgcactctttaacatattgcgagacaccttgtacagtaatacccaaagatgtcttacagagtctaatgatttacccattattcttcagttaacttactgctaacaccaatttgtatacaaaagttgtctgaacatgtttctccgttccagCCTCCAAAGTTCGAATTTTATGATCCAAAAACTCCTTTCTTCACCTCACCTCGATACTTACCTCCAGCAAGATTGGAGAAGTGCAAG

Basic information

species Oryza sativa
transcript LOC_Os01g44220.6
intron # 11
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|116875182|gb|EC365690.1|EC365690
EST:     TTGGAACAATCAAATCATTTTTTGACGCTAACTTGGCCCTCACCGAGCAG                         CCTCCAAAGTTCGAATTTTATGATCCAAAAACTCCTTTCTTCACCTCACCT
genomic: TTGGAACAATCAAATCATTTTTTGATGCTAACTTGGCCCTCACCGAGCAGgtattgccac ... tccgttccagCCTCCAAAGTTCGAATTTTATGATCCAAAAACTCCTTTCTTCACCTCACCT
EST: gi|2797455|gb|AA750749.1|AA750749
EST:     TTGGAACAATCAAATCATTTTTTGACGCTAACTTGGCCCTCACCGAGCAG                         CCTCCAAAGTTCGAATTTAATGATCCCAAAACTCCTTTCTTCACCTCA
genomic: TTGGAACAATCAAATCATTTTTTGATGCTAACTTGGCCCTCACCGAGCAGgtattgccac ... tccgttccagCCTCCAAAGTTCGAATTTTATGATCCAAAAACTCCTTTCTTCACCTCA
EST: gi|29680979|gb|CB677254.1|CB677254
EST:     TTGGAACAATCAAATCATTTTTTGATGCTAACTTGGCCCTCACCGAGCAG                         CCTCCAAAGTTCGAATTTTATGATCCAAAAACTCCTTTCTTCACCTCACCT
genomic: TTGGAACAATCAAATCATTTTTTGATGCTAACTTGGCCCTCACCGAGCAGgtattgccac ... tccgttccagCCTCCAAAGTTCGAATTTTATGATCCAAAAACTCCTTTCTTCACCTCACCT
EST: gi|116875001|gb|EC365509.1|EC365509
EST:     TTGGAACAATCAAATCATTTTTTGACGCTAACTTGGCCCTCACCGAGCAG                         CCTCCAAAGTTCGAATTTTATGATCCAAAAACTCCTTTCTTCACCTCACCT
genomic: TTGGAACAATCAAATCATTTTTTGATGCTAACTTGGCCCTCACCGAGCAGgtattgccac ... tccgttccagCCTCCAAAGTTCGAATTTTATGATCCAAAAACTCCTTTCTTCACCTCACCT
EST: gi|66915625|gb|CX102473.1|CX102473
EST:     TTGGAACAATCAAATCATTTTTTGACGCTAACTTGGCCCTCAACGAGCAG                         CCTCCAAAGTTCGAATTTTATGATCCAAAAACTCCTTTCTTCACCTCACCT
genomic: TTGGAACAATCAAATCATTTTTTGATGCTAACTTGGCCCTCACCGAGCAGgtattgccac ... tccgttccagCCTCCAAAGTTCGAATTTTATGATCCAAAAACTCCTTTCTTCACCTCACCT
EST: gi|29668852|gb|CB665127.1|CB665127
EST:     TTGGAACAATCAAATCATTTTTTGATGCTAACTTGGCCCTCACCGAGCAG                         CCTCCAAAGTTCGAATTTTATGATCCAAAAACTCCTTTCTTCACCTCACCT
genomic: TTGGAACAATCAAATCATTTTTTGATGCTAACTTGGCCCTCACCGAGCAGgtattgccac ... tccgttccagCCTCCAAAGTTCGAATTTTATGATCCAAAAACTCCTTTCTTCACCTCACCT
EST: gi|116875027|gb|EC365535.1|EC365535
EST:     TTGGAACAATCAAATCATTTTTTGACGCTAACTTGGCCCTCACCGAGCAG                         CCTCCAAAGTTCGAATTTTATGATCCAAAAACTCCCTTCTTCACCTCACCT
genomic: TTGGAACAATCAAATCATTTTTTGATGCTAACTTGGCCCTCACCGAGCAGgtattgccac ... tccgttccagCCTCCAAAGTTCGAATTTTATGATCCAAAAACTCCTTTCTTCACCTCACCT
EST: gi|1631864|gb|C19593.1|C19593
EST:     TTGGAACAATCAAATCATTTTTTGATGCTAACTTGGCCCTCACCGAGCAG                         CCTCCAAAGTTCGAATTTTATGATCCAAAAACTCCTTTCTT-ACCTCAACC
genomic: TTGGAACAATCAAATCATTTTTTGATGCTAACTTGGCCCTCACCGAGCAGgtattgccac ... tccgttccagCCTCCAAAGTTCGAATTTTATGATCCAAAAACTCCTTTCTTCACCTCA-CC
EST: gi|88693552|gb|CI737127.1|CI737127
EST:     ACTTGGCCCTCACCGAGCAG                         CCTCCAAAGTTCGAATTTTATGATCCAAAAACTCCTTTCTTCACCTCACCT
genomic: ACTTGGCCCTCACCGAGCAGgtattgccac ... tccgttccagCCTCCAAAGTTCGAATTTTATGATCCAAAAACTCCTTTCTTCACCTCACCT

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: 619

GCATGTGTCTTCACAGAATATTGGGAGGATATTGGAACAATCAAATCATTTTTTGATGCTAACTTGGCCCTCACCGAGCAGgtattgccac ... tccgttccagCCTCCAAAGTTCGAATTTTATGATCCAAAAACTCCTTTCTTCACCTCACCTCGATACTTACCTCCAGCAAGATTGGAGAAGTGCAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

actgctaacaccaatttgtatacaaaagttgtctgaacatgtttctccgttccagCCTCCAAAGTTCGAATTTTATGATCCAAAAACTCCTTTCTTCACCTCACCTCGATACTTACCTCCAGCAAGATTGGAGAAGTGCAAG
  tgctaac  putative branch site (score: 619)
                                       tgtttctccgttcc  putative PPT
            aatttgtatacaaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtattgccacatatgtattctgtacaactgatgcactctttaacatattgcgagacaccttgtacagtaatacccaaagatgtcttacagagtctaatgatttacccattattcttcagttaacttactgctaacaccaatttgtatacaaaagttgtctgaacatgtttctccgttccagCCTCCAAAGTTCGAATTTTATGATCCAAAAACTCCTTTCTTCACCTCACCTCGATACTTACCTCCAGCAAGATTGGAGAAGTGCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT