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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactactacactacactacatctctctttctttctttttcagtttccttcccttctcaattagattaattaattaattaattaattacttgtgctactgcctgctaatgatggaaaacgcatagTGAAATCGGAAGTGGAACATGGGACTCTTGGTTAATGCCTCTTCAGAAACAG

Basic information

species Oryza sativa
transcript LOC_Os03g01150.1
intron # 2
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|88577066|gb|CI673617.1|CI673617
EST:     AAGTTCACCCGCCTTCTCGCCGACTGGTCCGCCTCCCATGGCTACTGCCT                         TGAAATCGGAAGTGGAACATGGGACTCTTGGTTAATGCCTCTTCAGAAACA
genomic: AAGTTCACCCGCCTTCTCGCCGACTGGTCCGCCTCCCATGGCTACTGCCTgtactactac ... aaacgcatagTGAAATCGGAAGTGGAACATGGGACTCTTGGTTAATGCCTCTTCAGAAACA
EST: gi|88432450|gb|CI567489.1|CI567489
EST:     AAGTTCACCCGCCTTCTCGCCGACTGGTCCGCCTCCCATGGCTACTGCCT                         TGAAATCGGAAGTGGAACATGGGACTCTTGGTTAATGCCTCTTCAGAAACA
genomic: AAGTTCACCCGCCTTCTCGCCGACTGGTCCGCCTCCCATGGCTACTGCCTgtactactac ... aaacgcatagTGAAATCGGAAGTGGAACATGGGACTCTTGGTTAATGCCTCTTCAGAAACA
EST: gi|29619262|gb|CB624274.1|CB624274
EST:     AAGTTCACCCGCCTTCTCGCCGACTGGTCCGCCTCCCATGGCTACTGCCT                         TGAAATCGGAAGTGGAACATGGGACTCTTGGTTAATGCCTCTTCAGAAACA
genomic: AAGTTCACCCGCCTTCTCGCCGACTGGTCCGCCTCCCATGGCTACTGCCTgtactactac ... aaacgcatagTGAAATCGGAAGTGGAACATGGGACTCTTGGTTAATGCCTCTTCAGAAACA
EST: gi|88340848|gb|CI637008.1|CI637008
EST:     AAGTTCACCCGCCTTCTCGCCGACTGGTCCGCCTCCCATGGCTACTGCCT                         TGAAATCGGAAGTGGAACATGGGACTCTTGGTTAATGCCTCTTCAGAAACA
genomic: AAGTTCACCCGCCTTCTCGCCGACTGGTCCGCCTCCCATGGCTACTGCCTgtactactac ... aaacgcatagTGAAATCGGAAGTGGAACATGGGACTCTTGGTTAATGCCTCTTCAGAAACA
EST: gi|66916126|gb|CX102974.1|CX102974
EST:     AAGTTCACCCGCCTTCTCGCCGACTGGTCCGCCTCCCATGGCTACTGCCT                         TGAAATCGGAAGTGGAACATGGGACTCTTGGTTAATGCCTCTTCAGAAACA
genomic: AAGTTCACCCGCCTTCTCGCCGACTGGTCCGCCTCCCATGGCTACTGCCTgtactactac ... aaacgcatagTGAAATCGGAAGTGGAACATGGGACTCTTGGTTAATGCCTCTTCAGAAACA
EST: gi|29661631|gb|CB657906.1|CB657906
EST:     AAGTTCACCCGCCTTCTCGCCGACTGGTCCGCCTCCCATGGCTACTGCCT                         TGAAATCGGAAGTGGAACATGGGACTCTTGGTTAATGCCTCTTCAGAAACA
genomic: AAGTTCACCCGCCTTCTCGCCGACTGGTCCGCCTCCCATGGCTACTGCCTgtactactac ... aaacgcatagTGAAATCGGAAGTGGAACATGGGACTCTTGGTTAATGCCTCTTCAGAAACA
EST: gi|11025710|gb|AU162311.1|AU162311
EST:     AAGTTCACCCGCCTTCTCGCCGACTGGTCCGCCTCCCATGGCTACTGCCT                         TGAAATCGGAAGTGGAACATGGGACTCTTGGTTAATGCCTCTTCAGAAACA
genomic: AAGTTCACCCGCCTTCTCGCCGACTGGTCCGCCTCCCATGGCTACTGCCTgtactactac ... aaacgcatagTGAAATCGGAAGTGGAACATGGGACTCTTGGTTAATGCCTCTTCAGAAACA
EST: gi|88324289|gb|CI566102.1|CI566102
EST:     AAGTTCACCCGCCTTCTCGCCGACTGGTCCGCCTCCCATGGGTACTGCCT                         TGAAATCGGAAGTGGAACATGGGACTCTTGGTTAATGCCTCTTCAGAAACA
genomic: AAGTTCACCCGCCTTCTCGCCGACTGGTCCGCCTCCCATGGCTACTGCCTgtactactac ... aaacgcatagTGAAATCGGAAGTGGAACATGGGACTCTTGGTTAATGCCTCTTCAGAAACA
EST: gi|88735407|gb|CI758915.1|CI758915
EST:     AAGTTCACCCGCCTTCTCGCCGACTGGTCCGCCTCCCATGGCTACTGCCT                         TGAAATCGGAAGTGGAACATGGGACTCTTGGTTAATGCCTCTTCAGAAACA
genomic: AAGTTCACCCGCCTTCTCGCCGACTGGTCCGCCTCCCATGGCTACTGCCTgtactactac ... aaacgcatagTGAAATCGGAAGTGGAACATGGGACTCTTGGTTAATGCCTCTTCAGAAACA
EST: gi|88447741|gb|CI579817.1|CI579817
EST:     AAGTTCACCCGCCTTCTCGCCGACTGGTCCGCCTCCCATGGGTACTGCCT                         TGAAATCGGAAGTGGAACATGGGACTCTTGGTTAATGCCTCTTCAGAAACA
genomic: AAGTTCACCCGCCTTCTCGCCGACTGGTCCGCCTCCCATGGCTACTGCCTgtactactac ... aaacgcatagTGAAATCGGAAGTGGAACATGGGACTCTTGGTTAATGCCTCTTCAGAAACA
EST: gi|58678057|gb|CK066744.1|CK066744
EST:     AAGTTCACCCGCCTTCTCGCCGACTGGTCCGCCTCCCATGGCTACTGCCT                         TGAAATCGGAAGTGGAACATGGGACTCTTGGTTAATGCCTCTTCAGAAACA
genomic: AAGTTCACCCGCCTTCTCGCCGACTGGTCCGCCTCCCATGGCTACTGCCTgtactactac ... aaacgcatagTGAAATCGGAAGTGGAACATGGGACTCTTGGTTAATGCCTCTTCAGAAACA
EST: gi|88389314|gb|CI598112.1|CI598112
EST:     AAGTTCACCCGCCTTCTCGCCGACTGGTCCGCCTCCCATGGCTACTGCCT                         TGAAATCGGAAGTGGAACATGGGACTCTTGGTTAATGCCTCTTCAGAAACA
genomic: AAGTTCACCCGCCTTCTCGCCGACTGGTCCGCCTCCCATGGCTACTGCCTgtactactac ... aaacgcatagTGAAATCGGAAGTGGAACATGGGACTCTTGGTTAATGCCTCTTCAGAAACA
EST: gi|25797306|gb|CA753267.1|CA753267
EST:     AAGTTCACCCGCCTTCTCGCCGACTGGTCCGCCTCCCATGGCTACTGCCT                         TGAAATCGGAAGTGGAACATGGGACTCTTGGTTAATGCCTCTTCAGAAACA
genomic: AAGTTCACCCGCCTTCTCGCCGACTGGTCCGCCTCCCATGGCTACTGCCTgtactactac ... aaacgcatagTGAAATCGGAAGTGGAACATGGGACTCTTGGTTAATGCCTCTTCAGAAACA
EST: gi|117235882|gb|CT847837.1|CT847837
EST:     AAGTTCACCCGCCTTCTCGCCGACTGGTCCGCCTCCCATGGCTACTGCCT                         TGAAATCGGAAGTGGAACATGGGACTCTTGGTTAATGCCTCTTCAGAAACA
genomic: AAGTTCACCCGCCTTCTCGCCGACTGGTCCGCCTCCCATGGCTACTGCCTgtactactac ... aaacgcatagTGAAATCGGAAGTGGAACATGGGACTCTTGGTTAATGCCTCTTCAGAAACA
EST: gi|88743128|gb|CI766636.1|CI766636
EST:     AAGTTCACCCGCCTTCTCGCCGACTGGTCCGCCTCCCATGGCTACTGCCT                         TGAAATCGGAAGTGGAACATGGGACTCTTGGTTAATGCCTCTTCAGAAACA
genomic: AAGTTCACCCGCCTTCTCGCCGACTGGTCCGCCTCCCATGGCTACTGCCTgtactactac ... aaacgcatagTGAAATCGGAAGTGGAACATGGGACTCTTGGTTAATGCCTCTTCAGAAACA

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), 52 (downstream exon)
Score: 11

GGATCGGAGACCAGTGCGCCAACCATGGTGTCGCCAAGTTCACCCGCCTTCTCGCCGACTGGTCCGCCTCCCATGGCTACTGCCTgtactactac ... aaacgcatagTGAAATCGGAAGTGGAACATGGGACTCTTGGTTAATGCCTCTTCAGAAACAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taattaattaattaattacttgtgctactgcctgctaatgatggaaaacgcatagTGAAATCGGAAGTGGAACATGGGACTCTTGGTTAATGCCTCTTCAGAAACAG
                                tgctaat  putative branch site (score: 11)
     aattaattaattactt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtactactacactacactacatctctctttctttctttttcagtttccttcccttctcaattagattaattaattaattaattaattacttgtgctactgcctgctaatgatggaaaacgcatagTGAAATCGGAAGTGGAACATGGGACTCTTGGTTAATGCCTCTTCAGAAACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA