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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgccccttcagattcagatttgtgactttctctattttgattgtaattttaagatacacgtgcggtgtagtatagtacctgagatccctttttgcttgttagacctcactacaaaatagagatcctgaattctaattctgttaggtagATGGAAATTGCACGGCAACGGGAATTAGAAGGCCAAGGGAGTGAGAATGCAGGGAGTATATATAATGGGTTACTTCATAGATCAGAGGTTACACAAGAAG

Basic information

species Oryza sativa
transcript LOC_Os01g68010.4
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|88336570|gb|CI656841.1|CI656841
EST:     AGAAGAGATCACAGTACGCAGCCTTTAAAGAAGAATTCCTTAGCAACCCT                         ATGGAAATTGCACGGCAACGGGAATTAGAAGGCCA
genomic: AGAAGAGATCACAGTACGCAGCCTTTAAAGAAGAATTCCTTAGCAACCCTgtatgcccct ... tgttaggtagATGGAAATTGCACGGCAACGGGAATTAGAAGGCCA
EST: gi|88339196|gb|CI633767.1|CI633767
EST:     AGAAGAGATCACAGTACGCAGCCTTTAAAGAAGAATTCCTTAGCAACCCT                         ATGGAAATTGCACGGCAACGGGAATTAGAAGGCCAAGGGAGTGAGAATGGA
genomic: AGAAGAGATCACAGTACGCAGCCTTTAAAGAAGAATTCCTTAGCAACCCTgtatgcccct ... tgttaggtagATGGAAATTGCACGGCAACGGGAATTAGAAGGCCAAGGGAGTGAGAATGCA
EST: gi|88742952|gb|CI766460.1|CI766460
EST:     AGAAGAGATCACAGTACGCAGCCTTTAAAGAAGAATTCCTTAGCAACCCT                         G
genomic: AGAAGAGATCACAGTACGCAGCCTTTAAAGAAGAATTCCTTAGCAACCCTgtatgcccct ... tgttaggtag-
EST: gi|88742952|gb|CI766460.1|CI766460
EST:     AGAAGAGATCACAGTACGCAGCCTTTAAAGAAGAATTCCTTAGCAACCCT                         G
genomic: AGAAGAGATCACAGTACGCAGCCTTTAAAGAAGAATTCCTTAGCAACCCTgtatgcccct ... tgttaggtag-
EST: gi|88742952|gb|CI766460.1|CI766460
EST:     AGAAGAGATCACAGTACGCAGCCTTTAAAGAAGAATTCCTTAGCAACCCT                         G
genomic: AGAAGAGATCACAGTACGCAGCCTTTAAAGAAGAATTCCTTAGCAACCCTgtatgcccct ... tgttaggtag-
EST: gi|88370350|gb|CI587740.1|CI587740
EST:     AGAAGAGATCACAGTACGCAGCCTTTAAAGAAGAATTCCTTAGCAACCCT                         ATGGAAATTGCACGGCAACGGGAATTAGAAGGCCAAGGGAGTGAGAATGCA
genomic: AGAAGAGATCACAGTACGCAGCCTTTAAAGAAGAATTCCTTAGCAACCCTgtatgcccct ... tgttaggtagATGGAAATTGCACGGCAACGGGAATTAGAAGGCCAAGGGAGTGAGAATGCA
EST: gi|88341320|gb|CI640077.1|CI640077
EST:     AGAAGAGATCACAGTACGCAGCCTTTAAAGAAGAATTCCTTAGCAACCCT                         ATGGAAATTGCACGGCAACGGGAATTAGAAGGCCAAGGGAGTGAGAATGCA
genomic: AGAAGAGATCACAGTACGCAGCCTTTAAAGAAGAATTCCTTAGCAACCCTgtatgcccct ... tgttaggtagATGGAAATTGCACGGCAACGGGAATTAGAAGGCCAAGGGAGTGAGAATGCA
EST: gi|9866162|gb|AU101912.1|AU101912
EST:     AGAAGAGATCACAGTACGCAGCCTTTAAAGAAGAATTCCTTAGCAACCCT                         ATGGAAATTGCACGGCAACGGGAATTAGAAGGCCAAGGGAGTGAGAATGCA
genomic: AGAAGAGATCACAGTACGCAGCCTTTAAAGAAGAATTCCTTAGCAACCCTgtatgcccct ... tgttaggtagATGGAAATTGCACGGCAACGGGAATTAGAAGGCCAAGGGAGTGAGAATGCA
EST: gi|88364426|gb|CI644504.1|CI644504
EST:     AGAAGAGATCACAGTACGCAGCCTTTAAAGAAGAATTCCTTAGCAACCCT                         ATGGAAATTGCACGGCAACGGGAATTAGAAGGCCAAGGGAGTGAGAATGCA
genomic: AGAAGAGATCACAGTACGCAGCCTTTAAAGAAGAATTCCTTAGCAACCCTgtatgcccct ... tgttaggtagATGGAAATTGCACGGCAACGGGAATTAGAAGGCCAAGGGAGTGAGAATGCA
EST: gi|88737467|gb|CI759348.1|CI759348
EST:     AGAAGAGATCACAGTACGCAGCCTTTAAAGAAGAATTCCTTAGCAACCCT                         G
genomic: AGAAGAGATCACAGTACGCAGCCTTTAAAGAAGAATTCCTTAGCAACCCTgtatgcccct ... tgttaggtag-
EST: gi|88737467|gb|CI759348.1|CI759348
EST:     AGAAGAGATCACAGTACGCAGCCTTTAAAGAAGAATTCCTTAGCAACCCT                         G
genomic: AGAAGAGATCACAGTACGCAGCCTTTAAAGAAGAATTCCTTAGCAACCCTgtatgcccct ... tgttaggtag-
EST: gi|88737467|gb|CI759348.1|CI759348
EST:     AGAAGAGATCACAGTACGCAGCCTTTAAAGAAGAATTCCTTAGCAACCCT                         G
genomic: AGAAGAGATCACAGTACGCAGCCTTTAAAGAAGAATTCCTTAGCAACCCTgtatgcccct ... tgttaggtag-
EST: gi|58672453|gb|CK061139.1|CK061139
EST:     AGAAGAGATCACAGTACGCAGCCTTTAAAGAAGAATTCCTTAGCAACCCT                         ATGGAAATTGCACGGCAACGGGAATTAGAAGGCCAAGGGAGTGAGAATGCA
genomic: AGAAGAGATCACAGTACGCAGCCTTTAAAGAAGAATTCCTTAGCAACCCTgtatgcccct ... tgttaggtagATGGAAATTGCACGGCAACGGGAATTAGAAGGCCAAGGGAGTGAGAATGCA
EST: gi|58652950|gb|CK041630.1|CK041630
EST:     AGAAGAGATCACAGTACGCAGCCTTTAAAGAAGAATTCCTTAGCAACCCT                         ATGGAAATTGCACGGCAACGGGAATTAGAAGGCCAAGGGAGTGAGAATGCA
genomic: AGAAGAGATCACAGTACGCAGCCTTTAAAGAAGAATTCCTTAGCAACCCTgtatgcccct ... tgttaggtagATGGAAATTGCACGGCAACGGGAATTAGAAGGCCAAGGGAGTGAGAATGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcttgttagacctcactacaaaatagagatcctgaattctaattctgttaggtagATGGAAATTGCACGGCAACGGGAATTAGAAGGCCAAGGGAGTGAGAATGCAGGGAGTATATATAATGGGTTACTTCATAGATCAGAGGTTACACAAGAAG
                                    ttctaat  putative branch site (score: 2)
                                          ttctgtt  CT-rich tract
                                  aattctaatt  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
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---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgccccttcagattcagatttgtgactttctctattttgattgtaattttaagatacacgtgcggtgtagtatagtacctgagatccctttttgcttgttagacctcactacaaaatagagatcctgaattctaattctgttaggtagATGGAAATTGCACGGCAACGGGAATTAGAAGGCCAAGGGAGTGAGAATGCAGGGAGTATATATAATGGGTTACTTCATAGATCAGAGGTTACACAAGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG