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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaacttctcctctcatggcctctgcttcttgctctgttttttttttctttcttggctgatgtctctggttgaatcgtgcagCGCCGCGCGCGAAGAGGGAGCGGAAGAACCAGTACCGCGGGATCAGGCAGCGGCCGTGGGGGAAGTGGGCGGCGGAGATCCGCGACCCGGTGAAGGGGGT

Basic information

species Oryza sativa
transcript LOC_Os01g21120.1
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|3759821|gb|C97079.1|C97079
EST:     CTGGCCCGACGCCGACGACTCCGACCCCCACACCCCCGCTCCCGAGAAAC                         CGCCGCGCGCGAAGAGGGAGCGGAAGAACCAGTACCGCGGGATCAGGCAGC
genomic: CTGGCCCGACGCCGACGACTCCGACCCCCACACCCCCGCTCCCGAGAAACgtaacttctc ... aatcgtgcagCGCCGCGCGCGAAGAGGGAGCGGAAGAACCAGTACCGCGGGATCAGGCAGC
EST: gi|88334842|gb|CI647224.1|CI647224
EST:     CTGGCCCGACGCCGACGACTCCGACCCCCACACCCCCGCTCCCGAGAAAC                         CGCCGGGCGCGAAGAGGGAGCGGAAGAAC-AGTACCGCGGGATCAGGCAGC
genomic: CTGGCCCGACGCCGACGACTCCGACCCCCACACCCCCGCTCCCGAGAAACgtaacttctc ... aatcgtgcagCGCCGCGCGCGAAGAGGGAGCGGAAGAACCAGTACCGCGGGATCAGGCAGC
EST: gi|88578023|gb|CI674649.1|CI674649
EST:     CTGGCCCGACGCCGACGACTCCGACCCCCACACCCCCGCTCCCGAGAAAC                         CGCCGCGCGCGAAGAGGGAGCGGAAGAACCAGTACCGCGGGATCAGGCA
genomic: CTGGCCCGACGCCGACGACTCCGACCCCCACACCCCCGCTCCCGAGAAACgtaacttctc ... aatcgtgcagCGCCGCGCGCGAAGAGGGAGCGGAAGAACCAGTACCGCGGGATCAGGCA
EST: gi|287181|gb|D15986.1|D15986
EST:     CTGGCCCGACGNCGACGACTCCGACCCCCACANCCNCGCTCCCGAGAAAC                         CGCCGCGCGCGAAGAGGGAGCGGAAGAACCAGTACCGCGGGATCAGGCAGC
genomic: CTGGCCCGACGCCGACGACTCCGACCCCCACACCCCCGCTCCCGAGAAACgtaacttctc ... aatcgtgcagCGCCGCGCGCGAAGAGGGAGCGGAAGAACCAGTACCGCGGGATCAGGCAGC
EST: gi|88340471|gb|CI659677.1|CI659677
EST:     CTGGCCCGACGCCGACGACTCCGACCCCCACACCCCCGCTCCCGANAAAC                         CGCCGNGCGCGAAGAGGGAGCGGAAAAACCAGTACCGCGGGATCAGGCAGN
genomic: CTGGCCCGACGCCGACGACTCCGACCCCCACACCCCCGCTCCCGAGAAACgtaacttctc ... aatcgtgcagCGCCGCGCGCGAAGAGGGAGCGGAAGAACCAGTACCGCGGGATCAGGCAGC
EST: gi|7219927|gb|AU065506.2|AU065506
EST:     CTGGCCCGACGCCGACGACTCCGACCCCCACACCCCCGCTCCCGAGAAAC                         CGCCGCGCGCGAAGAGGGAGCGGAAGAACCAGTACCGCGGGATCAGGCAGC
genomic: CTGGCCCGACGCCGACGACTCCGACCCCCACACCCCCGCTCCCGAGAAACgtaacttctc ... aatcgtgcagCGCCGCGCGCGAAGAGGGAGCGGAAGAACCAGTACCGCGGGATCAGGCAGC
EST: gi|4968603|gb|AU065507.1|AU065507
EST:     CTGGCCCGACGCCGACGACTCCGACCCNCACACCCTCGNTCCCGAGAAAC                         CGNCGCGCGCGAAGAGGGAGCGGAAGAACCAGTACCGCGGGATCAGGCAGC
genomic: CTGGCCCGACGCCGACGACTCCGACCCCCACACCCCCGCTCCCGAGAAACgtaacttctc ... aatcgtgcagCGCCGCGCGCGAAGAGGGAGCGGAAGAACCAGTACCGCGGGATCAGGCAGC
EST: gi|23513657|gb|BU673243.1|BU673243
EST:     TTGGCCCGACGCCGACGACTCCGACCCCCACACCCCCGCTCCCGAGAAAC                         CGCCGCGCGCGAAGAGGGAGCGGAAGAACCAGTACCGCGGGATCAGGCAGC
genomic: CTGGCCCGACGCCGACGACTCCGACCCCCACACCCCCGCTCCCGAGAAACgtaacttctc ... aatcgtgcagCGCCGCGCGCGAAGAGGGAGCGGAAGAACCAGTACCGCGGGATCAGGCAGC
EST: gi|871919|gb|D22672.1|D22672
EST:     CTGGCCCGACGCCGACGACTCCNACCCCCACACCCCCGCTCCCGAGAAAC                         CGCCGCGCGCNAAGAGGGAGCGGAAGAACCAGTACCGCGGGATCAGGCAGC
genomic: CTGGCCCGACGCCGACGACTCCGACCCCCACACCCCCGCTCCCGAGAAACgtaacttctc ... aatcgtgcagCGCCGCGCGCGAAGAGGGAGCGGAAGAACCAGTACCGCGGGATCAGGCAGC
EST: gi|12404843|gb|AU166444.1|AU166444
EST:     CTGGCCCGACGCCGACGACTCCGACCCCCACACCCCCGCTCCCGAGAAAC                         CGCCGCGCGCGAAGAGGGAGCGGAAGAACCAGTACCGCGGGATCAGGCAGC
genomic: CTGGCCCGACGCCGACGACTCCGACCCCCACACCCCCGCTCCCGAGAAACgtaacttctc ... aatcgtgcagCGCCGCGCGCGAAGAGGGAGCGGAAGAACCAGTACCGCGGGATCAGGCAGC

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: 57 (upstream exon), 53 (downstream exon)
Score: 11

ATCATCTACGACTACATCCCGGCGCGCCGCCGGTTGTGCGCCTCCGACTTCTGGCCCGACGCCGACGACTCCGACCCCCACACCCCCGCTCCCGAGAAACgtaacttctc ... aatcgtgcagCGCCGCGCGCGAAGAGGGAGCGGAAGAACCAGTACCGCGGGATCAGGCAGCGGCCGTGGGGGAAGTGGGCGGCGGAGATCCGCGACCCGGTGAAGGGGGT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcttgctctgttttttttttctttcttggctgatgtctctggttgaatcgtgcagCGCCGCGCGCGAAGAGGGAGCGGAAGAACCAGTACCGCGGGATCAGGCAGCGGCCGTGGGGGAAGTGGGCGGCGGAGATCCGCGACCCGGTGAAGGGGGT
                           ggctgat  putative branch site (score: 11)
          ttttttttttctttct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaacttctcctctcatggcctctgcttcttgctctgttttttttttctttcttggctgatgtctctggttgaatcgtgcagCGCCGCGCGCGAAGAGGGAGCGGAAGAACCAGTACCGCGGGATCAGGCAGCGGCCGTGGGGGAAGTGGGCGGCGGAGATCCGCGACCCGGTGAAGGGGGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC