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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCCTACATCCGCTGCTATAGATGGCCCCCTTGAACCTTCTTCGTCGTCCACTGTTCTAGTTTCTAATGCCCCTGATGAATCATTGACTGATTATTTCAGTgtatgttctctcctttaaactccctgctattgcattctaccttttattttttttcatgttcatcaaataatatacaatagcttgcctcagatcctagtaa...

Basic information

species Oryza sativa
transcript LOC_Os12g06020.1
intron # 6
splice site 5'
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|29684686|gb|CB680961.1|CB680961
EST:     CTGTTCTAGTTTCTAATGCCCCTGATGAATCATTGACTGATTATTTCAGT                         GGCGCTGTTAATGTTGGGAATGTATCAATTACACCAATGGTTGGAAGAACT
genomic: CTGTTCTAGTTTCTAATGCCCCTGATGAATCATTGACTGATTATTTCAGTgtatgttctc ... aaatctgcagGGCGCTGTTAATGTTGGGAATGTATCAATTACACCAATGGTTGGAAGAACT
EST: gi|29639083|gb|CB644092.1|CB644092
EST:     GATTATTTCAGT                         GGCGCTGTTAATGTTGGGAATGTATCAATTACACCAATGGTTGGAAGAACT
genomic: GATTATTTCAGTgtatgttctc ... aaatctgcagGGCGCTGTTAATGTTGGGAATGTATCAATTACACCAATGGTTGGAAGAACT
EST: gi|29639129|gb|CB644138.1|CB644138
EST:     TCATTGACTGATTATTTCAGT                         GGCGCTGTTAATGTTGGGAATGTATCAATTACACCAATGGTTGGAAGAACT
genomic: TCATTGACTGATTATTTCAGTgtatgttctc ... aaatctgcagGGCGCTGTTAATGTTGGGAATGTATCAATTACACCAATGGTTGGAAGAACT
EST: gi|29676701|gb|CB672976.1|CB672976
EST:     CTGTTCTAGTTTCTAATGCCCCTGATGAATCATTGACTGATTATTTCAGT                         GGCGCTGTTAATGTTGGGAATGTATCAATTACACCAATGGTTGGAAGAACT
genomic: CTGTTCTAGTTTCTAATGCCCCTGATGAATCATTGACTGATTATTTCAGTgtatgttctc ... aaatctgcagGGCGCTGTTAATGTTGGGAATGTATCAATTACACCAATGGTTGGAAGAACT
EST: gi|33793549|gb|CF322657.1|CF322657
EST:     CTGTTCTAGTTTCTAATGCCCCTGATGAATCATTGACTGATTATTTCAGT                         GGCGCTGTTAATGTTGGGAATGTATCAATTACACCAATGGTTGGAAGAACT
genomic: CTGTTCTAGTTTCTAATGCCCCTGATGAATCATTGACTGATTATTTCAGTgtatgttctc ... aaatctgcagGGCGCTGTTAATGTTGGGAATGTATCAATTACACCAATGGTTGGAAGAACT
EST: gi|58686519|gb|CK075206.1|CK075206
EST:     CTGTTCTAGTTTCTAATGCCCCTGATGAATCATTGACTGATTATTTCAGT                         GGCGCTGTTAATGTTGGGAATGTATCAATTACACCAATGGTTGGAAGAACT
genomic: CTGTTCTAGTTTCTAATGCCCCTGATGAATCATTGACTGATTATTTCAGTgtatgttctc ... aaatctgcagGGCGCTGTTAATGTTGGGAATGTATCAATTACACCAATGGTTGGAAGAACT
EST: gi|29639082|gb|CB644091.1|CB644091
EST:     CTGTTCTAGTTTCTAATGCCCCTGATGAATCATTGACTGATTATTTCAGT                         GGCGCTGTTAATGTTGGGAATGTATCAATTACACCAATGGTTGGAAGAACT
genomic: CTGTTCTAGTTTCTAATGCCCCTGATGAATCATTGACTGATTATTTCAGTgtatgttctc ... aaatctgcagGGCGCTGTTAATGTTGGGAATGTATCAATTACACCAATGGTTGGAAGAACT
EST: gi|58601073|gb|CK011601.1|CK011601
EST:     CTGTTCTAGTTTCTAATGCCCCTGATGAATCATTGACTGATTATTTCAGT                         GGCCCTGTTAATGTTGGGAATGTATCAATTACACCAATGGTTGGAAGAACT
genomic: CTGTTCTAGTTTCTAATGCCCCTGATGAATCATTGACTGATTATTTCAGTgtatgttctc ... aaatctgcagGGCGCTGTTAATGTTGGGAATGTATCAATTACACCAATGGTTGGAAGAACT
EST: gi|29669200|gb|CB665475.1|CB665475
EST:     CTGTTCTAGTTTCTAATGCCCCTGATGAATCATTGACTGATTATTTCAGT                         GGCGCTGTTAATGTTGGGAATGTATCAATTACACCAATGGTTGGAAGAACT
genomic: CTGTTCTAGTTTCTAATGCCCCTGATGAATCATTGACTGATTATTTCAGTgtatgttctc ... aaatctgcagGGCGCTGTTAATGTTGGGAATGTATCAATTACACCAATGGTTGGAAGAACT
EST: gi|38482214|gb|CF966266.1|CF966266
EST:     CTGTTCTAGTTTCTAATGCCCCTGATGAATCATTGACTGATTATTTCAGT                         GGCGCTGTGAATGTTGGGAATGTATCAATTACACCAATGGTTGGAAGAACT
genomic: CTGTTCTAGTTTCTAATGCCCCTGATGAATCATTGACTGATTATTTCAGTgtatgttctc ... aaatctgcagGGCGCTGTTAATGTTGGGAATGTATCAATTACACCAATGGTTGGAAGAACT
EST: gi|33793116|gb|CF322439.1|CF322439
EST:     CTGTTCTAGTTTCTAATGCCCCTGATGAATCATTGACTGATTATTTCAGT                         GGCGCTGTTAATGTTGGGAATGTATCAATTACACCAATGGTTGGAAGAACT
genomic: CTGTTCTAGTTTCTAATGCCCCTGATGAATCATTGACTGATTATTTCAGTgtatgttctc ... aaatctgcagGGCGCTGTTAATGTTGGGAATGTATCAATTACACCAATGGTTGGAAGAACT
EST: gi|29669201|gb|CB665476.1|CB665476
EST:     TGCCCCTGATGAATCATTGACTGATTATTTCAGT                         GGCGCTGTTAATGTTGGGAATGTATCAATTACACCAATGGTTGGAAGAACT
genomic: TGCCCCTGATGAATCATTGACTGATTATTTCAGTgtatgttctc ... aaatctgcagGGCGCTGTTAATGTTGGGAATGTATCAATTACACCAATGGTTGGAAGAACT
EST: gi|218494718|gb|FG969775.1|FG969775
EST:     CTGTTCTAGTTTCTAATGCCCCTGATGAATCATTGACTGATTATTTCAGT                         GGCGCTGTTAATGTTGGGAATGTATCAATTACACCAATGGTTGGAAGAACT
genomic: CTGTTCTAGTTTCTAATGCCCCTGATGAATCATTGACTGATTATTTCAGTgtatgttctc ... aaatctgcagGGCGCTGTTAATGTTGGGAATGTATCAATTACACCAATGGTTGGAAGAACT
EST: gi|29639128|gb|CB644137.1|CB644137
EST:     CTGTTCTAGTTTCTAATGCCCCTGATGAATCATTGACTGATTATTTCAGT                         GGCGCTGTTAATGTTGGGAATGTATCAATTACACCAATGGTTGGAAGAACT
genomic: CTGTTCTAGTTTCTAATGCCCCTGATGAATCATTGACTGATTATTTCAGTgtatgttctc ... aaatctgcagGGCGCTGTTAATGTTGGGAATGTATCAATTACACCAATGGTTGGAAGAACT

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: 41

TCCTACATCCGCTGCTATAGATGGCCCCCTTGAACCTTCTTCGTCGTCCACTGTTCTAGTTTCTAATGCCCCTGATGAATCATTGACTGATTATTTCAGTgtatgttctc ... aaatctgcagGGCGCTGTTAATGTTGGGAATGTATCAATTACACCAATGGTTGGAAGAACTCATCAGCCTATCGAGTCTGTTGCATCCTCACACGTACCATTGATCATCC




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCCTACATCCGCTGCTATAGATGGCCCCCTTGAACCTTCTTCGTCGTCCACTGTTCTAGTTTCTAATGCCCCTGATGAATCATTGACTGATTATTTCAGTgtatgttctctcctttaaactccctgctattgcattctaccttttattttttttcatgttcatcaaataatatacaatagcttgcctcagatcctagtaa

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttctctcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctccctgc