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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATCAGAAGAATGCTAGGAGATATTCCGTGGGGCCCTTATCTAATGGGAGACCAGCCGTTAATTACTCATACTTGAGCGCTAACACCCCGGCAAGAGCAGgtatacccatttaagatggtttgtcatgctcatttcataggggaggatttgtggctgttgcacttggaattataacaaactataattacctccttgtag

Basic information

species Oryza sativa
transcript LOC_Os06g02550.2
intron # 16
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|29638209|gb|CB643218.1|CB643218
EST:     ACCAGCCGTTAATTACTCATACTTGAGCGCTAACACCCCGGCAAGAGCAG                         CTGGTGTGCAAAGGAAGCTGGAGTTGGATCACCAGGTGAATATGAATTCTT
genomic: ACCAGCCGTTAATTACTCATACTTGAGCGCTAACACCCCGGCAAGAGCAGgtatacccat ... ctccttgtagCTGGTGTGCAAAGGAAGCTGGAGTTGGATCACCAGGTGAATATGAATTCTT
EST: gi|58685705|gb|CK074392.1|CK074392
EST:     ACCAGCCGTTAATTACTCATACTTGAGCGCTAACACCCCGGCAAGAGCAG                         CTGGTGTGCAAAGGAAGCTGGAGTTGGATCACCAGGTGAATATGAATTCTT
genomic: ACCAGCCGTTAATTACTCATACTTGAGCGCTAACACCCCGGCAAGAGCAGgtatacccat ... ctccttgtagCTGGTGTGCAAAGGAAGCTGGAGTTGGATCACCAGGTGAATATGAATTCTT
EST: gi|88691087|gb|CI735166.1|CI735166
EST:     ACCAGCCGTTAATTACTCATACTTGAGCGCTAACACCCCGGCAAGAGCAG                         CTGGTGTGCAAAGGAAGCTGGAGTTGGATCACCAGGTGAATATGAATTCTT
genomic: ACCAGCCGTTAATTACTCATACTTGAGCGCTAACACCCCGGCAAGAGCAGgtatacccat ... ctccttgtagCTGGTGTGCAAAGGAAGCTGGAGTTGGATCACCAGGTGAATATGAATTCTT
EST: gi|88691956|gb|CI735531.1|CI735531
EST:     ACCAGCCGTTAATTACTCATACTTGAGCGCTAACACCCCGGCAAGAGCAG                         CTGGTGTGCAAAGGAAGCTGGAGTTGGATCACCAGGTGAATATGAATTCTT
genomic: ACCAGCCGTTAATTACTCATACTTGAGCGCTAACACCCCGGCAAGAGCAGgtatacccat ... ctccttgtagCTGGTGTGCAAAGGAAGCTGGAGTTGGATCACCAGGTGAATATGAATTCTT
EST: gi|218500572|gb|FG950928.1|FG950928
EST:     ACCAGCCGTTAATTACTCATACTTGAGCGCTAACACCCCGGCAAGAGCAG                         CTGGTGTGCAAAGGAAGCT
genomic: ACCAGCCGTTAATTACTCATACTTGAGCGCTAACACCCCGGCAAGAGCAGgtatacccat ... ctccttgtagCTGGTGTGCAAAGGAAGCT
EST: gi|66916087|gb|CX102935.1|CX102935
EST:     ACCAGCCGTTAATTACTCATACTTGAGCGCTAACACCCCGGCAAGAGCAG                         CTGGTGTGCAAAGGAAGCTGGAGTTGGATCACCAGGTGAATATGAATTCTT
genomic: ACCAGCCGTTAATTACTCATACTTGAGCGCTAACACCCCGGCAAGAGCAGgtatacccat ... ctccttgtagCTGGTGTGCAAAGGAAGCTGGAGTTGGATCACCAGGTGAATATGAATTCTT
EST: gi|58687727|gb|CK076414.1|CK076414
EST:     CCAGCCGTTAACTTACTCATACTTGAGCGCTAACACCCCGGCAAGAGCAG                         CTGGTGTGCAAAGGAAGCTGGAGTT
genomic: CCAGCCGTTAA-TTACTCATACTTGAGCGCTAACACCCCGGCAAGAGCAGgtatacccat ... ctccttgtagCTGGTGTGCAAAGGAAGCTGGAGTT
EST: gi|29641487|gb|CB646494.1|CB646494
EST:     ACCAGCCGTTAATTACTCATACTTGAGCGCTAACACCCCGGCAAGAGCAG                         CTGGTGTGCAAAGGAAGCTGGAGTTGGATCACCAGGTGAATATGAATTCTT
genomic: ACCAGCCGTTAATTACTCATACTTGAGCGCTAACACCCCGGCAAGAGCAGgtatacccat ... ctccttgtagCTGGTGTGCAAAGGAAGCTGGAGTTGGATCACCAGGTGAATATGAATTCTT
EST: gi|58593890|gb|CF992198.1|CF992198
EST:     ACCAGCCGTTAATTACTCATACTTGAGCGCTAACACCCCGGCAAGAGCAG                         CTGGTGTGCAAAGGAAGCTGGAGTTGGATCACCAGGTGAATATGAATTCTT
genomic: ACCAGCCGTTAATTACTCATACTTGAGCGCTAACACCCCGGCAAGAGCAGgtatacccat ... ctccttgtagCTGGTGTGCAAAGGAAGCTGGAGTTGGATCACCAGGTGAATATGAATTCTT
EST: gi|29666198|gb|CB662473.1|CB662473
EST:     ACCAGCCGTTAATTACTCATACTTGAGCGCTAACACCCCGGCAAGAGCAG                         CTGGTGTGCAAAGGAAGCTGGAGTTGGATCACCAGGTGAATATGAATTCTT
genomic: ACCAGCCGTTAATTACTCATACTTGAGCGCTAACACCCCGGCAAGAGCAGgtatacccat ... ctccttgtagCTGGTGTGCAAAGGAAGCTGGAGTTGGATCACCAGGTGAATATGAATTCTT
EST: gi|29626826|gb|CB631837.1|CB631837
EST:     ACCAGCCGTTAATTACTCATACTTGAGCGCTAACACCCCGGCAAGAGCAG                         CTGGTGTGCAAAGGAAGCTGGAGTTGGATCACCAGGTGAATATGAATTCTT
genomic: ACCAGCCGTTAATTACTCATACTTGAGCGCTAACACCCCGGCAAGAGCAGgtatacccat ... ctccttgtagCTGGTGTGCAAAGGAAGCTGGAGTTGGATCACCAGGTGAATATGAATTCTT
EST: gi|58684250|gb|CK072937.1|CK072937
EST:     ACCAGCCGTTAATTACTCATACTTGAGCGCTAACACCCCGGCAAGAGCAG                         CTGGTGTGCAAAGGAAGCTGGAGTTGGATCACCAGGTGAATATGAATTCTT
genomic: ACCAGCCGTTAATTACTCATACTTGAGCGCTAACACCCCGGCAAGAGCAGgtatacccat ... ctccttgtagCTGGTGTGCAAAGGAAGCTGGAGTTGGATCACCAGGTGAATATGAATTCTT
EST: gi|88689214|gb|CI732790.1|CI732790
EST:     ACCACCCGTTAATTACTCATACTTGAGCGCTAACACCCCGGCAAGAGCAG                         CTGGTGTGCAAAGGAAGCTGGAGTTGGATCACCAGGTGAATATGAATTCTT
genomic: ACCAGCCGTTAATTACTCATACTTGAGCGCTAACACCCCGGCAAGAGCAGgtatacccat ... ctccttgtagCTGGTGTGCAAAGGAAGCTGGAGTTGGATCACCAGGTGAATATGAATTCTT
EST: gi|29626870|gb|CB631881.1|CB631881
EST:     ACCAGCCGTTAATTACTCATACTTGAGCGCTAACACCCCGGCAAGAGCAG                         CTGGTGTGCAAAGGAAGCTGGAGTTGGATCACCAGGTGAATATGAATTCTT
genomic: ACCAGCCGTTAATTACTCATACTTGAGCGCTAACACCCCGGCAAGAGCAGgtatacccat ... ctccttgtagCTGGTGTGCAAAGGAAGCTGGAGTTGGATCACCAGGTGAATATGAATTCTT
EST: gi|88691942|gb|CI735517.1|CI735517
EST:     ACCAGCCGTTAATTACTCATACTTGAGCGCTAACACCCCGGCAAGAGCAG                         CTGGTGTGCAAAGGAAGCTGGAGTTGGATCACCAGGTGAATATGAATTCTT
genomic: ACCAGCCGTTAATTACTCATACTTGAGCGCTAACACCCCGGCAAGAGCAGgtatacccat ... ctccttgtagCTGGTGTGCAAAGGAAGCTGGAGTTGGATCACCAGGTGAATATGAATTCTT
EST: gi|88688550|gb|CI732126.1|CI732126
EST:     ACCAGCCGTTAATTACTCATACTTGAGCGCTAACACCCCGGCAAGAGCAG                         CTGGTGTGCAAAGGAAGCTGGAGTTGGATCACCAGGTGAATATGAATTCTT
genomic: ACCAGCCGTTAATTACTCATACTTGAGCGCTAACACCCCGGCAAGAGCAGgtatacccat ... ctccttgtagCTGGTGTGCAAAGGAAGCTGGAGTTGGATCACCAGGTGAATATGAATTCTT

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), 74 (downstream exon)
Score: 52

GATCAGAAGAATGCTAGGAGATATTCCGTGGGGCCCTTATCTAATGGGAGACCAGCCGTTAATTACTCATACTTGAGCGCTAACACCCCGGCAAGAGCAGgtatacccat ... ctccttgtagCTGGTGTGCAAAGGAAGCTGGAGTTGGATCACCAGGTGAATATGAATTCTTGTCAGGCTCCAGAGGGTAACCATAAACTGACAAAGGCAGAGGCAATGAA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GATCAGAAGAATGCTAGGAGATATTCCGTGGGGCCCTTATCTAATGGGAGACCAGCCGTTAATTACTCATACTTGAGCGCTAACACCCCGGCAAGAGCAGgtatacccatttaagatggtttgtcatgctcatttcataggggaggatttgtggctgttgcacttggaattataacaaactataattacctccttgtag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG