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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgtatatatagtcttgttctagctagtgcagtcgcagtagcaaaatcgtactagtagcagtcatatgctcatcactacagagatatattactgaactctccagctttggatttttcagCATGGTATGAAAGGCGGCAAATGAGGAAGATATATTCCCCTCTTCTTGAAGGAATCTTGGCTTTCTACCTTGGCTTTGAGTGGATCCAG

Basic information

species Oryza sativa
transcript LOC_Os03g01014.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g01014.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G005859_T02 (Zea mays), 3'ss of exon 7
gtgtatatatagtcttgttctagctagtgcagtcgcagtagcaaaatcgtactagtagcagtcatatgctcatcactacagagatatattactgaac-tctccagctttggatttttcagCATGGTATGAAAGGCGGCAAATGAGGAAGATATATTCCCCTCTTCTTGAAGGAATCTTGGCTTTCTACCTTGGCTTTGAGTGGATCCAG
  || | | | ||| | |   | ||| |  ||   |  |   ||| | |||   || |   |  |  ||  |  | |  |||  | ||    |  || | | ||    |||||||  |||| ||||| || ||| ||||||||||||||||||| || || ||||| ||||||||||||||||||||||||||||| || |||||||||
--gtttgtttggtcatat---atctactatagattctttt-taaatttgtagccgtggtgatgtt--gcaaagtagt-tagatttttagcctttgacatatgcatgcatggatttg-cagCTTGGTACGAGAGGAGGCAAATGAGGAAGATATACTCGCCGCTTCTGGAAGGAATCTTGGCTTTCTACCTTGGCTTCGAATGGATCCAG
















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|86889444|gb|CI317244.1|CI317244
EST:     TCAAATACT-GGCGAGAGAATCTCAAGAAACTA-TTGCAG                         CATGGTATGAAA-GCGGCAAATGA-GAAGATATATTCCCCTCTTCTTGAAG
genomic: TCAAATACTGGGCGAGAGAATCTCAAGAAACTATTTGCAGgtgtatatat ... gatttttcagCATGGTATGAAAGGCGGCAAATGAGGAAGATATATTCCCCTCTTCTTGAAG
EST: gi|86502916|gb|CI145549.1|CI145549
EST:     AGCAATGCGTTCAAATACTGGGCGAGAGAATCTCAAGAAACTATTTGCAG                         CATGGTATGAAAGGCGGCAAATGAGGAAGATATATTCCCCTCTTCTTGAAG
genomic: AGCAATGCGTTCAAATACTGGGCGAGAGAATCTCAAGAAACTATTTGCAGgtgtatatat ... gatttttcagCATGGTATGAAAGGCGGCAAATGAGGAAGATATATTCCCCTCTTCTTGAAG
EST: gi|87015730|gb|CI277688.1|CI277688
EST:     GCGAGAGAATCTCAAGAAACTATTTGCAG                         CATGGTATGAAAGGCGGCAAATGAGGAAGATATATTCCCCTCTTCTTGAAG
genomic: GCGAGAGAATCTCAAGAAACTATTTGCAGgtgtatatat ... gatttttcagCATGGTATGAAAGGCGGCAAATGAGGAAGATATATTCCCCTCTTCTTGAAG
EST: gi|66931443|gb|CX118291.1|CX118291
EST:     AGCAATGCGTTCAAATACTGGGCGAGAGAATCTCAAGAAACTATTTGCAG                         CATGGTATGAAAGGCGGCAAATGAGGAAGATATATTCCCCTCTTCTTGAAG
genomic: AGCAATGCGTTCAAATACTGGGCGAGAGAATCTCAAGAAACTATTTGCAGgtgtatatat ... gatttttcagCATGGTATGAAAGGCGGCAAATGAGGAAGATATATTCCCCTCTTCTTGAAG
EST: gi|86501807|gb|CI144440.1|CI144440
EST:     AGCAATGCGTTCAAATACTGGGCGAGAGAATCTCAAGAAACTATTTGCAG                         CATGGTATGAAAGGCGGCAAATGAGGAAGATATATTCCCCTCTTCTTGAAG
genomic: AGCAATGCGTTCAAATACTGGGCGAGAGAATCTCAAGAAACTATTTGCAGgtgtatatat ... gatttttcagCATGGTATGAAAGGCGGCAAATGAGGAAGATATATTCCCCTCTTCTTGAAG
EST: gi|58693667|gb|CK082354.1|CK082354
EST:     AGCAATGCGTTCAAATACTGGGCGAGAGAATCTCAAGAAACTATTTGCAG                         CATGGTATGAAAGGCGGCAAATGAGGAAGATATATTCCCCTCTTCTTGAAG
genomic: AGCAATGCGTTCAAATACTGGGCGAGAGAATCTCAAGAAACTATTTGCAGgtgtatatat ... gatttttcagCATGGTATGAAAGGCGGCAAATGAGGAAGATATATTCCCCTCTTCTTGAAG
EST: gi|29615143|gb|CB620156.1|CB620156
EST:     AGCAATGCGTTCAAATACTGGGCGAGAGAATCTCAAGAAACTATTTGCAG                         CATGGTATGAAAGGCGGCAAATGAGGAAGATATATTCCCCTCTTCTTGAAG
genomic: AGCAATGCGTTCAAATACTGGGCGAGAGAATCTCAAGAAACTATTTGCAGgtgtatatat ... gatttttcagCATGGTATGAAAGGCGGCAAATGAGGAAGATATATTCCCCTCTTCTTGAAG
EST: gi|29684278|gb|CB680553.1|CB680553
EST:     AGCAATGCGTTCAAATACTGGGCGAGAGAATCTCAAGAAACTATTTGCAG                         CATGGTATGAAAGGCGGCAAATGAGGAAGATATATTCCCCTCTTCTTGAAG
genomic: AGCAATGCGTTCAAATACTGGGCGAGAGAATCTCAAGAAACTATTTGCAGgtgtatatat ... gatttttcagCATGGTATGAAAGGCGGCAAATGAGGAAGATATATTCCCCTCTTCTTGAAG
EST: gi|29642142|gb|CB647149.1|CB647149
EST:     AGCAATGCGTTCAAATACTGGGCGAGAGAATCTCAAGAAACTATTTGCAG                         CATGGTATGAAAGGCGGCAAATGAGGAAGATATATTCCCCTCTTCTTGAAG
genomic: AGCAATGCGTTCAAATACTGGGCGAGAGAATCTCAAGAAACTATTTGCAGgtgtatatat ... gatttttcagCATGGTATGAAAGGCGGCAAATGAGGAAGATATATTCCCCTCTTCTTGAAG
EST: gi|88958690|gb|CI096205.1|CI096205
EST:     TGGGCGAGAGAATCTCAAGAAACTATTTGCAG                         CATGGTATGAAAGGCGGCAAATGAGGAAGATATATTCCCCTCTTCTTGAAG
genomic: TGGGCGAGAGAATCTCAAGAAACTATTTGCAGgtgtatatat ... gatttttcagCATGGTATGAAAGGCGGCAAATGAGGAAGATATATTCCCCTCTTCTTGAAG
EST: gi|29685648|gb|CB681923.1|CB681923
EST:     AGCAATGCGTTCAAATACTGGGCGAGAGAATCTCAAGAAACTATTTGCAG                         CATGGTATGAAAGGCGGCAAATGAGGAAGATATATTCCCCTCTTCTTGAAG
genomic: AGCAATGCGTTCAAATACTGGGCGAGAGAATCTCAAGAAACTATTTGCAGgtgtatatat ... gatttttcagCATGGTATGAAAGGCGGCAAATGAGGAAGATATATTCCCCTCTTCTTGAAG
EST: gi|29684277|gb|CB680552.1|CB680552
EST:     AGCAATGCGTTCAAATACTGGGCGAGAGAATCTCAAGAAACTATTTGCAG                         CATGGTATGAAAGGCGGCAAATGAGGAAGATATATTCCCCTCTTCTTGAAG
genomic: AGCAATGCGTTCAAATACTGGGCGAGAGAATCTCAAGAAACTATTTGCAGgtgtatatat ... gatttttcagCATGGTATGAAAGGCGGCAAATGAGGAAGATATATTCCCCTCTTCTTGAAG
EST: gi|87009421|gb|CI313894.1|CI313894
EST:     GGGCGAGAGAATCTCAAGAAACTATTTGCAG                         CATGGTATGAAAGGCGGCAAATGAGGGAGATATATTCCCCTCTTCTTGAAG
genomic: GGGCGAGAGAATCTCAAGAAACTATTTGCAGgtgtatatat ... gatttttcagCATGGTATGAAAGGCGGCAAATGAGGAAGATATATTCCCCTCTTCTTGAAG
EST: gi|88977251|gb|CI024988.1|CI024988
EST:     AGCAATGCGTTCAAATACTGGGCGAGAGAATCTCAAGAAACTATTTGCAG                         CATGGTATGAAAGGCGGCAAATGAGGAAGATATATTCCCCTCTTCTTGAAG
genomic: AGCAATGCGTTCAAATACTGGGCGAGAGAATCTCAAGAAACTATTTGCAGgtgtatatat ... gatttttcagCATGGTATGAAAGGCGGCAAATGAGGAAGATATATTCCCCTCTTCTTGAAG
EST: gi|29669725|gb|CB666000.1|CB666000
EST:     AGCAATGCGTTCAAATACTGGGCGAGAGAATCTCAAGAAACTATTTGCAG                         CATGGTATGAAAGGCGGCAAATGAGGAAGATATATTCCCCTCTTCTTGAAG
genomic: AGCAATGCGTTCAAATACTGGGCGAGAGAATCTCAAGAAACTATTTGCAGgtgtatatat ... gatttttcagCATGGTATGAAAGGCGGCAAATGAGGAAGATATATTCCCCTCTTCTTGAAG
EST: gi|29668135|gb|CB664410.1|CB664410
EST:     AGCAATGCGTTCAAATATTGGGCGAGAGAATCTCAAGAAACTATTTGCAG                         CATGGTATGAAAGGCGGCAAATGAGGAAGATATATTCCCCTCTTCTTGAAG
genomic: AGCAATGCGTTCAAATACTGGGCGAGAGAATCTCAAGAAACTATTTGCAGgtgtatatat ... gatttttcagCATGGTATGAAAGGCGGCAAATGAGGAAGATATATTCCCCTCTTCTTGAAG

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: 66 (upstream exon), 75 (downstream exon)
Score: 52

ATCCTACTTATGTGGTGACACCAGCAATGCGTTCAAATACTGGGCGAGAGAATCTCAAGAAACTATTTGCAGgtgtatatat ... gatttttcagCATGGTATGAAAGGCGGCAAATGAGGAAGATATATTCCCCTCTTCTTGAAGGAATCTTGGCTTTCTACCTTGGCTTTGAGTGGATCCAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatgctcatcactacagagatatattactgaactctccagctttggatttttcagCATGGTATGAAAGGCGGCAAATGAGGAAGATATATTCCCCTCTTCTTGAAGGAATCTTGGCTTTCTACCTTGGCTTTGAGTGGATCCAG
                                               tttttc  CT-rich tract
                 agatatatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgtatatatagtcttgttctagctagtgcagtcgcagtagcaaaatcgtactagtagcagtcatatgctcatcactacagagatatattactgaactctccagctttggatttttcagCATGGTATGAAAGGCGGCAAATGAGGAAGATATATTCCCCTCTTCTTGAAGGAATCTTGGCTTTCTACCTTGGCTTTGAGTGGATCCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA