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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGATATGAGCCAAAACAACCTTGGTGGTGGCCAACAGATACAGTACAATCTTCCCACTAATAAGCTTGAGAGGCTgtaagttcctcaaatgaagttgtggtttagaaagtacatcagcttttctggtgtctgtgtgctaagtggttattgtttgcag

Basic information

species Oryza sativa
transcript LOC_Os03g08550.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g08550.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G153393_T01 (Zea mays), 5'ss of exon 4
CGATATGAGCCAAAACAACCTTGGTGGTGGCCAACAGATACAGTACAATCTTCCCACTAATAAGCTTGAGAGGCTgtaagttcctcaaatgaagttgtg-gtttagaaagtacatcagcttttctggtgtc-tgtgtgctaagtggttattgtt-tgcag
 || ||||||||||| |||||||| |||||    || ||||||||||||||||||| ||  ||||||||||  ||||||||||||  | | ||  ||||  |||  ||| | |   | || || ||||| | ||  || ||  || || ||| | | |||
TGACATGAGCCAAAATAACCTTGGCGGTGGAGGTCAAATACAGTACAATCTTCCCAATATGAAGCTTGAGAAACTgtaagttcctacagtcaatctgtgcatttgaaaatttctctaactattatggtggcatggctgttagatgattcttgctgtacag

upper sequence: LOC_Os03g08550.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G330907_T01 (Zea mays), 5'ss of exon 4
CGATATGAGCCAAAACAACCTTGGTGGTGGCCAACAGATACAGTACAATCTTCCCACTAATAAGCTTGAGAGGCTgtaagttcctcaaatgaagttgtg-gtttagaaagtacatcagcttttctggtgtc-tgtgtgctaagtggttattgtt-tgcag
 ||  |||||||||| ||||||||||||||    || ||||||||||||||||||| |   ||||||||||  |||||||||| |  | |||| |||||  |||  |   | ||  | ||  |||| || | |   || ||  || || || || | |||
TGACTTGAGCCAAAATAACCTTGGTGGTGGAGGCCAAATACAGTACAATCTTCCCAATGTGAAGCTTGAGAAACTgtaagttcatacagtgaatttgtgcatttgaatttttcactaactaatctgatggcatagctgttagatgattcttcttgtacag
















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|3107717|gb|D43457.1|D43457
EST:     GGTGGCCAACAGATACAGTACAATCTTCCCACTAATAAGCTTGAGAGGCT                         CAATCTCGCAGGAAACCAGTTCACTGGAAATTTACCCTACTCGATTTTCTC
genomic: GGTGGCCAACAGATACAGTACAATCTTCCCACTAATAAGCTTGAGAGGCTgtaagttcct ... ttgtttgcagCAATCTCGCAGGAAACCAGTTCACTGGAAATTTACCCTACTCGATTTTCTC
EST: gi|44665230|gb|CR278664.1|CR278664
EST:     GGTGGCCAACAGATACAGTACAATCTTCCCACTAATAAGCTTGAGAGGCT                         CAATCTCGCAGGAAACCAGTTCACTGGAAATTTACCCTACTCGATTTTCTC
genomic: GGTGGCCAACAGATACAGTACAATCTTCCCACTAATAAGCTTGAGAGGCTgtaagttcct ... ttgtttgcagCAATCTCGCAGGAAACCAGTTCACTGGAAATTTACCCTACTCGATTTTCTC
EST: gi|88421797|gb|CI621441.1|CI621441
EST:     GGTGGCCAACAGATACAGTACAATCTTCCCACTAATAAGCTTGAGAGGCT                         CAATCTCGCAGGAAACCAGTTC
genomic: GGTGGCCAACAGATACAGTACAATCTTCCCACTAATAAGCTTGAGAGGCTgtaagttcct ... ttgtttgcagCAATCTCGCAGGAAACCAGTTC
EST: gi|29644649|gb|CB649656.1|CB649656
EST:     GGTGGCCAACAGATACAGTACAATCTTCCCACTAATAAGCTTGAGAGGCT                         CAATCTCGCAGGAAACCAGTTCACTGGAAATTTACCCTACTCGATTTTCTC
genomic: GGTGGCCAACAGATACAGTACAATCTTCCCACTAATAAGCTTGAGAGGCTgtaagttcct ... ttgtttgcagCAATCTCGCAGGAAACCAGTTCACTGGAAATTTACCCTACTCGATTTTCTC
EST: gi|29624948|gb|CB629959.1|CB629959
EST:     GGTGGCCAACAGATACAGTACAATCTTCCCACTAATAAGCTTGAGAGGCT                         CAATCTCGCAGGAAACCAGTTCACTGGAAATTTACCCTACTCGATTTTCTC
genomic: GGTGGCCAACAGATACAGTACAATCTTCCCACTAATAAGCTTGAGAGGCTgtaagttcct ... ttgtttgcagCAATCTCGCAGGAAACCAGTTCACTGGAAATTTACCCTACTCGATTTTCTC
EST: gi|66914683|gb|CX101531.1|CX101531
EST:     GGTGGCCAACAGATACAGTACAATCTTCCCACTAATAAGCTTGAGAGGCT                         CAATCTCGCAGGAAACCAGTTCACTGGAAATTTACCCTACTCGATTTTCTC
genomic: GGTGGCCAACAGATACAGTACAATCTTCCCACTAATAAGCTTGAGAGGCTgtaagttcct ... ttgtttgcagCAATCTCGCAGGAAACCAGTTCACTGGAAATTTACCCTACTCGATTTTCTC
EST: gi|88386689|gb|CI682838.1|CI682838
EST:     GGTGGCCAACAGATACAGTACAATC-TCCCACTAATAAGCTTGAGAGGCT                         CAATCTCGCAGGAAACCAGTTCACTGGAAATTTACCCTACTCGATTTTCTC
genomic: GGTGGCCAACAGATACAGTACAATCTTCCCACTAATAAGCTTGAGAGGCTgtaagttcct ... ttgtttgcagCAATCTCGCAGGAAACCAGTTCACTGGAAATTTACCCTACTCGATTTTCTC
EST: gi|88432225|gb|CI565258.1|CI565258
EST:     GGTGGCCAACAGATACAGTACAATCTTCCCACTAATAAGCTTGAGAGGCT                         CAATCTCGCAGGAAACCAGTTCACTGGAAATT
genomic: GGTGGCCAACAGATACAGTACAATCTTCCCACTAATAAGCTTGAGAGGCTgtaagttcct ... ttgtttgcagCAATCTCGCAGGAAACCAGTTCACTGGAAATT
EST: gi|117225926|gb|CT846035.1|CT846035
EST:     GGTGGCCAACAGATACAGTACAATCTTCCCACTAATAAGCTTGAGAGGCT                         CAATCTCGCAGGAAACCAGTTCACTGGAAATTTACCCTACTCGATTTTCTC
genomic: GGTGGCCAACAGATACAGTACAATCTTCCCACTAATAAGCTTGAGAGGCTgtaagttcct ... ttgtttgcagCAATCTCGCAGGAAACCAGTTCACTGGAAATTTACCCTACTCGATTTTCTC
EST: gi|29681108|gb|CB677383.1|CB677383
EST:     GGTGGCCAACAGATACAGTACAATCTTCCCACTAATAAGCTTGAGAGGCT                         CAATCTCGCAGGAAACCAGTTCACTGGAAATTTACCCTACTCGATTTTCTC
genomic: GGTGGCCAACAGATACAGTACAATCTTCCCACTAATAAGCTTGAGAGGCTgtaagttcct ... ttgtttgcagCAATCTCGCAGGAAACCAGTTCACTGGAAATTTACCCTACTCGATTTTCTC
EST: gi|88399209|gb|CI618399.1|CI618399
EST:     GGTGGCCAACAGATACAGTACAATCTTCCCACTAATAAGCTTGAGAGGCT                         CAATCTCGCAGGAAACC
genomic: GGTGGCCAACAGATACAGTACAATCTTCCCACTAATAAGCTTGAGAGGCTgtaagttcct ... ttgtttgcagCAATCTCGCAGGAAACC
EST: gi|88358901|gb|CI619405.1|CI619405
EST:     GGTGGCCAACAGATACAGTACAATCTTCCCACTAATAAGCTTGAGAGGCT                         CAATCTCGCAGGA
genomic: GGTGGCCAACAGATACAGTACAATCTTCCCACTAATAAGCTTGAGAGGCTgtaagttcct ... ttgtttgcagCAATCTCGCAGGA

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: 67 (upstream exon), 51 (downstream exon)
Score: 37

CGATATGAGCCAAAACAACCTTGGTGGTGGCCAACAGATACAGTACAATCTTCCCACTAATAAGCTTGAGAGGCTgtaagttcct ... ttgtttgcagCAATCTCGCAGGAAACCAGTTCACTGGAAATTTACCCTACTCGATTTTCTCGATGTCTAATCTTAAGTATTT




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CGATATGAGCCAAAACAACCTTGGTGGTGGCCAACAGATACAGTACAATCTTCCCACTAATAAGCTTGAGAGGCTgtaagttcctcaaatgaagttgtggtttagaaagtacatcagcttttctggtgtctgtgtgctaagtggttattgtttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGAGG