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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CATCAGTGATGAGTTCAAGCGTGTAATTGGGTCACTCAAAGGGCATGATGATAAAATACGTATAGTTCTGAACAAAGCAGACCAAGTTGATGCACAACAAgtgagtgttattgctatccctttatagtgtgataacatattccattttcatcctctttatgcataggaaaaaaaatcatggagtgtgataagaaacattgatttgttttttacatttcaagtggagacaaaaaagagtagctatgttgattgaaagcaaataacgactttgcttctgacaaatttatcctcag

Basic information

species Oryza sativa
transcript LOC_Os04g57350.1
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g57350.1 (Oryza sativa), 5'ss of exon 12
lower sequence: GRMZM2G065012_T02 (Zea mays), 5'ss of exon 12
CATCAGTGATGAGTTCAAGCGTGTAATTGGGTCACTCAAAGGGCATGATGATAAAATACGTATAGTTCTGAACAAAGCAGACCAAGTTGATGCACAACAAgtgagtgttattgctatccctttatagtgtgataacatattccattttcatcctctttatgcataggaaaaaaaatcatggagtgtgataagaaacattgatttgttttttacatttcaagtggagacaaaaaagagtagctatgttgattgaaagcaaataacgactttgcttctgacaaatttatcctcag
|||||| ||||||||||||||||| || ||||| |||   ||||||||||| || ||||| |||||||| ||||| || ||||||||||||||||| || | |||| || |    || ||    ||  |  ||||     |   || ||    ||  | |    | |  |  | ||       | |     |    | || | |                                                                                         
CATCAGCGATGAGTTCAAGCGTGTGATCGGGTCTCTCCGCGGGCATGATGACAAGATACGCATAGTTCTCAACAAGGCCGACCAAGTTGATGCACAGCAGgcgagtattgt----attcccgattaccgccataatgcccttttttctctctatccctctcagcaagtcagcatattccattttcttgct-gctgtagtgctata----------------------------------------------------------------------------------------

upper sequence: LOC_Os04g57350.1 (Oryza sativa), 5'ss of exon 12
lower sequence: GLYMA02G46350.1 (Glycine max), 5'ss of exon 12
CATCAGTGATGAGTTCAAGCGTGTAATTGGGTCACTCAAAGGGCATGATGATAAAATACGTATAGTTCTGAACAAAGCAGACCAAGTTGATGCACAACAAgtgagtgttattgctatccc-tttatagtgtgataacatattccattttcatcctctttatgcataggaaaaaaaatcatggagtgtgataagaaacattgatttgttttttacatttcaagtggagacaaaaaagagtagctatgttgattgaaagcaaataacgactttgcttctgacaaatttatcctcag
|||||||||||||||||| ||||| ||    ||  |    ||||||||||| ||||| ||  | ||| ||||||| ||||||||||||||| | |||||||| || | |  ||   ||    ||    | |  |||  | ||  || ||   |  | |  | |   | ||   ||   ||   | |   || |   ||                                                                                                
CATCAGTGATGAGTTCAATCGTGTGATATCATCCTTACGGGGGCATGATGACAAAATCCGAGTGGTTTTGAACAAGGCAGACCAAGTTGATACCCAACAAgtaagagcttgtgtagtcaaacttccgtttttttaatcttttgaatctttcacaacctggtccggtgaaatctaacctatattgggctctatggtgcag-----------------------------------------------------------------------------------------------

upper sequence: LOC_Os04g57350.1 (Oryza sativa), 5'ss of exon 12
lower sequence: GLYMA18G10150.1 (Glycine max), 5'ss of exon 12
CATCAGTGATGAGTTCAAGCGTGTAATTGGGTCACTCAAAGGGCATGATGATAAAATACGTATAGTTCTGAACAAAGCAGACCAAGTTGATGCACAACAAgtgagtgt---tattgctatccctttatagtgtgataacatattccattttcatcctctttatgcataggaaaaaaaatcatgga-gtgtgataagaaacattgatttgttttttacatttcaagtggagacaaaaaagagtagctatgttgattgaaagcaaataacgactttgcttctgacaaatttatcctcag
  | |||||||||||||||||||| ||    || ||    || |||||||| ||||| ||  | ||  ||||||||||||||||||||||| | |||||||| |       | || |||    | |||  |    ||||| | || |||   ||    || | | | |  |   |     ||    ||||||| | |                                                                                                    
TGTTAGTGATGAGTTCAAGCGTGTGATATCATCCCTACGGGGACATGATGACAAAATTCGAGTTGTCTTGAACAAAGCAGACCAAGTTGATACCCAACAAgtaaaaacatatgttactaatattctatttttacttaaca-aatctattaaaatttcattaaagaaaaaaattgacctatatatctgtgtgatcaaatgttacag--------------------------------------------------------------------------------------------

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|25806656|gb|CA762617.1|CA762617
EST:     TCTGAACAAAGCAGACCAAGTTGATGCACAACAA                         CTCATGAGAGTCTATGGAGCACTGCTATGGTCGC-TGGGAAAGTTCTGAAC
genomic: TCTGAACAAAGCAGACCAAGTTGATGCACAACAAgtgagtgtta ... ttatcctcagCTCATGAGAGTCTATGGAGCACTGCTATGGTCGCTTGGGAAAGTTCTGAAC
EST: gi|86477340|gb|CI119973.1|CI119973
EST:     ATAAAATACGTATAGTTCTGAACAAAGCAGACCAAGTTGATGCACAACAA                         CTCATGAGAGTCTATGGAGCACTGCTATGGTCGCTTGGGAAAGTTCTGAAC
genomic: ATAAAATACGTATAGTTCTGAACAAAGCAGACCAAGTTGATGCACAACAAgtgagtgtta ... ttatcctcagCTCATGAGAGTCTATGGAGCACTGCTATGGTCGCTTGGGAAAGTTCTGAAC
EST: gi|87022084|gb|CI259156.1|CI259156
EST:     TATAGTTCTGAACAAAGCAGACCAAGTTGATGCACAACAA                         CTCATGAGAGTCTATGGAGCACTGCTATGGTCGCTTGGGAAAGTTCTGAAC
genomic: TATAGTTCTGAACAAAGCAGACCAAGTTGATGCACAACAAgtgagtgtta ... ttatcctcagCTCATGAGAGTCTATGGAGCACTGCTATGGTCGCTTGGGAAAGTTCTGAAC
EST: gi|66928201|gb|CX115049.1|CX115049
EST:     ATAAAATACGTATAGTTCTGAACAAAGCAGACCAAGTTGATGCACAACAA                         CTCATGAGAGTCTATGGAGCACTGCTATGGTCGCTTGGGAAAGTTCTGAAC
genomic: ATAAAATACGTATAGTTCTGAACAAAGCAGACCAAGTTGATGCACAACAAgtgagtgtta ... ttatcctcagCTCATGAGAGTCTATGGAGCACTGCTATGGTCGCTTGGGAAAGTTCTGAAC

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: 71 (upstream exon), 74 (downstream exon)
Score: 65

CATCAGTGATGAGTTCAAGCGTGTAATTGGGTCACTCAAAGGGCATGATGATAAAATACGTATAGTTCTGAACAAAGCAGACCAAGTTGATGCACAACAAgtgagtgtta ... ttatcctcagCTCATGAGAGTCTATGGAGCACTGCTATGGTCGCTTGGGAAAGTTCTGAACACACCAGAAGTCATGCGTGTGTACATAGG




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