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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGATTGGTGCTGGTTTGGAATCCATGTCCATAAATTCCATTGCTTGGGAAGGACAAGTTAACCCAAAAgtaaggattataaccacaatgtaaattgaaatagttttttcctttttacacaaaaaggaaactctcgtaacacatttttctctctccttgcag

Basic information

species Zea mays
transcript GRMZM5G848768_T04
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G848768_T02 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os02g57260.1 (Oryza sativa), 5'ss of exon 6
GGATTGGTGCTGGTTTGGAATCCATGTCCATAAATTCCATTGCTTGGGAAGGACAAGTTAACCCAAAAgtaaggattataaccacaatgtaaattgaaatagttttttcctttttacacaaaaaggaaactctcgtaacacatttttctctctccttgcag
|||||||||| ||  |||||||||||||  ||||| | || | ||||||||||||||| ||||| |||||| | ||| ||    ||    |   |    |   ||| |  | ||  |     | |      || |||||||    | || | |        
GGATTGGTGCAGGCCTGGAATCCATGTCAGTAAATGCTATGGGTTGGGAAGGACAAGTAAACCCTAAAgtatgaattctatgagcaccagagcatcctctgtatttctgttgttctctggtgatg-----ccttgtaacaccacgtactttgtag------
















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|213184067|gb|FM191388.1|FM191388
EST:     AATCCATGTCCATAAATTCCATTGCTTGGGAAGGACAAGTTAACCCAAAA                         ATAAGCGCATTCCAGAAAGCACAGGATTGTCTTCTGCCCATGGGAATTACG
genomic: AATCCATGTCCATAAATTCCATTGCTTGGGAAGGACAAGTTAACCCAAAAgtaaggatta ... ctccttgcagATAAGCGCATTCCAGAAAGCACAGGATTGTCTTCTGCCCATGGGAATTACT
EST: gi|60672291|gb|DN475055.1|DN475055
EST:     AATCCATGTCCATAAATTCCATTGCTTGGGAAGGACAAGTTAACCCAAAA                         ATAAGCGCATTCCAGAAAGCACAGGATTGTCTTCTGCCCATGGGAATTACG
genomic: AATCCATGTCCATAAATTCCATTGCTTGGGAAGGACAAGTTAACCCAAAAgtaaggatta ... ctccttgcagATAAGCGCATTCCAGAAAGCACAGGATTGTCTTCTGCCCATGGGAATTACT
EST: gi|148952059|gb|EC897848.2|EC897848
EST:     AATCCATGTCCATAAATTCCATTGCTTGGGAAGGACAAGTTAACCCAAAA                         ATAAGCGCATTCCAGAAAGCACAGGATTGTCTTCTGCCCATGGGAATTACT
genomic: AATCCATGTCCATAAATTCCATTGCTTGGGAAGGACAAGTTAACCCAAAAgtaaggatta ... ctccttgcagATAAGCGCATTCCAGAAAGCACAGGATTGTCTTCTGCCCATGGGAATTACT
EST: gi|32859848|gb|CD999529.1|CD999529
EST:     AATCCATGTCCATAAATTCCATTGCTTGGGAAGGACAAGTTAACCCAAAA                         ATAAGCGCATTCCAGAAAGCACAGGATTGTCTTCTGCCCATGGGAATTACG
genomic: AATCCATGTCCATAAATTCCATTGCTTGGGAAGGACAAGTTAACCCAAAAgtaaggatta ... ctccttgcagATAAGCGCATTCCAGAAAGCACAGGATTGTCTTCTGCCCATGGGAATTACT
EST: gi|6012216|gb|AW061758.1|AW061758
EST:     AATCCATGTCCATAAATTCCATTGCTTGGGAAGGACAAGTTAACCCAAAA                         ATAAGCGCATTCCAGAAAGCACAGGATTGTCTTCTGCCCATGGGAATTACG
genomic: AATCCATGTCCATAAATTCCATTGCTTGGGAAGGACAAGTTAACCCAAAAgtaaggatta ... ctccttgcagATAAGCGCATTCCAGAAAGCACAGGATTGTCTTCTGCCCATGGGAATTACT

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 4 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 214

GGATTGGTGCTGGTTTGGAATCCATGTCCATAAATTCCATTGCTTGGGAAGGACAAGTTAACCCAAAAgtaaggatta ... ctccttgcagATAAGCGCATTCCAGAAAGCACAGGATTGTCTTCTGCCCATGGGAATTACTTCTGAAAATGTTGCCCATCGATATGGTGTAACCAGGCAAGAGCAAGATC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 844

GGATTGGTGCTGGTTTGGAATCCATGTCCATAAATTCCATTGCTTGGGAAGGACAAGTTAACCCAAAAgtaaggatta ... ctccttgcagATAAGCGCATTCCAGAAAGCACAGGATTGTCTTCTGCCCATGGGAATTACTTCTGAAAATGTTGCCCATCGATATGGTGTAACCAGGCAAGAGCAAGATC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 593

GGATTGGTGCTGGTTTGGAATCCATGTCCATAAATTCCATTGCTTGGGAAGGACAAGTTAACCCAAAAgtaaggatta ... ctccttgcagATAAGCGCATTCCAGAAAGCACAGGATTGTCTTCTGCCCATGGGAATTACTTCTGAAAATGTTGCCCATCGATATGGTGTAACCAGGCAAGAGCAAGATC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 472

GGATTGGTGCTGGTTTGGAATCCATGTCCATAAATTCCATTGCTTGGGAAGGACAAGTTAACCCAAAAgtaaggatta ... ctccttgcagATAAGCGCATTCCAGAAAGCACAGGATTGTCTTCTGCCCATGGGAATTACTTCTGAAAATGTTGCCCATCGATATGGTGTAACCAGGCAAGAGCAAGATC