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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATCGATCTTCTTGGGAAGGTGGACGAGTTATTTATCGACATATATGACAGATATGAACCTACCAATGACTCATCAGCAGACAATTGTTTCATCTCAACAgtaagcattatctgacacgcacctttgatagaattttcaaatatccttatttccatttcaattaactaccttttcag

Basic information

species Zea mays
transcript GRMZM2G047431_T01
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G047431_T01 (Zea mays), 5'ss of exon 10
lower sequence: LOC_Os07g16970.2 (Oryza sativa), 5'ss of exon 10
GATCGATCTTCTTGGGAAGGTGGACGAGTTATTTATCGACATATATGACAGATATGAACCTACCAATGACTCATCAGCAGACAATTGTTTCATCTCAACAgtaag-catt------atctgacacgcacctttgataga---attttcaaatatccttattt-------ccatttcaattaactaccttttcag
||| || |||||||||   ||||| ||  ||||||| || | ||| ||||||| ||||||||| |||||| ||||  |||||||||||||||||||||||||||| |||       || | |   | |  |  | ||||   ||   |||| | |   ||||        ||||| | |  | |  ||||||||
GATAGACCTTCTTGGGCCAGTGGATGAACTATTTATTGATACATACGACAGATTTGAACCTACTAATGACCCATCTTCAGACAATTGTTTCATCTCAACAgtaagtcatcgcagaaatatcaagtgtatgtaggttagacatatgaccaaaaaactgcatttgaaataaacatttaattcgatttgcttttcag
















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|22489519|gb|BU049442.1|BU049442
EST:     GATATGAACCTACCAATGACTCATCAGCAGACAATTGTTTCATCTCAACA                         AGTTATGATGCCACAACACACTTTGAGTCCACTGTTATGGATGTACTTTCC
genomic: GATATGAACCTACCAATGACTCATCAGCAGACAATTGTTTCATCTCAACAgtaagcatta ... accttttcagAGTTATGATGCCACAACACACTTTGAGTCCACTGTTATGGATGTACTTTCC
EST: gi|8551599|gb|BE128944.1|BE128944
EST:     GATATGAACCTACCAATGACTCATCAGCAGACAATTGTTTCATCTCAACA                         AGTTATGATGCCACAACACACTTTGAGTCCACTGTTATGGATGTACTTTCC
genomic: GATATGAACCTACCAATGACTCATCAGCAGACAATTGTTTCATCTCAACAgtaagcatta ... accttttcagAGTTATGATGCCACAACACACTTTGAGTCCACTGTTATGGATGTACTTTCC
EST: gi|211044538|gb|FL475091.1|FL475091
EST:     GATATGAACCTACCAATGACTCATCAGCAGACAATTGTTTCATCTCAACA                         AGTTATGATGCCACAACACACTTTGAGTCCACTGTTATGGATGTACTTTCC
genomic: GATATGAACCTACCAATGACTCATCAGCAGACAATTGTTTCATCTCAACAgtaagcatta ... accttttcagAGTTATGATGCCACAACACACTTTGAGTCCACTGTTATGGATGTACTTTCC
EST: gi|211200480|gb|FL442520.1|FL442520
EST:     GATATGAACCTACCAATGACTCATCAGCAGACAATTGTTTCATCTCAACA                         AGTTATGATGCCACAACACACTTTGAGTCCACTGTTATGGATGTACTTTCC
genomic: GATATGAACCTACCAATGACTCATCAGCAGACAATTGTTTCATCTCAACAgtaagcatta ... accttttcagAGTTATGATGCCACAACACACTTTGAGTCCACTGTTATGGATGTACTTTCC
EST: gi|4804534|gb|AI665406.2|AI665406
EST:     GATATGAACCTACCAATGACTCATCAGCAGNCAATTGTTTCATCTCAACA                         AGTTATGATGCCCCACCCCCCTTTGAGTCCCCTGTTATGGATGTACTTTCC
genomic: GATATGAACCTACCAATGACTCATCAGCAGACAATTGTTTCATCTCAACAgtaagcatta ... accttttcagAGTTATGATGCCACAACACACTTTGAGTCCACTGTTATGGATGTACTTTCC
EST: gi|32832146|gb|CD971824.1|CD971824
EST:     GATATGAACCTACCAATGACTCATCAGCAGACAATTGTTTCATCTCAACA                         AGTTATGATGCCACAACACACTTTGAGTCCACTGTTATGGATGT
genomic: GATATGAACCTACCAATGACTCATCAGCAGACAATTGTTTCATCTCAACAgtaagcatta ... accttttcagAGTTATGATGCCACAACACACTTTGAGTCCACTGTTATGGATGT
EST: gi|211340571|gb|FL245012.1|FL245012
EST:     GATATGAACCTACCAATGACTCATCAGCAGACAATTGTTTCATCTCAACA                         AGTTATGATGCCACAACACACTTTGAGTCCACTGTTATGGATGTACTTTCC
genomic: GATATGAACCTACCAATGACTCATCAGCAGACAATTGTTTCATCTCAACAgtaagcatta ... accttttcagAGTTATGATGCCACAACACACTTTGAGTCCACTGTTATGGATGTACTTTCC
EST: gi|17921693|gb|BM259344.1|BM259344
EST:     GATATGAACCTACCAATGACTCATCAGCAGACAATTGTTTCATCTCAACA                         AGTTATGATGCCACAACACACTTTGAGTCCACTGTTATGGATGTACTTTCC
genomic: GATATGAACCTACCAATGACTCATCAGCAGACAATTGTTTCATCTCAACAgtaagcatta ... accttttcagAGTTATGATGCCACAACACACTTTGAGTCCACTGTTATGGATGTACTTTCC

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), 40 (downstream exon)
Score: 42

GATCGATCTTCTTGGGAAGGTGGACGAGTTATTTATCGACATATATGACAGATATGAACCTACCAATGACTCATCAGCAGACAATTGTTTCATCTCAACAgtaagcatta ... accttttcagAGTTATGATGCCACAACACACTTTGAGTCCACTGTTATGGATGTACTTTCCCTTTACACAAAGATCACCGGAAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 64

GATCGATCTTCTTGGGAAGGTGGACGAGTTATTTATCGACATATATGACAGATATGAACCTACCAATGACTCATCAGCAGACAATTGTTTCATCTCAACAgtaagcatta ... accttttcagAGTTATGATGCCACAACACACTTTGAGTCCACTGTTATGGATGTACTTTCCCTTTACACAAAGATCACCGGAAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 93

GATCGATCTTCTTGGGAAGGTGGACGAGTTATTTATCGACATATATGACAGATATGAACCTACCAATGACTCATCAGCAGACAATTGTTTCATCTCAACAgtaagcatta ... accttttcagAGTTATGATGCCACAACACACTTTGAGTCCACTGTTATGGATGTACTTTCCCTTTACACAAAGATCACCGGAAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 184

GATCGATCTTCTTGGGAAGGTGGACGAGTTATTTATCGACATATATGACAGATATGAACCTACCAATGACTCATCAGCAGACAATTGTTTCATCTCAACAgtaagcatta ... accttttcagAGTTATGATGCCACAACACACTTTGAGTCCACTGTTATGGATGTACTTTCCCTTTACACAAAGATCACCGGAAAG