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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGCAAGCCATCATCTTCGCCTTATAGGTTTCAAGCCATTGGATTGCTTGAAAGATTACCATAACTTAAGACCATCGACATTTATTTATCCGAGTGATGAGgtattgtgttcttctgggattgcgtcagcgtccaactgtagttttctgctgtactgcagctatccacttaattcggaggctgagaatgtcgttatttttc...

Basic information

species Zea mays
transcript GRMZM2G414496_T07
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G414496_T07 (Zea mays), 5'ss of exon 11
lower sequence: LOC_Os07g08729.1 (Oryza sativa), 5'ss of exon 12
TGCAAGCCATCATCTTCGCCTTATAGGTTTCAAGCCATTGGATTGCTTGAAAGATTACCATAACTTAAGACCATCGACATTTATTTATCCGAGTGATGAGgtattg-tgttcttctgggattgcgtcagcgtccaactgtagttttctgctgtactgcagct-atccacttaattcggaggctgagaatgtcgttatttttc
| |||| |||||||| |||||| |||| ||||||||| |||| | | | |||||||| || ||||||||||| || ||||||||||| || |||||||||||| |    ||  |    |      | | | || | ||  ||         | || ||  |  |||||     |   |  |||| | ||  ||   |     
TTCAAGTCATCATCTACGCCTTTTAGGATTCAAGCCACTGGACTACCTTAAAGATTATCACAACTTAAGACCGTCAACATTTATTTACCCCAGTGATGAGgtaataacattacttcatgtacttcttaacttcaatcttgaggccctcttggcacagctccggatccaagatttcttggagctgggtattccgagctcca--

upper sequence: GRMZM2G414496_T07 (Zea mays), 5'ss of exon 11
lower sequence: Vv05s0062g01170.t01 (Vitis vinifera), 5'ss of exon 12
TGCAAGCCATCATCTTCGCCTTATAGGTTTCAAGCCATTGGATTGCTTGAAAGATTACCATAACTTAAGACCATCGACATTTATTTATCCGAGTGATGAGgt-attgtg--ttcttctgggattgcgtcagcgtccaactgtagttttctgctgtactgcagctatccacttaattcggaggctgagaatgtcgttatttttc
| |||     |||||||||||| |||| ||||| || |||  |||||| ||||||||||| ||||| || ||||| |||||  ||| ||| | |||  |||| | | ||  ||  | | |  |||| ||    |   | | || |||| | |     | ||   ||| |    | |     | ||  || ||  ||  |    
TTCAACTGGACATCTTCGCCTTCTAGGATTCAAACCTTTGAGTTGCTTAAAAGATTACCACAACTTGAGGCCATCAACATTCGTTTTTCCTACTGACAAGgttactctgacttgcttttgttttgcttcttgttttcattctactttttttccccctttcaaggatctatcacaatattgagttgctaaggtatttgctg---
















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|32931709|gb|CF036521.1|CF036521
EST:     AAGATTACCATAACTTAAGACCATCGACATTTATTTATCCGAGTGATGAG                         CGTATATTTGGAAGCACCTGTGTTTTCGTTGCTTTACATAGCTCAATGTTA
genomic: AAGATTACCATAACTTAAGACCATCGACATTTATTTATCCGAGTGATGAGgtattgtgtt ... tctgatgcagCGTATATTTGGAAGCACCTGTGTTTTCGTTGCTTTACATAGCTCAATGTTA
EST: gi|76285513|gb|DV025081.1|DV025081
EST:     AAGATTACCATAACTTAAGACCATCGACATTTATTTATCCGAGTGATGAG                         CGTATATTTGGAAGCACCTGTGTTTTCGTTGCTTTACATAGCTCAATGTTA
genomic: AAGATTACCATAACTTAAGACCATCGACATTTATTTATCCGAGTGATGAGgtattgtgtt ... tctgatgcagCGTATATTTGGAAGCACCTGTGTTTTCGTTGCTTTACATAGCTCAATGTTA
EST: gi|32935327|gb|CF040139.1|CF040139
EST:     AAGATTACCATAACTTAAGACCATCGACATTTATTTATCCGAGTGATGAG                         CGTATATTTGGAAGCACCTGTGTTTTCGTTGCTTTACATAGCTCAATGTTA
genomic: AAGATTACCATAACTTAAGACCATCGACATTTATTTATCCGAGTGATGAGgtattgtgtt ... tctgatgcagCGTATATTTGGAAGCACCTGTGTTTTCGTTGCTTTACATAGCTCAATGTTA

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: 507

TGCAAGCCATCATCTTCGCCTTATAGGTTTCAAGCCATTGGATTGCTTGAAAGATTACCATAACTTAAGACCATCGACATTTATTTATCCGAGTGATGAGgtattgtgtt ... tctgatgcagCGTATATTTGGAAGCACCTGTGTTTTCGTTGCTTTACATAGCTCAATGTTACGTCTTGGAAG


Block sizes: 49 (upstream exon), 43 (downstream exon)
Score: 68

TGCAAGCCATCATCTTCGCCTTATAGGTTTCAAGCCATTGGATTGCTTGAAAGATTACCATAACTTAAGACCATCGACATTTATTTATCCGAGTGATGAGgtattgtgtt ... tctgatgcagCGTATATTTGGAAGCACCTGTGTTTTCGTTGCTTTACATAGCTCAATGTTACGTCTTGGAAG


Block sizes: 44 (upstream exon), 48 (downstream exon)
Score: 94

TGCAAGCCATCATCTTCGCCTTATAGGTTTCAAGCCATTGGATTGCTTGAAAGATTACCATAACTTAAGACCATCGACATTTATTTATCCGAGTGATGAGgtattgtgtt ... tctgatgcagCGTATATTTGGAAGCACCTGTGTTTTCGTTGCTTTACATAGCTCAATGTTACGTCTTGGAAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 120

TGCAAGCCATCATCTTCGCCTTATAGGTTTCAAGCCATTGGATTGCTTGAAAGATTACCATAACTTAAGACCATCGACATTTATTTATCCGAGTGATGAGgtattgtgtt ... tctgatgcagCGTATATTTGGAAGCACCTGTGTTTTCGTTGCTTTACATAGCTCAATGTTACGTCTTGGAAG