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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AATCTGGAAAAGAGAATCCAAATGAAGATGGTCCTGAAAATAACCCTCAGTTTACTACTGTTTATGTTGGCAATCTTCCTCACGAGgtattactcttccaatagaacagctgctgtctatgtttactgtgcttgtgtttggctttctatttgctcttaccttttttttgttagctttctttttattgtctaatttgtcttattttttttcag

Basic information

species Zea mays
transcript GRMZM5G835213_T01
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G835213_T02 (Zea mays), 5'ss of exon 10
lower sequence: LOC_Os11g40510.1 (Oryza sativa), 5'ss of exon 10
AATCTGGAAAAGAGAATCCAAATGAAGATGGTCCTGAAAATAACCCTCAGTTTACTACTGTTTATGTTGGCAATCTTCCTCACGAGgtattactcttccaatagaacagctgctgtctatgtttactgtgcttgtgtttggctttctatttgctcttaccttttttttgttagctttctttttattgtctaatttgtcttattttttttcag
||  |||||| || ||| |||||||||||||||||||||| ||||| ||||  || |||||||||||||||||||||||||| || |||   |||| ||| |     | |   | ||| | | |  |||||| || ||| | | | | |     |        ||| ||      || | |||| |                          
AAGGTGGAAAGGATAATGCAAATGAAGATGGTCCTGAAAACAACCCACAGTACACGACTGTTTATGTTGGCAATCTTCCTCATGATgtaac-ctctcccatttctgaaacaaatttctttttgttttgtgct-gtattttgttgtttttccataccagtaacgtttctgcc--tcttatatttactag------------------------

upper sequence: GRMZM5G835213_T02 (Zea mays), 5'ss of exon 10
lower sequence: Vv09s0002g00880.t01 (Vitis vinifera), 5'ss of exon 10
AATCTGGAAAAGAGAATCCAAATGAAGATGGTCCTGAAAATAACCCTCAGTTTACTACTGTTTATGTTGGCAATCTTCCTCACGAGgtattactcttccaatagaacagctgctgtctatgtttactgtgcttgtgtttggctttctatttgctcttaccttttttttgttagctttctttttatt-gtctaatttgtcttattttttttcag
||  ||| |||||||   ||| | | || | |||||| || |||||||||| ||| ||||||||||| ||||||||| |||  ||||||  |  |         || |  | |  | | |  ||  | |  |||| | ||   ||   ||||  | |  | ||   |||| |   | |||||| ||  |||  | ||                
AAGATGGTAAAGAGACAGCAACTAATGAGGCTCCTGACAACAACCCTCAGTATACAACTGTTTATGTGGGCAATCTTGCTCCAGAGgtaggaaacaattcgccaaaaattttccctttttactttatttatttgtttatg--ctttggtttgg-catctcattaacttgtgaaaatcctttttgttcatctgctatgcag-------------
















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|24934275|gb|CA452493.1|CA452493
EST:     AAAATAACCCTCAGTTTACTACTGTTTATGTTGGCAATCTTCCTCACGAG                         GCTACCATGAATGATGTGCACCTGTTTTTCCATTCACTGGGGGCTGGTTCA
genomic: AAAATAACCCTCAGTTTACTACTGTTTATGTTGGCAATCTTCCTCACGAGgtattactct ... tttttttcagGCTACCATGAATGATGTGCACCTGTTTTTCCATTCACTGGGGGCTGGTTCA
EST: gi|71436375|gb|DR817425.1|DR817425
EST:     AAAATAACCCTCAGTTTACTACTGTTTATGTTGGCAATCTTCCTCACGAG                         GCTACCATGAATGATGTGCACCTGTTTTTCCATTCACTGGGGGCTGGTTCA
genomic: AAAATAACCCTCAGTTTACTACTGTTTATGTTGGCAATCTTCCTCACGAGgtattactct ... tttttttcagGCTACCATGAATGATGTGCACCTGTTTTTCCATTCACTGGGGGCTGGTTCA
EST: gi|71324258|gb|DR798829.1|DR798829
EST:     AAAATAACCCTCAGTTTACTACTGTTTATGTTGGCAATCTTCCTCACGAG                         GCTACCATGAATGATGTGCACCTGTTTTTCCATTCACTGGGGGCTGGTTCA
genomic: AAAATAACCCTCAGTTTACTACTGTTTATGTTGGCAATCTTCCTCACGAGgtattactct ... tttttttcagGCTACCATGAATGATGTGCACCTGTTTTTCCATTCACTGGGGGCTGGTTCA
EST: gi|31361403|gb|CD445760.1|CD445760
EST:     AAAATAACCCTCAGTTTACTACTGTTTATGTTGGCAATCTTCCTCACGAG                         GCTACCATGAATGATGTGCACCTGTTTTTCCATTCACTGGGGGCTGGTTCA
genomic: AAAATAACCCTCAGTTTACTACTGTTTATGTTGGCAATCTTCCTCACGAGgtattactct ... tttttttcagGCTACCATGAATGATGTGCACCTGTTTTTCCATTCACTGGGGGCTGGTTCA
EST: gi|22546594|gb|BU098905.1|BU098905
EST:     AAAATAACCCTCAGTTTACTACTGTTTATGTTGGCAATCTTCCTCACGAG                         GCTACCATGAATGATGTGCACCTGTTTTTCCATTCACTGGGGGCTGGTTCA
genomic: AAAATAACCCTCAGTTTACTACTGTTTATGTTGGCAATCTTCCTCACGAGgtattactct ... tttttttcagGCTACCATGAATGATGTGCACCTGTTTTTCCATTCACTGGGGGCTGGTTCA
EST: gi|22545671|gb|BU098030.1|BU098030
EST:     AAAATAACCCTCAGTTTACTACTGTTTATGTTGGCAATCTTCCTCACGAG                         GCTACCATGAATGATGTGCACCTGTTTTTCCATTCACTGGGGGCTGG
genomic: AAAATAACCCTCAGTTTACTACTGTTTATGTTGGCAATCTTCCTCACGAGgtattactct ... tttttttcagGCTACCATGAATGATGTGCACCTGTTTTTCCATTCACTGGGGGCTGG
EST: gi|33091883|gb|CF051877.1|CF051877
EST:     AAAATAACCCTCAGTTTACTACTGTTTATGTTGGCAATCTTCCTCACGAG                         GCTACCATGAATGATGTGCACCTGTTTTTCCATTCACTGGGGGCTGGTTCA
genomic: AAAATAACCCTCAGTTTACTACTGTTTATGTTGGCAATCTTCCTCACGAGgtattactct ... tttttttcagGCTACCATGAATGATGTGCACCTGTTTTTCCATTCACTGGGGGCTGGTTCA
EST: gi|194717059|gb|FK934212.1|FK934212
EST:     AAAATAACCCTCAGTTTACTACTGTTTATGTTGGCAATCTTCCTCACGAG                         GCTACCATGAATGATGTGCACCTGTTTTTCCATTCACTGGGGGCTGGTTCA
genomic: AAAATAACCCTCAGTTTACTACTGTTTATGTTGGCAATCTTCCTCACGAGgtattactct ... tttttttcagGCTACCATGAATGATGTGCACCTGTTTTTCCATTCACTGGGGGCTGGTTCA
EST: gi|26456698|gb|CA828281.1|CA828281
EST:     AAAATAACCCTCAGTTTACTACTGTTTATGTTGGCAATCTTCCTCACGAG                         GCTACCATGAATGATGTGCACCTGTTTTTCCATTCACTGGGGGCTGGTTCA
genomic: AAAATAACCCTCAGTTTACTACTGTTTATGTTGGCAATCTTCCTCACGAGgtattactct ... tttttttcagGCTACCATGAATGATGTGCACCTGTTTTTCCATTCACTGGGGGCTGGTTCA
EST: gi|32850339|gb|CD990020.1|CD990020
EST:     AAAATAACCCTCAGTTTACTACTGTTTATGTTGGCAATCTTCCTCACGAG                         GCTACCATGAATGATGTGCACCTGTTTTTCCATTCACTGGGGGCTGGTTCA
genomic: AAAATAACCCTCAGTTTACTACTGTTTATGTTGGCAATCTTCCTCACGAGgtattactct ... tttttttcagGCTACCATGAATGATGTGCACCTGTTTTTCCATTCACTGGGGGCTGGTTCA
EST: gi|32866442|gb|CF006124.1|CF006124
EST:     AAAATAACCCTCAGTTTACTACTGTTTATGTTGGCAATCTTCCTCACGAG                         GCTACCATGAATGATGTGCACCTGTTTTTCCATTCACTGGGGGCTGGTTCA
genomic: AAAATAACCCTCAGTTTACTACTGTTTATGTTGGCAATCTTCCTCACGAGgtattactct ... tttttttcagGCTACCATGAATGATGTGCACCTGTTTTTCCATTCACTGGGGGCTGGTTCA

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: 994

AATCTGGAAAAGAGAATCCAAATGAAGATGGTCCTGAAAATAACCCTCAGTTTACTACTGTTTATGTTGGCAATCTTCCTCACGAGgtattactct ... tttttttcagGCTACCATGAATGATGTGCACCTGTTTTTCCATTCACTGGGGGCTGGTTCAATTGAGGAAGTCCGTGTAACTCGTGATAAAGGCTTTGGCTTTGTGAGGT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 491

AATCTGGAAAAGAGAATCCAAATGAAGATGGTCCTGAAAATAACCCTCAGTTTACTACTGTTTATGTTGGCAATCTTCCTCACGAGgtattactct ... tttttttcagGCTACCATGAATGATGTGCACCTGTTTTTCCATTCACTGGGGGCTGGTTCAATTGAGGAAGTCCGTGTAACTCGTGATAAAGGCTTTGGCTTTGTGAGGT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 601

AATCTGGAAAAGAGAATCCAAATGAAGATGGTCCTGAAAATAACCCTCAGTTTACTACTGTTTATGTTGGCAATCTTCCTCACGAGgtattactct ... tttttttcagGCTACCATGAATGATGTGCACCTGTTTTTCCATTCACTGGGGGCTGGTTCAATTGAGGAAGTCCGTGTAACTCGTGATAAAGGCTTTGGCTTTGTGAGGT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 1205

AATCTGGAAAAGAGAATCCAAATGAAGATGGTCCTGAAAATAACCCTCAGTTTACTACTGTTTATGTTGGCAATCTTCCTCACGAGgtattactct ... tttttttcagGCTACCATGAATGATGTGCACCTGTTTTTCCATTCACTGGGGGCTGGTTCAATTGAGGAAGTCCGTGTAACTCGTGATAAAGGCTTTGGCTTTGTGAGGT