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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCAACTCAGTACGGGAAGAGCTAATCTTCCTGCACTACAGCCACCGGGATCAGTTGATGGTTTTGAAATGTTCGGGTTGCTGTCACCGGCAATAGTTCAGgtgaggaaagtattcacttgaccgcattctgaaacacactacacctcaagaaatggggaaaaaaagaagaaacactgaagcacaccaatgccatgagcag...

Basic information

species Zea mays
transcript GRMZM2G140524_T02
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G140524_T02 (Zea mays), 5'ss of exon 12
lower sequence: LOC_Os05g10770.1 (Oryza sativa), 5'ss of exon 11
GCAACTCAGTACGGGAAGAGCTAATCTTCCTGCACTACAGCCACCGGGATCAGTTGATGGTTTTGAAATGTTCGGGTTGCTGTCACCGGCAATAGTTCAGgtgaggaaagtat-tcacttgaccgcattctgaaacacactacacctcaagaaatggggaaaaaaagaagaaacactgaagcacaccaatgccatgagcag
|||||| | || ||||| | | ||||||||| || | ||||| || ||||||||||||||| |||||||||| || ||  | |||||  ||||||||||||||||  |   || ||   |  || |||  |  | | |   |  |||  |        |  |          | | |   |            || ||   
GCAACTTAATATGGGAAAATCAAATCTTCCTACATTGCAGCCTCCAGGATCAGTTGATGGTCTTGAAATGTTTGGTTTATTATCACCACCAATAGTTCAGgtgagacattaatgtctggtatcctcatgattgatctc-taaggcctgtattggcattgcgaggccctttttataatagtgatttatgcacttataagtga
















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|37389000|gb|CF631716.1|CF631716
EST:     AAATGTTCGGGTNGCTGTCACCGGCAATAGTTCAG                         GCAATCGAGGCACGGGATAGAGATCGCATCTGCACAGAGTACTGGAGATCC
genomic: AAATGTTCGGGTTGCTGTCACCGGCAATAGTTCAGgtgaggaaag ... ttcatcccagGCAATCGAGGCACGGGATAGAGATCGCATCTGCACAGAGTACTGGAGATCC
EST: gi|211431329|gb|FL160081.1|FL160081
EST:     CAGTTGATGGTTTTGAAATGTTCGGGTTGCTGTCACCGGCAATAGTTCAG                         GCAATCGAGGCACGGGATAGAGATCGCATCTGCACAGAGTACTGGAGATCC
genomic: CAGTTGATGGTTTTGAAATGTTCGGGTTGCTGTCACCGGCAATAGTTCAGgtgaggaaag ... ttcatcccagGCAATCGAGGCACGGGATAGAGATCGCATCTGCACAGAGTACTGGAGATCC
EST: gi|74239883|gb|DT647797.1|DT647797
EST:     CAGTTGATGGTTTTGAAATGTTCCGGTTGCTGTCACCGGCAATTGTTCAG                         GCAATCGAGGCACGGGATAGAGATCGCATCTGCACAGAGTACTGGAGATCC
genomic: CAGTTGATGGTTTTGAAATGTTCGGGTTGCTGTCACCGGCAATAGTTCAGgtgaggaaag ... ttcatcccagGCAATCGAGGCACGGGATAGAGATCGCATCTGCACAGAGTACTGGAGATCC
EST: gi|22819921|gb|BU500011.1|BU500011
EST:     CAGTTGATGGTTTTGAAATGTTCGGGTTGCTGTCACCGGCAATAGTTCAG                         GCAATCGAGGCACGGGATAGAGATCGCATCTGCACAGAGTACTGGAGATCC
genomic: CAGTTGATGGTTTTGAAATGTTCGGGTTGCTGTCACCGGCAATAGTTCAGgtgaggaaag ... ttcatcccagGCAATCGAGGCACGGGATAGAGATCGCATCTGCACAGAGTACTGGAGATCC
EST: gi|211431328|gb|FL160080.1|FL160080
EST:     CAGTTGATGGTTTTGAAATGTTCGGGTTGCTGTCACCGGCAATAGTTCAG                         GCAATCGAGGCACGGGATAGAGATCGCATCTGCACAGAGTACTGGAGATCC
genomic: CAGTTGATGGTTTTGAAATGTTCGGGTTGCTGTCACCGGCAATAGTTCAGgtgaggaaag ... ttcatcccagGCAATCGAGGCACGGGATAGAGATCGCATCTGCACAGAGTACTGGAGATCC
EST: gi|87156370|gb|DY401159.1|DY401159
EST:     CAGTTGATGGTTTTGAAATGTTCGGGTTGCTGTCACCGGCAATAGTTCAG                         GCAATCGAGGCACGGGATAGAGATCGCATCTGCACAGAGTACTGGAGATCC
genomic: CAGTTGATGGTTTTGAAATGTTCGGGTTGCTGTCACCGGCAATAGTTCAGgtgaggaaag ... ttcatcccagGCAATCGAGGCACGGGATAGAGATCGCATCTGCACAGAGTACTGGAGATCC
EST: gi|26560092|gb|CA832327.1|CA832327
EST:     CAGTTGATGGTTTTGAAATGTTCGGGTTGCTGTCACCGGCAATAGTTCAG                         GCAATCGAGGCACGGGATAGAGATCGCATCTGCACAGAGTACTGGAGATCC
genomic: CAGTTGATGGTTTTGAAATGTTCGGGTTGCTGTCACCGGCAATAGTTCAGgtgaggaaag ... ttcatcccagGCAATCGAGGCACGGGATAGAGATCGCATCTGCACAGAGTACTGGAGATCC
EST: gi|60355691|gb|DN222664.1|DN222664
EST:     CAGTTGATGGTTTTGAAATGTTCGGGTTGCTGTCACCGGCAATAGTTCAG                         GCAATCGAGGCACGGGATAGAGATCGCATCTGCACAGAGTACTGGAGATCC
genomic: CAGTTGATGGTTTTGAAATGTTCGGGTTGCTGTCACCGGCAATAGTTCAGgtgaggaaag ... ttcatcccagGCAATCGAGGCACGGGATAGAGATCGCATCTGCACAGAGTACTGGAGATCC

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: 46 (upstream exon), 49 (downstream exon)
Score: 95

GCAACTCAGTACGGGAAGAGCTAATCTTCCTGCACTACAGCCACCGGGATCAGTTGATGGTTTTGAAATGTTCGGGTTGCTGTCACCGGCAATAGTTCAGgtgaggaaag ... ttcatcccagGCAATCGAGGCACGGGATAGAGATCGCATCTGCACAGAGTACTGGAGATCCAGGCCTCATGTTGTCACTGAAGATCGTGCGACGGCGCCACCTCAGGCTC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 53

GCAACTCAGTACGGGAAGAGCTAATCTTCCTGCACTACAGCCACCGGGATCAGTTGATGGTTTTGAAATGTTCGGGTTGCTGTCACCGGCAATAGTTCAGgtgaggaaag ... ttcatcccagGCAATCGAGGCACGGGATAGAGATCGCATCTGCACAGAGTACTGGAGATCCAGGCCTCATGTTGTCACTGAAGATCGTGCGACGGCGCCACCTCAGGCTC


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 62

GCAACTCAGTACGGGAAGAGCTAATCTTCCTGCACTACAGCCACCGGGATCAGTTGATGGTTTTGAAATGTTCGGGTTGCTGTCACCGGCAATAGTTCAGgtgaggaaag ... ttcatcccagGCAATCGAGGCACGGGATAGAGATCGCATCTGCACAGAGTACTGGAGATCCAGGCCTCATGTTGTCACTGAAGATCGTGCGACGGCGCCACCTCAGGCTC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 60

GCAACTCAGTACGGGAAGAGCTAATCTTCCTGCACTACAGCCACCGGGATCAGTTGATGGTTTTGAAATGTTCGGGTTGCTGTCACCGGCAATAGTTCAGgtgaggaaag ... ttcatcccagGCAATCGAGGCACGGGATAGAGATCGCATCTGCACAGAGTACTGGAGATCCAGGCCTCATGTTGTCACTGAAGATCGTGCGACGGCGCCACCTCAGGCTC