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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cgcacacaaacacatgacatgacatgacatgacacaccagacttgacgctctcctgtctttatatgccggcgcggcgcgcgggcgtgcgtgcgcgcgcagATGGCGGAGGAGGAGCAGATGGCGGAGCTGGTGATGGCGCAGTGCGGGGTGCCGAGCGGCGGTGAGGGGGGCGCGTGGCCGCCGGGATTCGCGTGGGACG

Basic information

species Zea mays
transcript GRMZM2G139372_T05
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G139372_T04 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os02g02820.1 (Oryza sativa), 3'ss of exon 5
cgcacacaaacacatgacatgacatgacatg-acacaccagacttgacgctctcctgtctttatatgccggcgcggcgcgcgggc--gtgcgtgcgcgcgcagATGGCGGAGGAGGAGCAGATGGCGGAGCTGGTGATGGCGCAGTGCGG-GGTGCCGAGCGGCGGTGAGGGGGGCGCGTGGCCGCCGGGATTCGCGTGGGACG
|    |    |  |   | ||   | |  || || || | | |||  || | |   |  |  ||  |       |    | |||    |  |||   | |||||||||||||||| |||||||||||||||| || |||||||||||||| || | || ||| ||| || |  || | | ||| | || |     ||  |||  
caacgaacgccggagagcttgcggttagctgcacgcaacggcctttgcgtttt---gcatggatgggttatatagatttgtgggttgatcggtgttggtgcagATGGCGGAGGAGCAGCAGATGGCGGAGCTTGTCATGGCGCAGTGCGGCGGCGGCG-GCGCCGGGGACGACGGTGGGGGGCAGGCGTGGCCGCCGCCGGAGA
















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|149096501|gb|EE182246.2|EE182246
EST:     TGCTGGTGCCCGTCGCCGGCGGCCTCGTCGAGCTCTTCGCGGCGAGATAC                         ATGGCGGAGGAGGAGCAGATGGCGGAGCTGGTGATGGCGCAGTGCGGGGTG
genomic: TGCTGGTGCCCGTCGCCGGCGGCCTCGTCGAGCTCTTCGCGGCGAGATACgtgcgtaagc ... gcgcgcgcagATGGCGGAGGAGGAGCAGATGGCGGAGCTGGTGATGGCGCAGTGCGGGGTG
EST: gi|149099194|gb|EE185222.2|EE185222
EST:     TGCTGGTGCCCGTCGCCGGCGGCCTCGTCGAGCTCTTCGCGGCGAGATAC                         ATGGCGGAGGAGGAGCAGATGGCGGAGCTGGTGATGGCGCAGTGCGGGGTG
genomic: TGCTGGTGCCCGTCGCCGGCGGCCTCGTCGAGCTCTTCGCGGCGAGATACgtgcgtaagc ... gcgcgcgcagATGGCGGAGGAGGAGCAGATGGCGGAGCTGGTGATGGCGCAGTGCGGGGTG
EST: gi|149090656|gb|EE179979.2|EE179979
EST:     TGCTGGTGCCCGTCGCCGGCGGCCTCGTCGAGCTCTTCGCGGCGAGATAC                         ATGGCGGAGGAGGAGCAGATGGCGGAGCTGGTGATGGCGCAGTGCGGGGTG
genomic: TGCTGGTGCCCGTCGCCGGCGGCCTCGTCGAGCTCTTCGCGGCGAGATACgtgcgtaagc ... gcgcgcgcagATGGCGGAGGAGGAGCAGATGGCGGAGCTGGTGATGGCGCAGTGCGGGGTG
EST: gi|148933084|gb|EE286018.2|EE286018
EST:     TGCTGGTGCCCGTCGCCGGCGGCCTCGTCGAGCTCTTCGCGGCGAGATAC                         ATGGCGGAGGAGGAGCAGATGGCGGAGCTGGTGATGGCGCAGTGCGGGGTG
genomic: TGCTGGTGCCCGTCGCCGGCGGCCTCGTCGAGCTCTTCGCGGCGAGATACgtgcgtaagc ... gcgcgcgcagATGGCGGAGGAGGAGCAGATGGCGGAGCTGGTGATGGCGCAGTGCGGGGTG
EST: gi|149103852|gb|EE289263.2|EE289263
EST:     TGCTGGTGCCCGTCGCCGGCGGCCTCGTCGAGCTCTTCGCGGCGAGATAC                         ATGGCGGAGGAGGAGCAGATGGCGGAGCTGGTGATGGCGCAGTGCGGGGTG
genomic: TGCTGGTGCCCGTCGCCGGCGGCCTCGTCGAGCTCTTCGCGGCGAGATACgtgcgtaagc ... gcgcgcgcagATGGCGGAGGAGGAGCAGATGGCGGAGCTGGTGATGGCGCAGTGCGGGGTG
EST: gi|149073865|gb|EE162188.2|EE162188
EST:     TGCTGGTGCCCGTCGCCGGCGGCCTCGTCGAGCTCTTCGCGGCGAGATAC                         ATGGCGGAGGAGGAGCAGATGGCGGAGCTGGTGATGGCGCAGTGCGGGGTG
genomic: TGCTGGTGCCCGTCGCCGGCGGCCTCGTCGAGCTCTTCGCGGCGAGATACgtgcgtaagc ... gcgcgcgcagATGGCGGAGGAGGAGCAGATGGCGGAGCTGGTGATGGCGCAGTGCGGGGTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acgctctcctgtctttatatgccggcgcggcgcgcgggcgtgcgtgcgcgcgcagATGGCGGAGGAGGAGCAGATGGCGGAGCTGGTGATGGCGCAGTGCGGGGTGCCGAGCGGCGGTGAGGGGGGCGCGTGGCCGCCGGGATTCGCGTGGGACG
 acttgac  putative branch site (score: 4)
           tctttatat  TA-rich tract