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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaatttctgaagttttttttttaaaaactgtacgtattaaatcgtcaaagctcacactctggaagagcataatatgttttctgattaggatggccataattgaattacttttttttccttatttactctgctaaaaaaatcagttactgatacattttcatgaatttcagATAAACTACGCCTCTGCTCATGACAATGAAACACTATTTGATATTATTAGTCTAAAG

Basic information

species Zea mays
transcript GRMZM2G158043_T03
intron # 19
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G158043_T01 (Zea mays), 3'ss of exon 19
lower sequence: GLYMA10G34080.1 (Glycine max), 3'ss of exon 20
gtaaatttctgaagttttttttttaaaaactgtacgtattaaatcgtcaaagctcacactctggaagagcataatatgttttctgattaggatggccataattgaattacttttttttccttatttactctgctaaaaaaatcagttact-gatacattttcatgaatttcagATAAACTACGCCTCTGCTCATGACAATGAAACACTATTTGATATTATTAGTCTAAAG
||||  || |  | || | | ||    |||||| | |  |      | ||| ||             | |||  | ||| || |||  |  ||    | | || |||||    | ||        |  | ||    | | ||||  || | |  |  |||  |||  || ||||| || || |  |||||||||||||||||||| |||||||| ||| | ||  |||||
gtaagcttattcacttatatattcctcaactgttcttcctc-----ttaaatct------------aaacatgctctgtattttgagaaacatcaaga-atttaaattatcagtattgaacatcattttttgaaccagagatcatctaatcggcatctttagatgttttgcagATCAATTATGTTTCTGCTCATGACAATGAAACCCTATTTGACATTGTGAGCTTAAAG

upper sequence: GRMZM2G158043_T01 (Zea mays), 3'ss of exon 19
lower sequence: AT5G04360.1 (Arabidopsis thaliana), 3'ss of exon 20
gtaaatttctgaagttttttttttaaaaactgtacgtattaaatcgtcaaagctcacactctggaagagcataatatgttttctgattaggatggccataattgaattacttttttttccttatttactctgctaaaaaaatcagttactgatacattttcatgaatttcagATAAACTACGCCTCTGCTCATGACAATGAAACACTATTTGATATTATTAGTCTAAAG
                                                                       ||      || ||   ||  |    ||| ||| || |          ||  | | | |||||    |   |||  |||    |  |     ||  |||||||| || ||||  |||||||||||||||||||| || ||||| ||||| ||| | |||
----------------------------------------------------------------------gtatgcaacttcctttctatcactttcatcatttaagtgaaacaagcacc--aataaatctgc---gatgctca--taccagcatttccctgtgg-tttcagATTAATTACGTATCTGCTCATGACAATGAAACTCTCTTTGACATTATCAGTTTGAAG
















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|18648749|gb|BM497568.1|BM497568
EST:     GCTTCATCCCCTATAGAAACA                         ATAAACTACGCCTCTGCTCATGACAATGAAACACTATTTGATATTATTAGT
genomic: GCTTCATCCCCTATAGAAACAgtaaatttct ... tgaatttcagATAAACTACGCCTCTGCTCATGACAATGAAACACTATTTGATATTATTAGT
EST: gi|18450794|gb|BM429072.1|BM429072
EST:     CGATGGCTCACCAGTTGGCTATGCTTCATCCCCTATAGAAACA                         ATAAACTACGCCTCTGCTCATGACAATGAAACACTATTTGATATTATTAGT
genomic: CGATGGCTCACCAGTTGGCTATGCTTCATCCCCTATAGAAACAgtaaatttct ... tgaatttcagATAAACTACGCCTCTGCTCATGACAATGAAACACTATTTGATATTATTAGT
EST: gi|87152540|gb|DY397329.1|DY397329
EST:     GCACCTTCGATGGCTCACCAGTTGGCTATGCTTCATCCCCTATAGAAACA                         ATAAACTACGCCTCTGCTCATGACAATGAAACACTATTTGATATTATTAGT
genomic: GCACCTTCGATGGCTCACCAGTTGGCTATGCTTCATCCCCTATAGAAACAgtaaatttct ... tgaatttcagATAAACTACGCCTCTGCTCATGACAATGAAACACTATTTGATATTATTAGT
EST: gi|18648748|gb|BM497567.1|BM497567
EST:     GCACCTTCGATGGCTCACCAGTTGGCTATGCTTCATCCCCTATAGAAACA                         ATAAACTACGCCTCTGCTCATGACAATGAAACACTATTTGATATTATTAGT
genomic: GCACCTTCGATGGCTCACCAGTTGGCTATGCTTCATCCCCTATAGAAACAgtaaatttct ... tgaatttcagATAAACTACGCCTCTGCTCATGACAATGAAACACTATTTGATATTATTAGT
EST: gi|60396203|gb|DN229072.1|DN229072
EST:     GCACCTTCGATGGCTCACCAGTTGGCTATGCTTCATCCCCTATAGAAACA                         ATAAACTACGCCTCTGCTCATGACAATGAAACACTATTTGATATTATTAGT
genomic: GCACCTTCGATGGCTCACCAGTTGGCTATGCTTCATCCCCTATAGAAACAgtaaatttct ... tgaatttcagATAAACTACGCCTCTGCTCATGACAATGAAACACTATTTGATATTATTAGT
EST: gi|31360398|gb|CD444755.1|CD444755
EST:     GCACCTTCGATGGCTCACCAGTTGGCTATGCTTCATCCCCTATAGAAACA                         ATAAACTACGCCTCTGCTCATGACAATGAAACACTATTTGATATTATTAGT
genomic: GCACCTTCGATGGCTCACCAGTTGGCTATGCTTCATCCCCTATAGAAACAgtaaatttct ... tgaatttcagATAAACTACGCCTCTGCTCATGACAATGAAACACTATTTGATATTATTAGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tccttatttactctgctaaaaaaatcagttactgatacattttcatgaatttcagATAAACTACGCCTCTGCTCATGACAATGAAACACTATTTGATATTATTAGTCTAAAG
                             tactgat  putative branch site (score: 2)
                                       ttttcat  putative PPT
                taaaaaaatcagtta  TA-rich tract