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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aggttgatgccatgcaatacttgacactggtggtataatgcaaacatgctacacacatacgtgttgcttaaccatctgtttattttatttccgctcacagGGAGAGCCAATATGCAGTTTCTACAATCGCTACGGCATGTGCAAGTTCGGTCCAAATTGCAAATTCGATCACCCAATGGGAAATGCCATGTACGGCCAGG

Basic information

species Zea mays
transcript GRMZM2G146514_T03
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G146514_T02 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os11g28270.1 (Oryza sativa), 3'ss of exon 6
aggttgatgccatgcaatacttgacactggtggtata---atgca---aacatgctacacacatacgtgttgcttaaccatctgtttattttatttccgctcacagGGAGAGCCAATATGCAGTTTCTACAATCGCTACGGCATGTGCAAGTTCGGTCCAAATTGCAAATTCGATCACCCAATGGGAAATGCCATGTACGGCCAGG
  ||| ||  ||||||||  |  | || | |   | |   || ||   || ||   | |   | | ||||||| ||| | ||||||| ||||  | | |||  ||||||||||| |||||||  |||||   |||||| ||||| |||||||| ||||| ||||||||||| ||||| |||||||||| ||  ||||| || |  |
--gtttat--catgcaatgttcaaaaccgataaaacataaatacatacaatatagaagatggacaagtgttgcctaatcctctgtttctttt--tcctgcttgcagGGAGAGCCCATATGCACATTCTATTCTCGCTATGGCATCTGCAAGTTTGGTCCGAATTGCAAATTTGATCATCCAATGGGAACTGTGATGTATGGTCTCG

upper sequence: GRMZM2G146514_T02 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA09G38650.2 (Glycine max), 3'ss of exon 6
aggttgatgccatgcaatac--ttgacactggtggtataatgcaaacatgctacacacatacgtgttgcttaaccatctgtt-tattttatttccgctcacagGGAGAGCCAATATGCAGTTTCTACAATCGCTACGGCATGTGCAAGTTCGGTCCAAATTGCAAATTCGATCACCCAATGGGAAATGCCATGTACGGCCAGG
|||  ||||  |    || |  |||    |    || |  |    ||||   |      ||| || |  |  |  |   ||| | |   ||||   |  ||||||||||||  | ||    |||||    || |||||||| ||||| || ||||||| |||||| || |||||||||||||||     ||  ||   |    
agggagatgagaatatatgcaattgtttattacagtgttctcttcacat-tgattttggtacatgctaatagaggagaggttgtgtcccatttt--cctacagGGAGAGCCCCTGTGTGTGTTCTATTCACGTTACGGCATATGCAAATTTGGTCCAAGTTGCAAGTTTGATCACCCAATGGGAGTCTTCACCTATAACATAT
















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|19770493|gb|BQ035214.1|BQ035214
EST:     TTCCTACTCCCAATTGTGCACTGAGTCCATTAGGCCTACCTTTGCGCCCG                         GGAGAGCCAATATGCAGTTTCTACAATCGCTACGGCATGTGCAAGTTCGGT
genomic: TTCCTACTCCCAATTGTGCACTGAGTCCATTAGGCCTACCTTTGCGCCCGgtaagagtta ... ccgctcacagGGAGAGCCAATATGCAGTTTCTACAATCGCTACGGCATGTGCAAGTTCGGT
EST: gi|20300460|gb|BQ163403.1|BQ163403
EST:     TTCCTACTCCCAATTGTGCACTGAGTCCATTAGGCCTACCTTTGCGCCCG                         GGAGAGCCAATATGCAGTTTCTACAATCGCTACGGCATGTGCAAGTTCGGT
genomic: TTCCTACTCCCAATTGTGCACTGAGTCCATTAGGCCTACCTTTGCGCCCGgtaagagtta ... ccgctcacagGGAGAGCCAATATGCAGTTTCTACAATCGCTACGGCATGTGCAAGTTCGGT
EST: gi|87152782|gb|DY397571.1|DY397571
EST:     CTACTCCCAATTGTGCACTGAGTCCATTAGGCCTACCTTTGCGCCCG                         GGAGAGCCAATATGCAGTTTCTACAATCGCTACGGCATGTGCAAGTTCGGT
genomic: CTACTCCCAATTGTGCACTGAGTCCATTAGGCCTACCTTTGCGCCCGgtaagagtta ... ccgctcacagGGAGAGCCAATATGCAGTTTCTACAATCGCTACGGCATGTGCAAGTTCGGT
EST: gi|16926943|gb|BM080011.1|BM080011
EST:     TTCCTACTCCCAATTGTGCACTGAGTCCATTAGGCCTACCTTTGCGCCCG                         GGAGAGCCAATATGCAGTTTCTACAATCGCTACGGCATGTGCAAGTTCGGT
genomic: TTCCTACTCCCAATTGTGCACTGAGTCCATTAGGCCTACCTTTGCGCCCGgtaagagtta ... ccgctcacagGGAGAGCCAATATGCAGTTTCTACAATCGCTACGGCATGTGCAAGTTCGGT
EST: gi|113704058|gb|EE681562.1|EE681562
EST:     TTCCTACTCCCAATTGTGCACTGAGTCCATTAGGCCTACCTTTGCGCCCG                         GGAGAGCCAATATGCAGTTTCTACAATCGCTACGGCATGTGCAAGTTCGGT
genomic: TTCCTACTCCCAATTGTGCACTGAGTCCATTAGGCCTACCTTTGCGCCCGgtaagagtta ... ccgctcacagGGAGAGCCAATATGCAGTTTCTACAATCGCTACGGCATGTGCAAGTTCGGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgctacacacatacgtgttgcttaaccatctgtttattttatttccgctcacagGGAGAGCCAATATGCAGTTTCTACAATCGCTACGGCATGTGCAAGTTCGGTCCAAATTGCAAATTCGATCACCCAATGGGAAATGCCATGTACGGCCAGG
                    gcttaac  putative branch site (score: 3)
                                 tttattttatttcc  putative PPT
                            atctgtttattttatt  TA-rich tract