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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagattttacacttgcttgattaactttgctgtcgcctgtcatgctccatggtagctgattttaatatgttttaatattcaacttggcagTTAATTTTCCTGTGAAGAACTTGGAGTTGAAGGACTACATTCCATTACCTAAGCCGAAAGAGAATCATAAGCTACGTTCAAAGTATGACCTCATAGCAAA

Basic information

species Zea mays
transcript GRMZM2G091151_T01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G091151_T01 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os09g24250.1 (Oryza sativa), 3'ss of exon 7
gtgagattttacacttgcttgattaactttgctgtcgcctgtcatgctccatggtagctgattttaatatgttttaatattcaacttggcagTTAATTTTCCTGTGAAGAACTTGGAGTTGAAGGACTACATTCCATTACCTAAGCCGAAAGAGAATCATAAGCTACGTTCAAAGTATGACCTCATAGCAAA
|| | ||      |||| ||   | | ||   |  |  |||   | | |  |||||  |  || ||| ||||||  ||||| | |||  |||| ||||| || |||||||||||||| ||||| || ||||| |||||||||||||| |||||     | |||||||| ||||||||||| |||||||| ||
gtaaaatc-----cttgttt---tgatttaattagcctctgcagtccact-tggtacat--ttctaagatgtttacatatttatctta-cagTGAATTTCCCCGTGAAGAACTTGGAATTGAAAGATTACATCCCATTACCTAAGCCAAAAGATTCCGAGAAGCTACGCTCAAAGTATGATCTCATAGCCAA

upper sequence: GRMZM2G091151_T01 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA10G08500.2 (Glycine max), 3'ss of exon 8
gtgagattttacact-tgcttgattaactttgctgtcgcctgtcatgctccatggtagctgattttaatatgttttaatattcaact-tggcagTTAATTTTCCTGTGAAGAACTTGGAGTTGAAGGACTACATTCCATTACCTAAGCCGAAAGAGAATCATAAGCTACGTTCAAAGTATGACCTCATAGCAAA
||  || |||    |    |    |    ||  |      || ||| || |||  |  || | || |   |  |  | | || |  |    |||| || ||||||||||||||| ||||||||||||| |||||||| || || |  || ||||| ||| | ||  | ||  | || |||||  | || || ||
gtaggaatttctgttgcaatcttctgtaatttattcaagttgacat-ctgcatactt-ctaacttcaccctaatccattctttatttgcttcagTCAACTTTCCTGTGAAGAACCTGGAGTTGAAGGATTACATTCCCTTGCCAACACCAAAAGAAAATGAGAAATTGCGAACTAAATATGATTTGATTGCTAA

upper sequence: GRMZM2G091151_T01 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA13G22190.1 (Glycine max), 3'ss of exon 8
gtgagattttacact-tgcttgattaactttgctgtcgcctgtcatgctccatggtagctgattttaatatgttttaatattcaact-tggcagTTAATTTTCCTGTGAAGAACTTGGAGTTGAAGGACTACATTCCATTACCTAAGCCGAAAGAGAATCATAAGCTACGTTCAAAGTATGACCTCATAGCAAA
|| ||| |||    |    |    |    ||  |     ||| ||| || |||  |  || | || |   |     | | || |  |    |||| || ||||||||||||||| ||||||||||||| |||||||| || || |  || ||||| ||| | ||  | ||  | || |||||  | || || ||
gtaagaatttctgttgcaatcttctgtaatttattcaagctgacat-ctgcatactt-ctaacttcaccctaaaccattctttatttgcttcagTCAACTTTCCTGTGAAGAACCTGGAGTTGAAGGATTACATTCCCTTGCCAACACCAAAAGAAAATGAGAAATTGCGAACTAAATATGATTTGATTGCTAA

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|60348304|gb|DN215277.1|DN215277
EST:     GCGAAGGTTTACCAAAAATAACTTTTTTGTCGAGAAAAACCCTACTCTAG                         TTAATTTTCCTGTGAAGAACTTGGAGTTGAAGGACTACATTCCATTACCTA
genomic: GCGAAGGTTTACCAAAAATAACTTTTTTGTCGAGAAAAACCCTACTCTAGgtgagatttt ... aacttggcagTTAATTTTCCTGTGAAGAACTTGGAGTTGAAGGACTACATTCCATTACCTA
EST: gi|76927561|gb|DV171298.1|DV171298
EST:     GCGAAGGTTTACCAAAAATAACTTTTTTGTCGAGAAAAACCCTACTCTAG                         TTAATTTTCCTGTGAAGAACTTGGAGTTGAAGGACTACATTCCATTACCTA
genomic: GCGAAGGTTTACCAAAAATAACTTTTTTGTCGAGAAAAACCCTACTCTAGgtgagatttt ... aacttggcagTTAATTTTCCTGTGAAGAACTTGGAGTTGAAGGACTACATTCCATTACCTA
EST: gi|31250431|gb|CD219455.1|CD219455
EST:     GCGAAGGTTTACCAAAAATAACTTTTTTGTCGAGAAAAACCCTACTCTAG                         TTAATTTTCCTGTGAAGAACTTGGAGTTGAAGGACTACATTCCATTACCTA
genomic: GCGAAGGTTTACCAAAAATAACTTTTTTGTCGAGAAAAACCCTACTCTAGgtgagatttt ... aacttggcagTTAATTTTCCTGTGAAGAACTTGGAGTTGAAGGACTACATTCCATTACCTA
EST: gi|71434280|gb|DR815330.1|DR815330
EST:     GAAGGTTTTACCAAAAAATAACTTTTTTGTCGAGAAAAACCCTACTCTAG                         TTAATTTTCCTGTGAAGAACTTGGAGTTGAAGGACTACATTCCATTACCTA
genomic: GAAGGTTT-ACCAAAAA-TAACTTTTTTGTCGAGAAAAACCCTACTCTAGgtgagatttt ... aacttggcagTTAATTTTCCTGTGAAGAACTTGGAGTTGAAGGACTACATTCCATTACCTA
EST: gi|76927562|gb|DV171299.1|DV171299
EST:     GCGAAGGTTTACCAAAAATAACTTTTTTGTCGAGAAAA-CCCTACTCTAG                         TTAATTTTCCTGTGAAGAACTTGGAGTTGAGGGACTACATTCCATTACCTA
genomic: GCGAAGGTTTACCAAAAATAACTTTTTTGTCGAGAAAAACCCTACTCTAGgtgagatttt ... aacttggcagTTAATTTTCCTGTGAAGAACTTGGAGTTGAAGGACTACATTCCATTACCTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cctgtcatgctccatggtagctgattttaatatgttttaatattcaacttggcagTTAATTTTCCTGTGAAGAACTTGGAGTTGAAGGACTACATTCCATTACCTAAGCCGAAAGAGAATCATAAGCTACGTTCAAAGTATGACCTCATAGCAAA
                                  ttttaat  putative branch site (score: 3)
                     tgattttaatatgttt  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagattttacacttgcttgattaactttgctgtcgcctgtcatgctccatggtagctgattttaatatgttttaatattcaacttggcagTTAATTTTCCTGTGAAGAACTTGGAGTTGAAGGACTACATTCCATTACCTAAGCCGAAAGAGAATCATAAGCTACGTTCAAAGTATGACCTCATAGCAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA