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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tatgtaattgagttagtccctgaatttccatattttaaaatttccgtccctaaaatttttcaagcagtaggatgagatttagaatatggaaaattttcagAACTCTATTGGTGAGGAGTCACATTTGGCCATGGAAACAAGTGGGCATGGAGCGCTGAAAGAGAACCACTGGCTTGATGATGGAGCATACCTTATG

Basic information

species Zea mays
transcript GRMZM2G069676_T02
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G069676_T02 (Zea mays), 3'ss of exon 12
lower sequence: LOC_Os07g26610.1 (Oryza sativa), 3'ss of exon 13
tatgtaattgagttagtccctgaatttccatattttaaaatttccgtccctaaaatttttcaagcagtaggatgagatttagaatatggaaaattttcagAACTCTATTGGTGAGGAGTCACATTTGGCCATGGAAACAAGTGGGCATGGAGCGCTGAAAGAGAACCACTGGCTTGATGATGGAGCATACCTTATG
  |    |||   |  |     ||||   ||  | |  || ||   ||  |   |  |  |    | ||  |||  | | |      |  ||  ||||||||  |||||||||||||||||||||| || |||||||||||||| |||||||| ||||||||||| |||||||| |||||||| ||||| ||||||
-gttagtttgtactgattgtataattcagattgtcttgaaatttgttctatttcacctggctg--aataaaatgtaagtcattcctggtcaatctttcagAATACTATTGGTGAGGAGTCACATTTAGCTATGGAAACAAGTGGCCATGGAGCACTGAAAGAGAATCACTGGCTCGATGATGGTGCATATCTTATG

upper sequence: GRMZM2G069676_T02 (Zea mays), 3'ss of exon 12
lower sequence: GLYMA10G35490.2 (Glycine max), 3'ss of exon 12
------tatgtaattgagttagtccctgaatttccatattttaaaatttccgtccctaaaatttttcaagcagtaggatgagatttagaatatggaaaattttcagAACTCTATTGGTGAGGAGTCACATTTGGCCATGGAAACAAGTGGGCATGGAGCGCTGAAAGAGAACCACTGGCTTGATGATGGAGCATACCTTATG
      |    |||  | |||       | ||| |   |||| || ||    |   || ||| |   ||| |      | |  ||| |||     |    |  ||||| |||||||| ||||||||||||||||| || ||||| ||||| |||||||| || || || || || |||||||||||||| |||||||| |||
gaagcattctaaatcaaattatatatatagtttac---ttttgaatttcatatttttacaatat---aagtacatatttaacttttggaagcaatattgctgacagAATTCTATTGGCGAGGAGTCACATTTGGCAATTGAAACTAGTGGACATGGAGCTCTCAAGGAAAATCATTGGCTTGATGATGGTGCATACCTAATG

upper sequence: GRMZM2G069676_T02 (Zea mays), 3'ss of exon 12
lower sequence: GLYMA20G32030.1 (Glycine max), 3'ss of exon 12
tatgtaattgagttagtccctgaatttccatattttaaaatttccgtccctaaaatttttcaagcagtaggatgagatttagaatatggaa--aatttt-----cagAACTCTATTGGTGAGGAGTCACATTTGGCCATGGAAACAAGTGGGCATGGAGCGCTGAAAGAGAACCACTGGCTTGATGATGGAGCATACCTTATG
        |   ||  ||  |  || |  |||| |    | ||  |    | | |||||         || |  | |||||   | |||||  ||| ||     ||||| |||||||||||||||||||||||||| || ||||| ||||| |||||||| || || || || || |||||||||||||| |||||||| |||
-------cttgtttcttctatatatatatatatatacttacttttgaatttcatattttcaccatgtaagtaaaatatttaacttttggaagcaatattgctgacagAATTCTATTGGTGAGGAGTCACATTTGGCAATTGAAACTAGTGGACATGGAGCTCTCAAGGAAAATCATTGGCTTGATGATGGCGCATACCTAATG

upper sequence: GRMZM2G069676_T02 (Zea mays), 3'ss of exon 12
lower sequence: Vv13s0019g04370.t01 (Vitis vinifera), 3'ss of exon 13
tatgtaattgagttagtccctgaatttccatattttaaaatttccgtccctaaaatttttcaagcagtaggatgagatttagaatatggaaaatttt--cagAACTCTATTGGTGAGGAGTCACATTTGGCCATGGAAACAAGTGGGCATGGAGCGCTGAAAGAGAACCACTGGCTTGATGATGGAGCATACCTTATG
  | |||   |  |  | |||       | |   |||  |||        |    ||   |       |  ||   |  |  |  |   |   |  |  ||||| ||| ||||||||||||||||| |||| || || || ||||| |||||||| || || ||||| ||||||||||||||||| |||||||| |||
--tataaacaatcttcttccttgtcacactttggttactattctgcattttgggtttccactgctgagaatattttaactgaagcagtaatgttgctgacagAATTCTGTTGGTGAGGAGTCACATCTGGCTATTGAGACTAGTGGCCATGGAGCTCTCAAGGAGAATCACTGGCTTGATGATGGTGCATACCTCATG

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|211441851|gb|FL182588.1|FL182588
EST:     ACCGTTTCAAACGAGGGTACAAGAATGTAATAGACGAGGCTATTCGTCTG                         AACTCTATTGGTGAGGAGTCACATTTGGCCATGGAAACAAGTGGGCATGGA
genomic: ACCGTTTCAAACGAGGGTACAAGAATGTAATAGACGAGGCTATTCGTCTGgttagtttac ... aaattttcagAACTCTATTGGTGAGGAGTCACATTTGGCCATGGAAACAAGTGGGCATGGA
EST: gi|60341753|gb|DN208726.1|DN208726
EST:     ACCGTTTCAAACGAGGGTACAAGAATGTAATAGACGAGGCTATTCGTCTG                         AACTCTATTGGTGAGGAGTCACATTTGGCCATGGAAACAAGTGGGCATGGA
genomic: ACCGTTTCAAACGAGGGTACAAGAATGTAATAGACGAGGCTATTCGTCTGgttagtttac ... aaattttcagAACTCTATTGGTGAGGAGTCACATTTGGCCATGGAAACAAGTGGGCATGGA
EST: gi|20512826|gb|BQ280024.1|BQ280024
EST:     ACCGTTTCAAACGAGGGTACAAGAATGTAAGAGACGAGGCTATTCGTCTG                         AACTCTATTGGTGAGGAGTCACATTTGGCCATGGAAACAAGTGGGCATGGA
genomic: ACCGTTTCAAACGAGGGTACAAGAATGTAATAGACGAGGCTATTCGTCTGgttagtttac ... aaattttcagAACTCTATTGGTGAGGAGTCACATTTGGCCATGGAAACAAGTGGGCATGGA
EST: gi|32928442|gb|CF033254.1|CF033254
EST:     ACAAGAATGTAATAGACGAGGCTATTCGTCTG                         AACTCTATTGGTGAGGAGTCACATTTGGCCATGGAAACAAGTGCGCATGGA
genomic: ACAAGAATGTAATAGACGAGGCTATTCGTCTGgttagtttac ... aaattttcagAACTCTATTGGTGAGGAGTCACATTTGGCCATGGAAACAAGTGGGCATGGA
EST: gi|32928208|gb|CF033020.1|CF033020
EST:     ACAAGAATGTAATAGACGAGGCTATTCGTCTG                         AACTCTATTGGTGAGGAGTCACATTTGGCCATGGAAACAAGTGGGCATGGA
genomic: ACAAGAATGTAATAGACGAGGCTATTCGTCTGgttagtttac ... aaattttcagAACTCTATTGGTGAGGAGTCACATTTGGCCATGGAAACAAGTGGGCATGGA
EST: gi|32929540|gb|CF034352.1|CF034352
EST:     ACAAGAATGTAATAGACGAGGCTATTCGTCTG                         AACTCTATTGGTGAGGAGTCACATTTGGCCATGGAAACAAGTGGGCATGGA
genomic: ACAAGAATGTAATAGACGAGGCTATTCGTCTGgttagtttac ... aaattttcagAACTCTATTGGTGAGGAGTCACATTTGGCCATGGAAACAAGTGGGCATGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtccctaaaatttttcaagcagtaggatgagatttagaatatggaaaattttcagAACTCTATTGGTGAGGAGTCACATTTGGCCATGGAAACAAGTGGGCATGGAGCGCTGAAAGAGAACCACTGGCTTGATGATGGAGCATACCTTATG
  ccctaaa  putative branch site (score: 3)
                                                ttttc  putative PPT
                               atttagaatatggaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tatgtaattgagttagtccctgaatttccatattttaaaatttccgtccctaaaatttttcaagcagtaggatgagatttagaatatggaaaattttcagAACTCTATTGGTGAGGAGTCACATTTGGCCATGGAAACAAGTGGGCATGGAGCGCTGAAAGAGAACCACTGGCTTGATGATGGAGCATACCTTATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA