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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgaatatcagaactataaccattacttttgcatgatgcattttttcatgaactaatacatttaattttccattaatatcattgtcatgtgtgcatttcagGCCATACTGGCGGTGCTACTTTCCAAACACCCAGGCTATCATATATGTTGTTGATTCAAGCGATACAGATAGGCTTGTAACAGCAAAAGAAGAATTCCAT

Basic information

species Zea mays
transcript GRMZM2G147726_T03
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G147726_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os08g15040.2 (Oryza sativa), 3'ss of exon 4
tgaatatcagaactataaccattacttttgcatga--tgcattttttcatgaactaatacatttaattttccattaatatcattgtcatgtgtgcatttc-agGCCATACTGGCGGTGCTACTTTCCAAACACCCAGGCTATCATATATGTTGTTGATTCAAGCGATACAGATAGGCTTGTAACAGCAAAAGAAGAATTCCAT
    | | ||   |  |  |  |    ||   |||  | | |  ||| |   ||||   |||   |  || |  ||    ||||  ||| |   | |||  |||||||||||| | |||||||||||||| |||||||||||||| |||||||| |||||||| |||||||||||||||||||| ||||||||||| || |||
-ctttgttaggcatggattctcttagattatttgacttccttccttttaaagactag-gcatgacacgtttctcta-cgccattaacatattcacctttttagGCCATACTGGAGATGCTACTTTCCAAATACCCAGGCTATCATTTATGTTGTCGATTCAAGTGATACAGATAGGCTTGTAACGGCAAAAGAAGAGTTTCAT

upper sequence: GRMZM2G147726_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA17G07390.1 (Glycine max), 3'ss of exon 4
----tgaatatcagaactataaccattacttttgcatgatgcattttttcatgaactaatacatttaattttccattaatatcattgtcatgtgtgcatttcagGCCATACTGGCGGTGCTACTTTCCAAACACCCAGGCTATCATATATGTTGTTGATTCAAGCGATACAGATAGGCTTGTAACAGCAAAAGAAGAATTCCAT
    |   |||      ||||    |||    |    |||| | | |    | |  |    || ||  ||||   || || |  ||    | ||| |||   |||||||| ||| |||| ||||||||||| ||||| || || || ||||||||||||||||| ||    ||||||||||| | ||| || || || ||||||
acactttgtattgcctttatatatgttatacattatagatgtaatgtccatttatttctcccacttttttttggtttgat-tttttactttttgtccat---agGCCATATTGGAGGTGTTACTTTCCAAATACCCAAGCAATAATCTATGTTGTTGATTCAAGTGACGTTGATAGGCTTGTGATAGCTAAGGAGGAGTTCCAT

upper sequence: GRMZM2G147726_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA13G01270.1 (Glycine max), 3'ss of exon 4
---tgaatatcagaactata-accattacttttgcatgatgcattttttcatgaactaatacatttaattttccattaatatcattgtcatgtgtgcatttcagGCCATACTGGCGGTGCTACTTTCCAAACACCCAGGCTATCATATATGTTGTTGATTCAAGCGATACAGATAGGCTTGTAACAGCAAAAGAAGAATTCCAT
   |   ||| |  | |||     ||   || |  |||     |   || ||   ||   || |||  || |    |  | |  ||    | ||| |||   |||||||| ||| |||| ||||||||||| || || || || || ||||||||||||||||| ||    ||||||||||| | ||| || || || ||||||
cactttgtattaccattatgtgttatagattatcgatgtaatgtcaatttattt-ctcccacttttttttgtttgattgtttttttactttttgtccat---agGCCATATTGGAGGTGTTACTTTCCAAATACTCAAGCAATAATCTATGTTGTTGATTCAAGTGACGTTGATAGGCTTGTGATAGCTAAGGAGGAGTTCCAT

upper sequence: GRMZM2G147726_T01 (Zea mays), 3'ss of exon 6
lower sequence: Vv11s0052g01720.t01 (Vitis vinifera), 3'ss of exon 5
tgaatatcagaactataaccattacttttgcatgat--gcattttttcatgaactaatacatttaattttccattaatatcattgtcatgtgtgcatttcagGCCATACTGGCGGTGCTACTTTCCAAACACCCAGGCTATCATATATGTTGTTGATTCAAGCGATACAGATAGGCTTGTAACAGCAAAAGAAGAATTCCAT
  ||| |   || | || |  |   ||  |||| ||  | |  ||| ||| ||          | ||   |   |  | |  ||    | | |      ||||||||| ||| | ||||| |||||||| || || || || |||||||||||||||||||| ||||| |||||  | |||| ||| ||||| || || |||
-caatgtttcaatt-tacctttcttttgggcataatttgtaagtttgcatcaagggcacaggatcatcagctgcttgtttggtttatgttttttgggcacagGCCATATTGGAGATGCTATTTTCCAAATACTCAAGCCATAATATATGTTGTTGATTCAAGTGATACTGATAGATTGGTAATAGCTAAAGATGAGTTTCAT

upper sequence: GRMZM2G147726_T01 (Zea mays), 3'ss of exon 6
lower sequence: EFJ37645 (Selaginella moellendorffii), 3'ss of exon 4
tgaatatcagaactataaccattacttttgcatgatgcattttttcatgaactaatacatttaattttccattaatatcattgtcatgtgtgcat--ttcagGCCATACTGGCGGTGCTACTTTCCAAACACCCAGGCTATCATATATGTTGTTGATTCAAGCGATACAGATAGGCTTGTAACAGCAAAAGAAGAATTCCAT
                                   ||  |  |  |    | |  | | |||   |||| |  | | |  ||  |       |||  ||||| || |||||| | ||||||||||||||||| |||||| | || || ||||||||||| |  || || || ||  | | ||| ||||| || ||| |||| 
----------------------------------gtgagtgatcgcggtcattttttcttttg--tttcaaacactttggtttgctgacactcatcattcagACCTTACTGGAGATGCTACTTTCCAAACACACAGGCTGTGATTTACGTTGTTGATTCGACTGACACGGAAAGAATGGCAACTGCAAAGGACGAACTCCAC

upper sequence: GRMZM2G147726_T01 (Zea mays), 3'ss of exon 6
lower sequence: EFJ14920 (Selaginella moellendorffii), 3'ss of exon 4
tgaatatcagaactataaccattacttttgcatgatgcattttttcatgaactaatacatttaattttccattaatatcattgtcatgtgtgcat--ttcagGCCATACTGGCGGTGCTACTTTCCAAACACCCAGGCTATCATATATGTTGTTGATTCAAGCGATACAGATAGGCTTGTAACAGCAAAAGAAGAATTCCAT
                                                     | ||  |||  ||| | |  | | |  ||  |       |||  ||||| || |||||| | ||||||||||||||||| |||||| | || || ||||||||||| |  || || || ||  | | ||| ||||| || ||| |||| 
--------------------------------------------------gtgagtatcttttgttt-caaacactttggtttgctgacactcatcattcagACCTTACTGGAGATGCTACTTTCCAAACACACAGGCTGTGATTTACGTTGTTGATTCGACTGACACGGAAAGAATGGCAACTGCAAAGGACGAACTCCAC

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|211217104|gb|FL383487.1|FL383487
EST:     TACTCTGTGGTCAAACAAGCATCAG                         GCCATACTGGCGGTGCTACTTTCCAAACACCCAGGCTATCATATATGTTGT
genomic: TACTCTGTGGTCAAACAAGCATCAGgtaccggctc ... tgcatttcagGCCATACTGGCGGTGCTACTTTCCAAACACCCAGGCTATCATATATGTTGT
EST: gi|60396369|gb|DN229238.1|DN229238
EST:     GTGGTCAAACAAGCATCAG                         GCCATACTGGCGGTGCTACTTTCCAAACACCCAGGCTATCATATATGTTGT
genomic: GTGGTCAAACAAGCATCAGgtaccggctc ... tgcatttcagGCCATACTGGCGGTGCTACTTTCCAAACACCCAGGCTATCATATATGTTGT
EST: gi|32945768|gb|CF050587.1|CF050587
EST:     GTGGTCAAACAAGCATCAG                         GCCATACTGGCGGTGCTACTTTCCAAACACCCAGG-TNATCATATATGTTG
genomic: GTGGTCAAACAAGCATCAGgtaccggctc ... tgcatttcagGCCATACTGGCGGTGCTACTTTCCAAACACCCAGGCT-ATCATATATGTTG
EST: gi|31611779|gb|CD568401.1|CD568401
EST:     AACAAGCATCAG                         GCCATACTGGCGNG-GCTACTTTCCAAACACCCAGGCTATCATATATGTTG
genomic: AACAAGCATCAGgtaccggctc ... tgcatttcagGCCATACTGGCG-GTGCTACTTTCCAAACACCCAGGCTATCATATATGTTG
EST: gi|6994080|gb|AW453294.1|AW453294
EST:     GTGGTCAAACAAGCATCAG                         GCCATACTGGCGGTGCTACTTTCCAAACACTCAGGCTATCATATATGTTGT
genomic: GTGGTCAAACAAGCATCAGgtaccggctc ... tgcatttcagGCCATACTGGCGGTGCTACTTTCCAAACACCCAGGCTATCATATATGTTGT
EST: gi|71426509|gb|DR807559.1|DR807559
EST:     GTGGTCAAACAAGCATCAG                         GCCATACTGGCGGTGCTACTTTCCAAACACCCAGGCTATCATATATGTTGT
genomic: GTGGTCAAACAAGCATCAGgtaccggctc ... tgcatttcagGCCATACTGGCGGTGCTACTTTCCAAACACCCAGGCTATCATATATGTTGT
EST: gi|211068733|gb|FL060710.1|FL060710
EST:     GTGGTCAAACAAGCATCAG                         GCCATACTGGCGGTGCTACTTTCCAAACACTCAGGCTATCATATATGTTGT
genomic: GTGGTCAAACAAGCATCAGgtaccggctc ... tgcatttcagGCCATACTGGCGGTGCTACTTTCCAAACACCCAGGCTATCATATATGTTGT
EST: gi|211301270|gb|FL181609.1|FL181609
EST:     TACTCTGTGGTCAAACAAGCATCAG                         GCCATACTGGCGGTGCTACTTTCCAAACACCCAGGCTATCATATATGTTGT
genomic: TACTCTGTGGTCAAACAAGCATCAGgtaccggctc ... tgcatttcagGCCATACTGGCGGTGCTACTTTCCAAACACCCAGGCTATCATATATGTTGT
EST: gi|71775316|gb|DR973194.1|DR973194
EST:     GTGGTCAAACAAGCATCAG                         GCCATACTGGCGGTGCTACTTTCCAAACACCCAGGCTATCATATATGTTGT
genomic: GTGGTCAAACAAGCATCAGgtaccggctc ... tgcatttcagGCCATACTGGCGGTGCTACTTTCCAAACACCCAGGCTATCATATATGTTGT
EST: gi|78110076|gb|DV528491.1|DV528491
EST:     GTGGTCAAACAAGCATCAG                         GCCATACTGGCGGTGCTACTTTCCAAACACCCAGGCTATCATATATGTTGT
genomic: GTGGTCAAACAAGCATCAGgtaccggctc ... tgcatttcagGCCATACTGGCGGTGCTACTTTCCAAACACCCAGGCTATCATATATGTTGT
EST: gi|33092385|gb|CF052379.1|CF052379
EST:     GTGGTCAAACAAGCATCAG                         GCCATACTGGCGGTGCTACTTTCCAAACACCCAGGCTATCATATATGTTGT
genomic: GTGGTCAAACAAGCATCAGgtaccggctc ... tgcatttcagGCCATACTGGCGGTGCTACTTTCCAAACACCCAGGCTATCATATATGTTGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catgaactaatacatttaattttccattaatatcattgtcatgtgtgcatttcagGCCATACTGGCGGTGCTACTTTCCAAACACCCAGGCTATCATATATGTTGTTGATTCAAGCGATACAGATAGGCTTGTAACAGCAAAAGAAGAATTCCAT
       taatacatttaatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgaatatcagaactataaccattacttttgcatgatgcattttttcatgaactaatacatttaattttccattaatatcattgtcatgtgtgcatttcagGCCATACTGGCGGTGCTACTTTCCAAACACCCAGGCTATCATATATGTTGTTGATTCAAGCGATACAGATAGGCTTGTAACAGCAAAAGAAGAATTCCAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG