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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAATTGTCATCAGATTCATCCCAGCATGTTCGTTCAGCTTTAGCCTCAGTGATTATGGGAATGGCTCCTGTACTGGGAAAGgtgatatcagtgatgcaaacatgtgtttccagaatatggtgttgacaactgttgacattccatgtaagctgatcatctcttctttggcag

Basic information

species Zea mays
transcript GRMZM2G164352_T04
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G164352_T04 (Zea mays), 5'ss of exon 7
lower sequence: GLYMA10G42250.1 (Glycine max), 5'ss of exon 7
GAATTGTCATCAGATTCATCCCAGCATGTTCGTTCAGCTTTAGCCTCAGTGATTATGGGAATGGCTCCTGTACTGGGAAAGgtgatatcagtgatgcaaacatgtgtttccag--aatatggtgttgacaactgttgacattccatgtaagctga--tcatctcttctttggcag---------
||||||||||||||||| || |||||||| || || ||||| || ||||| || |||||||||||||| ||  |||||||||   ||| ||||    | |   || | | |||  | | |  | | ||||    |  |||||   ||||   |||  |  | |     |||   |         
GAATTGTCATCAGATTCTTCTCAGCATGTCCGGTCTGCTTTGGCTTCAGTAATAATGGGAATGGCTCCAGTGTTGGGAAAGg---tataagtgtcagatatcagtttctgcagttattgttctctagacaggaatacacattatctgtatcatgaagttgtttggggcttgagggcccttgtac

upper sequence: GRMZM2G164352_T04 (Zea mays), 5'ss of exon 7
lower sequence: GLYMA20G24790.1 (Glycine max), 5'ss of exon 7
GAATTGTCATCAGATTCATCCCAGCATGTTCGTTCAGCTTTAGCCTCAGTGATTATGGGAATGGCTCCTGTACTGGGAAAGgtgatatcagtgatgcaaacatgtgtttccag--aatatggtgttgacaactgttgacattccatgtaagctgatc-----atctcttctttggcag------
||||||||||||||||| || |||||||| || || ||||| || ||||| || |||||||||||||| ||  |||||||||   ||| ||||    | |  ||| | | |||  | | |  | | ||||    |  |||||    |||   |||       |||| || |||||         
GAATTGTCATCAGATTCTTCACAGCATGTCCGGTCTGCTTTGGCTTCAGTAATAATGGGAATGGCTCCAGTGTTGGGAAAGg---tataagtgtcaaatatctgtttctgcagttattgttctctagacagaaatacacattatcggtatcatgaaggtgaaatctgttgtttggggcttgagg

upper sequence: GRMZM2G164352_T04 (Zea mays), 5'ss of exon 7
lower sequence: Vv17s0000g03870.t01 (Vitis vinifera), 5'ss of exon 8
GAATTGTCATCAGATTCATCCCAGCATGTTCGTTCAGCTTTAGCCTCAGTGATTATGGGAATGGCTCCTGTACTGGGAAAGgtga---tatcagtgatgcaaacatgtgtttccagaatatggtgttgac--aactgttgacattccatgtaagctgatcatctcttctttggcag-----
||||| ||||||||||| ||||||||||||||||| ||||| || ||||| |||||||||||||| |||||  | |||||||| |   || ||     | |   || |  ||    |   ||| | |     |||  || |  | |  | ||   || |    |  |    ||||      
GAATTATCATCAGATTCTTCCCAGCATGTTCGTTCTGCTTTGGCTTCAGTTATTATGGGAATGGCACCTGTTTTAGGAAAGgtaagggtaccatattagtatgtatataattattcaggttggaggtagttgaaccatttatttactttctagtgtggtttcatacttgcaggcaaagctg

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|87156353|gb|DY401142.1|DY401142
EST:     GTTCAGCTTTAGCCTCAGTGATTATGGGAATGGCTCCTGTACTGGGAAAG                         GATGCTACCATTGAACAGCTTGTTCCAATTTTCCTCTCTTTGTTGAAAGAC
genomic: GTTCAGCTTTAGCCTCAGTGATTATGGGAATGGCTCCTGTACTGGGAAAGgtgatatcag ... tctttggcagGATGCTACCATTGAACAGCTTGTTCCAATTTTCCTCTCTTTGTTGAAAGAC
EST: gi|67016540|gb|CO445289.1|CO445289
EST:     GTTCAGCTTTACCCTCAGTGATTATGGGAATGGCTCCTGTACTGGGAAAG                         GATGCTACCATTGAACAGCTTGTTCCAATTTTCCTCTCTTTGTTGAAAGAC
genomic: GTTCAGCTTTAGCCTCAGTGATTATGGGAATGGCTCCTGTACTGGGAAAGgtgatatcag ... tctttggcagGATGCTACCATTGAACAGCTTGTTCCAATTTTCCTCTCTTTGTTGAAAGAC
EST: gi|87157118|gb|DY401907.1|DY401907
EST:     GTTCAGCTTTAGCCTCAGTGATTATGGGAATGGCTCCTGTACTGGGAAAG                         GATGCTACCATTGAACAGCTTGTTCCAATTTTCCTCTCTTTGTTGAAAGAC
genomic: GTTCAGCTTTAGCCTCAGTGATTATGGGAATGGCTCCTGTACTGGGAAAGgtgatatcag ... tctttggcagGATGCTACCATTGAACAGCTTGTTCCAATTTTCCTCTCTTTGTTGAAAGAC
EST: gi|26558526|gb|CA830761.1|CA830761
EST:     GTTCAGCTTTAGCCTCAGTGATTATGGGAATGGCTCCTGTACTGGGAAAG                         GATGCTACCATTGAACAGCTTGTTCCAATTTTCCTCTCTTTGTTGAAAGAC
genomic: GTTCAGCTTTAGCCTCAGTGATTATGGGAATGGCTCCTGTACTGGGAAAGgtgatatcag ... tctttggcagGATGCTACCATTGAACAGCTTGTTCCAATTTTCCTCTCTTTGTTGAAAGAC
EST: gi|67017790|gb|CO446539.1|CO446539
EST:     GTTCAGCTTTAGCCTCAGTGATTATGGGAATGGCTCCTGTACTGGGAAAG                         GATGCTACCATTGAACAGCTTGTTCCAATTTTCCTCTCTTTGTTGAAAGAC
genomic: GTTCAGCTTTAGCCTCAGTGATTATGGGAATGGCTCCTGTACTGGGAAAGgtgatatcag ... tctttggcagGATGCTACCATTGAACAGCTTGTTCCAATTTTCCTCTCTTTGTTGAAAGAC
EST: gi|32933390|gb|CF038202.1|CF038202
EST:     GGGAATGGCTCCTGTACTGGGAAAG                         GATGCTACCATTGAACAGCTTGTTCCAATTTTCCTCTCTTTGTTGAAAGAC
genomic: GGGAATGGCTCCTGTACTGGGAAAGgtgatatcag ... tctttggcagGATGCTACCATTGAACAGCTTGTTCCAATTTTCCTCTCTTTGTTGAAAGAC
EST: gi|211403483|gb|FL417168.1|FL417168
EST:     GTTCAGCTTTAGCCTCAGTGATTATGGGAATGGCTCCTGTACTGGGAAAG                         GATGCTACCATTGAACAGCTTGTTCCAATTTTCCTCTCTTTGTTGAAAGAC
genomic: GTTCAGCTTTAGCCTCAGTGATTATGGGAATGGCTCCTGTACTGGGAAAGgtgatatcag ... tctttggcagGATGCTACCATTGAACAGCTTGTTCCAATTTTCCTCTCTTTGTTGAAAGAC
EST: gi|22546073|gb|BU098394.1|BU098394
EST:     GTTCAGCTTTAGCCTCAGTGATTATGGGAATGGCTCCTGTACTGGGAAAG                         GATGCTACCATTGAACAGCTTGTTCCAATTTTCCTCTCTTTGTTGAAAGAC
genomic: GTTCAGCTTTAGCCTCAGTGATTATGGGAATGGCTCCTGTACTGGGAAAGgtgatatcag ... tctttggcagGATGCTACCATTGAACAGCTTGTTCCAATTTTCCTCTCTTTGTTGAAAGAC
EST: gi|31349427|gb|CD433784.1|CD433784
EST:     GTTCAGCTTTAGCCTCAGTGATTATGGGAATGGCTCCTGTACTGGGAAAA                         GATGCTACCAT
genomic: GTTCAGCTTTAGCCTCAGTGATTATGGGAATGGCTCCTGTACTGGGAAAGgtgatatcag ... tctttggcagGATGCTACCAT
EST: gi|31356642|gb|CD440999.1|CD440999
EST:     GTTCAGCTTTAGCCTCAGTGATTATGGGAATGGCTCCTGTACTGGGAAAG                         GATGCTACCATTGAACAGCTTGT-CCAATTTTTCCTCTC
genomic: GTTCAGCTTTAGCCTCAGTGATTATGGGAATGGCTCCTGTACTGGGAAAGgtgatatcag ... tctttggcagGATGCTACCATTGAACAGCTTGTTCCAATTTT-CCTCTC
EST: gi|42491785|gb|CK700831.1|CK700831
EST:     GTTCAGCTTTAGCCTCAGTGATTATGGGAATGGCTCCTGTACTGGGAAAG                         GATGCTACCATTGAACAGCTTGTTCCAATTTTCCTCTCTTTGTTGAAAGAC
genomic: GTTCAGCTTTAGCCTCAGTGATTATGGGAATGGCTCCTGTACTGGGAAAGgtgatatcag ... tctttggcagGATGCTACCATTGAACAGCTTGTTCCAATTTTCCTCTCTTTGTTGAAAGAC
EST: gi|23357737|gb|BU645386.1|BU645386
EST:     GTTCAGCTTTAGCCTCAGTGATTATGGGAATGGCTCCTGTACTGGGAAAG                         GATGCTACCATTGAACAGCTTGTTCCAATTTTCCTCTCTTTGTTGAAAGAC
genomic: GTTCAGCTTTAGCCTCAGTGATTATGGGAATGGCTCCTGTACTGGGAAAGgtgatatcag ... tctttggcagGATGCTACCATTGAACAGCTTGTTCCAATTTTCCTCTCTTTGTTGAAAGAC
EST: gi|67022121|gb|CO450870.1|CO450870
EST:     TATGGGCATGGCTCCTGTACTGGGAAAG                         GATGCTACCATTGAACAGCTTGTTCCAATTTTCCTCTCTTTGTTGAAAGAC
genomic: TATGGGAATGGCTCCTGTACTGGGAAAGgtgatatcag ... tctttggcagGATGCTACCATTGAACAGCTTGTTCCAATTTTCCTCTCTTTGTTGAAAGAC
EST: gi|211315613|gb|FL415838.1|FL415838
EST:     GTTCAGCTTTAGCCTCAGTGATTATGGGAATGGCTCCTGTACTGGGAAAG                         GATGCTACCATTGAACAGCTTGTTCCAATTTTCCTCTCTTTGTTGAAAGAC
genomic: GTTCAGCTTTAGCCTCAGTGATTATGGGAATGGCTCCTGTACTGGGAAAGgtgatatcag ... tctttggcagGATGCTACCATTGAACAGCTTGTTCCAATTTTCCTCTCTTTGTTGAAAGAC
EST: gi|26560084|gb|CA832319.1|CA832319
EST:     GTTCAGCTTTAGCCTCAGTGATTATGGGAATGGCTCCTGTACTGGGAAAG                         GATGCTACCATTGAACAGCTTGTTCCAATTTTCCTCTCTTTGTTGAAAGAC
genomic: GTTCAGCTTTAGCCTCAGTGATTATGGGAATGGCTCCTGTACTGGGAAAGgtgatatcag ... tctttggcagGATGCTACCATTGAACAGCTTGTTCCAATTTTCCTCTCTTTGTTGAAAGAC
EST: gi|67039515|gb|CO465770.1|CO465770
EST:     GTTCAGCTTTAGCCTCAGTGATTATGGGAATGGCTCCTGTACTGGGAAAG                         GATGCTACCATTGAACAGCTTGTTCCAATTTTCCTCTCTTTGTTGAAAGAC
genomic: GTTCAGCTTTAGCCTCAGTGATTATGGGAATGGCTCCTGTACTGGGAAAGgtgatatcag ... tctttggcagGATGCTACCATTGAACAGCTTGTTCCAATTTTCCTCTCTTTGTTGAAAGAC
EST: gi|31355734|gb|CD440091.1|CD440091
EST:     GTTCAGCTTTAGCCTCAGTGATTATGGGAATGGCTCCTGTACTGGGAAAG                         GATGCTACCATTGAACAGCTTGTTCCAATTTTCCTCTCTTTGTTGAAAGAC
genomic: GTTCAGCTTTAGCCTCAGTGATTATGGGAATGGCTCCTGTACTGGGAAAGgtgatatcag ... tctttggcagGATGCTACCATTGAACAGCTTGTTCCAATTTTCCTCTCTTTGTTGAAAGAC
EST: gi|13315895|gb|BG410243.1|BG410243
EST:     G-TCAGCTTTAGCCTCAG-GATTATGGGAATGGCTCCTGTACTGGGAAAG                         GATGCTACCATTGAACAGC-TGTTCCAATTTTCCTCTCTTTGTTGAAAGAC
genomic: GTTCAGCTTTAGCCTCAGTGATTATGGGAATGGCTCCTGTACTGGGAAAGgtgatatcag ... tctttggcagGATGCTACCATTGAACAGCTTGTTCCAATTTTCCTCTCTTTGTTGAAAGAC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAATTGTCATCAGATTCATCCCAGCATGTTCGTTCAGCTTTAGCCTCAGTGATTATGGGAATGGCTCCTGTACTGGGAAAGgtgatatcagtgatgcaaacatgtgtttccagaatatggtgttgacaactgttgacattccatgtaagctgatcatctcttctttggcag

- - - - - - - - - - - - - - - -  TCAGCT