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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGCAATAATTGAGTACATCCCATTGTTGGCGAGTCAATTAGGTGTTGGGTTTTTCGATGACAAGCTGGGGGCGCTCTGCATGCAATGGTTGGAAGACAAGgtttgtatcattagggttatgtcaaaacagtatctctttggagctgtctccagcgtctttatcttatatccttgagtgcatattggactttgtaatgtattgactaaaattgtcagtttaactaactaaaatttggatttcag

Basic information

species Zea mays
transcript GRMZM2G164352_T03
intron # 9
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 9
lower sequence: GLYMA10G42250.1 (Glycine max), 5'ss of exon 9
TGCAATAATTGAGTACATCCCATTGTTGGCGAGTCAATTAGGTGTTGGGTTTTTCGATGACAAGCTGGGGGCGCTCTGCATGCAATGGTTGGAAGACAAGgtttgtatcat-tagggttatgtcaaaacag-tatctctttggagctgtctccagcgtctttatcttatatccttgagtgcatattggactttgtaatgtattgactaaaattgtcagtttaactaactaaaatttggatttcag
|||||| || || || || || || ||||| |||||||| || ||| | ||||||||||||||||| || || || |||||||| |||||  | || |||||||||    |  |      ||  |     | |   | || ||| |||  |  |  |    |  |   | |  || |   ||  || |   |||||                                                 
TGCAATTATAGAATATATACCCTTATTGGCAAGTCAATTGGGGGTTAGTTTTTTCGATGACAAGCTTGGTGCTCTTTGCATGCAGTGGTTACAGGATAAGgtttgtgctctacacttccttgctagtgtgggtgcattttgggaactgcat--attgcacatgacggtttttgttaac--caccttagttattgtag------------------------------------------------

upper sequence: GRMZM2G164352_T04 (Zea mays), 5'ss of exon 9
lower sequence: AT3G25800.1 (Arabidopsis thaliana), 5'ss of exon 8
TGCAATAATTGAGTACATCCCATTGTTGGCGAGTCAATTAGGTGTTGGGTTTTTCGATGACAAGCTGGGGGCGCTCTGCATGCAATGGTTGGAAGACAAGgtttgtatcattagggttatgtcaaaacagtatctctttggagctgtctccagcgtctttatcttatatcc-ttgagtgcatattggactttgtaatgtattgactaaaattgtcagtttaactaactaaaatttggatttcag
||| ||||| ||||| ||||| |||||||| ||||| ||||||||||| || || || || ||||| || || || ||||||||||||||  |||||||||  | | || ||     | | ||  |    ||        || | |  |  | ||  | |   |||||    |||| |   | ||    ||| |  | | ||   |      |    | | | ||                   
TGCTATAATCGAGTATATCCCTTTGTTGGCAAGTCAGTTAGGTGTTGGCTTCTTTGACGATAAGCTTGGTGCTCTTTGCATGCAATGGTTACAAGACAAGg--tatttcttt----ctctctcttacttttactgggaatgatcagattataccgcttcttatttatagaaattgatttttttttttttttttttttttttttttttttgcggatgctctcattag------------------

upper sequence: GRMZM2G164352_T04 (Zea mays), 5'ss of exon 9
lower sequence: AT1G13320.2 (Arabidopsis thaliana), 5'ss of exon 9
TGCAATAATTGAGTACATCCCATTGTTGGCGAGTCAATTAGGTGTTGGGTTTTTCGATGACAAGCTGGGGGCGCTCTGCATGCAATGGTTGGAAGACAAGgtttgtatcattagggttatgtcaaaacagtatctctttggagctgtctccagcgtctttatcttatatccttgagtgcatattggactttgtaatgtattgactaaaattgtcagtttaactaactaaaatttggatttcag
 || ||||| ||||| || || |||||||| |||||||||||||| || || || ||||| ||||| || || || ||||||||||||||  ||||||||||   |     |     |   |  || ||   ||    |  |    | |   |  |||    |||  |   ||||    ||  |  | | |                                                    
GGCTATAATCGAGTATATTCCCTTGTTGGCCAGTCAATTAGGTGTAGGCTTCTTTGATGAGAAGCTTGGTGCTCTTTGCATGCAATGGTTACAAGACAAGgtccctcattctctaccttcattgaatca---tccagataaataaatttgtcgtctctactgcttgaaattttgaaataattataaattgtcag-------------------------------------------------

upper sequence: GRMZM2G164352_T04 (Zea mays), 5'ss of exon 9
lower sequence: AT1G25490.1 (Arabidopsis thaliana), 5'ss of exon 9
TGCAATAATTGAGTACATCCCATTGTTGGCGAGTCAATTAGGTGTTGGGTTTTTCGATGACAAGCTGGGGGCGCTCTGCATGCAATGGTTGGAAGACAAGgtttgt-----atcattagggtt-atgtcaaaacagtatctctttggagctgtctccagcgtctttatcttatatccttgagtgcatattggactttgtaatgtattgactaaaattgtcagtttaactaactaaaatttggatttcag
||||||||| |||||  | ||| ||||||| || || |||||| | || ||||||||||||||||| || || || |||||||||||| || ||||||||||||       ||| ||   |||    | ||      ||    |||    |||    |  | |  | |  |   ||||| ||                                                                   
TGCAATAATAGAGTATGTTCCACTGTTGGCCAGCCAGTTAGGTATAGGATTTTTCGATGACAAGCTCGGAGCCCTTTGCATGCAATGGCTGCAAGACAAGgtttaccttgaatctttgatgtttgcataaatttctcattcacttgttattgtagatattgacactgttct-cctccttcag-------------------------------------------------------------------

upper sequence: GRMZM2G164352_T04 (Zea mays), 5'ss of exon 9
lower sequence: PP1S214_34V6.1 (Physcomitrella patens), 5'ss of exon 8
TGCAATAATTGAGTACATCCCATTGTTGGCGAGTCAATTAGGTGTTGGGTTTTTCGATGACAAGCTGGGGGCGCTCTGCATGCAATGGTTGGAAGACAAGgtttgtatcattagggttatgtcaaaacagtatctctttggagctgtctccagcgtctttatcttatatccttgagtgcatattggactttgtaatgtattgactaaaattgtcagtttaactaactaaaatttggattt-cag
||| ||||||||||||||||| || ||||| || ||||||||||| |  |||||||| ||||| || || || || |||||||| ||| | | |||  |||||  |||        ||      || || | | ||  ||| |  || |    ||   |  || |      |    |   | ||    ||||     |    ||||     || |  | |  | | |    ||||||||   ||
TGCCATAATTGAGTACATCCCTTTATTGGCCAGCCAATTAGGTGTGGACTTTTTCGACGACAAACTAGGCGCTCTTTGCATGCAGTGGCTTGGAGATCAGgttcatat-------attcccatcaagcaatgtttcgatggtg--gtttgtgtcgagatggtcgtcctcaatcagatctcttttcatatttgcttctttagaactagttcagtaatataatttcattcttttttggattaatag

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:     TTTTCGATGACAAGCTGGGGGCGCTCTGCATGCAATGGTTGGAAGACAAG                         GTCTTTTCAATCAGAGATGCTGCCGCTAACAACTTGAAGCGCCTTGCAGAA
genomic: TTTTCGATGACAAGCTGGGGGCGCTCTGCATGCAATGGTTGGAAGACAAGgtttgtatca ... tggatttcagGTCTTTTCAATCAGAGATGCTGCCGCTAACAACTTGAAGCGCCTTGCAGAA
EST: gi|32847987|gb|CD987668.1|CD987668
EST:     TTTTCGATGACAAGCTGGGGGCGCTCTGCATGCAATGGTTGGAAGACAAG                         GTCTTTTCAATCAGAGATGCTGCCGCTAACAACTTGAAGCGCCTTGCAGAA
genomic: TTTTCGATGACAAGCTGGGGGCGCTCTGCATGCAATGGTTGGAAGACAAGgtttgtatca ... tggatttcagGTCTTTTCAATCAGAGATGCTGCCGCTAACAACTTGAAGCGCCTTGCAGAA
EST: gi|32929892|gb|CF034704.1|CF034704
EST:     TTTTCGATGACAAGCTGGGGGCGCTCTGCATGCAATGGTTGGAAGACAAG                         GTCTTTTCAATCAGAGATGCTGCCGCTAACAACTTGAAGCGCCTTGCAGAA
genomic: TTTTCGATGACAAGCTGGGGGCGCTCTGCATGCAATGGTTGGAAGACAAGgtttgtatca ... tggatttcagGTCTTTTCAATCAGAGATGCTGCCGCTAACAACTTGAAGCGCCTTGCAGAA
EST: gi|87157118|gb|DY401907.1|DY401907
EST:     TTTTCGATGACAAGCTGGGGGCGCTCTGCATGCAATGGTTGGAAGACAAG                         GTCTTTTCAATCAGAGATGCTGCCGCTAACAACTTGAAGCGCCTTGCAGAA
genomic: TTTTCGATGACAAGCTGGGGGCGCTCTGCATGCAATGGTTGGAAGACAAGgtttgtatca ... tggatttcagGTCTTTTCAATCAGAGATGCTGCCGCTAACAACTTGAAGCGCCTTGCAGAA
EST: gi|26558526|gb|CA830761.1|CA830761
EST:     TTTTCGATGACAAGCTGGGGGCGCTCTGCATGCAATGGTTGGAAGACAAG                         GTCTTTTCAATCAGAGATGCTGCCGCTAACAACTTGAAGCGCCTTGCAGAA
genomic: TTTTCGATGACAAGCTGGGGGCGCTCTGCATGCAATGGTTGGAAGACAAGgtttgtatca ... tggatttcagGTCTTTTCAATCAGAGATGCTGCCGCTAACAACTTGAAGCGCCTTGCAGAA
EST: gi|113682754|gb|DW833176.1|DW833176
EST:     GGGCGCTCTGCATGCAATGGTTGGAAGACAAG                         GTCTTTTCAATCAGAGATGCTGCCGCTAACAACTTGAAGCGCCTTGCAGAA
genomic: GGGCGCTCTGCATGCAATGGTTGGAAGACAAGgtttgtatca ... tggatttcagGTCTTTTCAATCAGAGATGCTGCCGCTAACAACTTGAAGCGCCTTGCAGAA
EST: gi|32933390|gb|CF038202.1|CF038202
EST:     TTTTCGATGACAAGCTGGGGGCGCTCTGCATGCAATGGTTGGAAGACAAG                         GTCTTTTCAATCAGAGATGCTGCCGCTAACAACTTGAAGCGCCTTGCAGAA
genomic: TTTTCGATGACAAGCTGGGGGCGCTCTGCATGCAATGGTTGGAAGACAAGgtttgtatca ... tggatttcagGTCTTTTCAATCAGAGATGCTGCCGCTAACAACTTGAAGCGCCTTGCAGAA
EST: gi|22546073|gb|BU098394.1|BU098394
EST:     TTTTCGATGACAAGCTGGGGGCGCTCTGCATGCAATGGTTGGAAGACAAG                         GTCTTTTCAATCAGAGATGCTGCCGCTAACAACTTGAAGCGCCTTGCAGAA
genomic: TTTTCGATGACAAGCTGGGGGCGCTCTGCATGCAATGGTTGGAAGACAAGgtttgtatca ... tggatttcagGTCTTTTCAATCAGAGATGCTGCCGCTAACAACTTGAAGCGCCTTGCAGAA
EST: gi|32847664|gb|CD987345.1|CD987345
EST:     TTTTCGATGACAAGCTGGGGGCGCTCTGCATGCAATGGTTGGAAGACAAG                         GTCTTTTCAATCAGAGATGCTGCCGCTAACAACTTGAAGCGCCTTGCAGAA
genomic: TTTTCGATGACAAGCTGGGGGCGCTCTGCATGCAATGGTTGGAAGACAAGgtttgtatca ... tggatttcagGTCTTTTCAATCAGAGATGCTGCCGCTAACAACTTGAAGCGCCTTGCAGAA
EST: gi|32939366|gb|CF044185.1|CF044185
EST:     TTTTCGATGACAAGCTGGGGGCGCTCTGCATGCAATGGTTGGAAGACAAG                         GTCTTTTCAATCAGAGATGCTGCCGCTAACAACTTGAAGCGCCTTGCAGAA
genomic: TTTTCGATGACAAGCTGGGGGCGCTCTGCATGCAATGGTTGGAAGACAAGgtttgtatca ... tggatttcagGTCTTTTCAATCAGAGATGCTGCCGCTAACAACTTGAAGCGCCTTGCAGAA
EST: gi|13557744|gb|BG549100.1|BG549100
EST:     TTTTCGATGACAAGCTGGGGGCGCTCTGCATGCAATGGTTGGAAGACAAG                         GTCTTTTCAATCAGAGATGCTGCCGCTAACAACTTGAAGCGCCTTGCAGAA
genomic: TTTTCGATGACAAGCTGGGGGCGCTCTGCATGCAATGGTTGGAAGACAAGgtttgtatca ... tggatttcagGTCTTTTCAATCAGAGATGCTGCCGCTAACAACTTGAAGCGCCTTGCAGAA
EST: gi|33103273|gb|CF063233.1|CF063233
EST:     TTTTCGATGACAAGCTGGGGGCGCTCTGCATGCAATGGTTGGAAGACAAG                         GTCTTTTCAATCAGAGATGCTGCCGCTAACAACTTGAAGCGCCTTGCAGAA
genomic: TTTTCGATGACAAGCTGGGGGCGCTCTGCATGCAATGGTTGGAAGACAAGgtttgtatca ... tggatttcagGTCTTTTCAATCAGAGATGCTGCCGCTAACAACTTGAAGCGCCTTGCAGAA
EST: gi|23357737|gb|BU645386.1|BU645386
EST:     TTTTCGATGACAAGCTGGGGGCGCTCTGCATGCAATGGTTGGAAGACAAG                         GTCTTTTCAATCAGAGATGCTGCCGCTAACAACTTGAAGCGCCTTGCAGAA
genomic: TTTTCGATGACAAGCTGGGGGCGCTCTGCATGCAATGGTTGGAAGACAAGgtttgtatca ... tggatttcagGTCTTTTCAATCAGAGATGCTGCCGCTAACAACTTGAAGCGCCTTGCAGAA
EST: gi|32928724|gb|CF033536.1|CF033536
EST:     TTTTCGATGACAAGCTGGGGGCGCTCTGCATGCAATGGTTGGAAGACAAG                         GTCTTTTCAATCAGAGATGCTGCCGCTAACAACTTGAAGCGCCTTGCAGAA
genomic: TTTTCGATGACAAGCTGGGGGCGCTCTGCATGCAATGGTTGGAAGACAAGgtttgtatca ... tggatttcagGTCTTTTCAATCAGAGATGCTGCCGCTAACAACTTGAAGCGCCTTGCAGAA
EST: gi|26560084|gb|CA832319.1|CA832319
EST:     TTTTCGATGACAAGCTGGGGGCGCTCTGCATGCAATGGTTGGAAGACAAG                         GTCTTTTCAATCAGAGATGCTGCCGCTAACAACTTGAAGCGCCTTGCAGAA
genomic: TTTTCGATGACAAGCTGGGGGCGCTCTGCATGCAATGGTTGGAAGACAAGgtttgtatca ... tggatttcagGTCTTTTCAATCAGAGATGCTGCCGCTAACAACTTGAAGCGCCTTGCAGAA
EST: gi|32846843|gb|CD986524.1|CD986524
EST:     TTTTCGATGACAAGCTGGGGGCGCTCTGCATGCAATGGTTGGAAGACAAG                         GTCTTTTCAATCAGAGATGCTGCCGCTAACAACTTGAAGCGCCTTGCAGAA
genomic: TTTTCGATGACAAGCTGGGGGCGCTCTGCATGCAATGGTTGGAAGACAAGgtttgtatca ... tggatttcagGTCTTTTCAATCAGAGATGCTGCCGCTAACAACTTGAAGCGCCTTGCAGAA
EST: gi|31355734|gb|CD440091.1|CD440091
EST:     TTTTCGATGACAAGCTGGGGGCGCTCTGCATGCAATGGTTGGAAGACAAG                         GTCTTTTCAATCAGAGATGCTGCCGCTAACAACTTGAAGCGCCTTGCAGAA
genomic: TTTTCGATGACAAGCTGGGGGCGCTCTGCATGCAATGGTTGGAAGACAAGgtttgtatca ... tggatttcagGTCTTTTCAATCAGAGATGCTGCCGCTAACAACTTGAAGCGCCTTGCAGAA
EST: gi|33102660|gb|CF062620.1|CF062620
EST:     TTTTCGATGACAAGCTGGGGGCGCTCTGCATGCAATGGTTGGAAGACAAG                         GTCTTTTCAATCAGAGATGCTGCCGCTAACAACTTGAAGCGCCTTGCAGAA
genomic: TTTTCGATGACAAGCTGGGGGCGCTCTGCATGCAATGGTTGGAAGACAAGgtttgtatca ... tggatttcagGTCTTTTCAATCAGAGATGCTGCCGCTAACAACTTGAAGCGCCTTGCAGAA
EST: gi|13315895|gb|BG410243.1|BG410243
EST:     TTTTCGATGACAAGCTGGGGGCGCTCTGCATGCAATGGTTGGAAGACAAG                         GTCTTTTCAATCAGAGATGCTGCCGCTAACAACTTGAAGCGCCTTGCAGAA
genomic: TTTTCGATGACAAGCTGGGGGCGCTCTGCATGCAATGGTTGGAAGACAAGgtttgtatca ... tggatttcagGTCTTTTCAATCAGAGATGCTGCCGCTAACAACTTGAAGCGCCTTGCAGAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGCAATAATTGAGTACATCCCATTGTTGGCGAGTCAATTAGGTGTTGGGTTTTTCGATGACAAGCTGGGGGCGCTCTGCATGCAATGGTTGGAAGACAAGgtttgtatcattagggttatgtcaaaacagtatctctttggagctgtctccagcgtctttatcttatatccttgagtgcatattggactttgtaatgtattgactaaaattgtcagtttaactaactaaaatttggatttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA