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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGATGCTAGTGTTATGTGGGACCAGAAAACAGGACGATCCAGAGGATTTGGTTTTGTTTCTTTCAGGAACCAGCAGgtagtgtcaccattttttaaaccctttgtgcattgttgccatgaacttttggagctgctgtttcatctcgttatgtcattattccttaacaggatgctca...

Basic information

species Zea mays
transcript GRMZM2G008611_T02
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G008611_T02 (Zea mays), 5'ss of exon 8
lower sequence: LOC_Os11g40510.1 (Oryza sativa), 5'ss of exon 7
AGATGCTAGTGTTATGTGGGACCAGAAAACAGGACGATCCAGAGGATTTGGTTTTGTTTCTTTCAGGAACCAGCAGgtagtgtcaccattttt-taaaccctttgtgcattgttgccatgaacttttggagc--tgctgtttcatctcgttatgtcattattccttaacaggatgctca
||||||||| || |||||||| |||||||| |||||||||||||| |||||||||||||||||||| || |||||||||||||||   |     |  |   ||| |  |||  | |  |    |||||| ||  ||||| || |||   ||      |||||| || ||||        
AGATGCTAGGGTAATGTGGGATCAGAAAACTGGACGATCCAGAGGTTTTGGTTTTGTTTCTTTCAGAAATCAGCAGgtagtgtcattgtgacagtttaatttttatttatttgtacttt---tttttggtgcggtgctgattgatcatctt----tgttattcattgacag--------

upper sequence: GRMZM2G008611_T02 (Zea mays), 5'ss of exon 8
lower sequence: GLYMA17G05530.1 (Glycine max), 5'ss of exon 7
AGATGCTAGTGTTATGTGGGACCAGAAAACAGGACGATCCAGAGGATTTGGTTTTGTTTCTTTCAGGAACCAGCAGgtagtgtcaccattttttaaaccctttgtgcattgttgccatgaacttttggagctgctgtttcatctcgttatgtcattattccttaacaggatgctca
 ||||| || || |||||||| ||||| ||||| || ||||| |||||||| |||||||||||  |||| ||||||| | ||  |   |   || |   |    |  ||| || |    | ||||||| | |     |||   | ||                             
TGATGCAAGGGTAATGTGGGATCAGAAGACAGGCCGTTCCAGGGGATTTGGgtttgtttcttttcggaatcagcaggca-tgaaatagtcacttcatttccacatttattcttac----agcttttggtgttttccattctaatggtag---------------------------

upper sequence: GRMZM2G008611_T02 (Zea mays), 5'ss of exon 8
lower sequence: GLYMA17G05530.4 (Glycine max), 5'ss of exon 8
AGATGCTAGTGTTATGTGGGACCAGAAAACAGGACGATCCAGAGGATTTGGTTTTGTTTCTTTCAGGAACCAGCAGgtagtgtcaccattttttaaaccctttgtgcattgttgccatgaacttttggagctgctgtttcatctcgtt--atgtcattattccttaacaggatgc-tca-
 ||||| || || |||||||| ||||| ||||| || ||||| |||||||| |||||||||||  |||| ||||||| | ||  |   |   || |   |    |  ||| || |    | ||||||| | |     |||   | ||   ||||  |  |||  | |    ||   ||| 
TGATGCAAGGGTAATGTGGGATCAGAAGACAGGCCGTTCCAGGGGATTTGGGTTTGTTTCTTTTCGGAATCAGCAGgca-tgaaatagtcacttcatttccacatttattcttac----agcttttggtgttttccattctaatggtaggatgttttggttctgtgattcaatttatcag

upper sequence: GRMZM2G008611_T02 (Zea mays), 5'ss of exon 8
lower sequence: GLYMA13G17200.2 (Glycine max), 5'ss of exon 7
AGATGCTAGTGTTATGTGGGACCAGAAAACAGGACGATCCAGAGGATTTGGTTTTGTTTCTTTCAGGAACCAGCAGgtagtgtcaccattttttaaaccctttgtgcattgttgccatgaacttttggagctgctgt----ttcatctcgttatgtcattattccttaacaggatg-ctca---------
 ||||| || || |||||||| ||||| ||||| || ||||| |||||||| |||||||||||  |||| ||||||| | ||  | | |   || |   ||   |  |||  |       | ||| |    |  |||    | |||     | | |||  ||   ||       ||  |||         
TGATGCAAGGGTAATGTGGGATCAGAAGACAGGCCGTTCCAGGGGATTTGGATTTGTTTCTTTTCGGAATCAGCAGgca-tgaaatcgtcacttcatttctacatttatt-ctcttgcagattttggtgttttttgtgttttccattctaatttatcaggatgttttggttctgtgattcaatttatcag

upper sequence: GRMZM2G008611_T02 (Zea mays), 5'ss of exon 8
lower sequence: AT1G54080.1 (Arabidopsis thaliana), 5'ss of exon 7
AGATGCTAGTGTTATGTGGGACCAGAAAACAGGACGATCCAGAGGATTTGGTTTTGTTTCTTTCAGGAACCAGCAGgtagtgtcaccattttttaaaccctttgtgcattgttgccatgaacttttggagctgctgtttcatctcgttatgtcattattccttaacaggatgctca
 || || || || ||||||||||||||||| ||||| || ||||| |||||||||||||| ||| | || ||||||||  | |    ||  ||| || | |  |||  || ||    | | ||     |     |||||    |  || |   ||  |||  |||   |  |    
GGACGCAAGAGTAATGTGGGACCAGAAAACTGGACGCTCAAGAGGCTTTGGTTTTGTTTCCTTCCGTAATCAGCAGgttttat----atccttttaatcatgagtgacttttttt--ttagctcc---attcattgtttacattgatttttaaatgtttctgtaatttgcag----

upper sequence: GRMZM2G008611_T02 (Zea mays), 5'ss of exon 8
lower sequence: AT1G54080.2 (Arabidopsis thaliana), 5'ss of exon 7
------------AGATGCTAGTGTTATGTGGGACCAGAAAACAGGACGATCCAGAGGATTTGGTTTTGTTTCTTTCAGGAACCAGCAGgtagtgtcaccattttttaaaccctttgtgcattgttgccatgaacttttggagctgctgtttcatctcgttatgtcattattccttaacaggatgctca
             || || || || ||||||||||||||||| ||||| || ||||| |||||||||||||| ||| | || ||||||||  | |    ||  ||| || | |  |||  || ||    | | ||     |     |||||    |  || |   ||  |||  |||   |  |    
TTCTTATTATAGGGACGCAAGAGTAATGTGGGACCAGAAAACTGGACGCTCAAGAGGCTTTGGTTTTGTTTCCTTCCGTAATCAGCAGgttttat----atccttttaatcatgagtgacttttttt--ttagctcc---attcattgtttacattgatttttaaatgtttctgtaatttgcag----

upper sequence: GRMZM2G008611_T02 (Zea mays), 5'ss of exon 8
lower sequence: AT1G17370.1 (Arabidopsis thaliana), 5'ss of exon 7
AGATGCTAGTGTTATGTGGGACCAGAAAACAGGACGATCCAGAGGATTTGGTTTTGTTTCTTTCAGGAACCAGCAGgtagtgtcaccattt--tttaaaccctttgtgcattg-ttgccatgaacttttggagctgctgtttcatctcgttatgtcattattcctta-acaggatgctca
 ||||| || ||||||||||| |||||||| || || || ||||||||||| |||||||| ||| | ||||| |||||| | | ||  | |   |   |  | ||||| || | ||| | |  |||||   |    ||| |  ||  |   |  || |  |||||||  |||        
GGATGCAAGAGTTATGTGGGATCAGAAAACTGGGCGTTCAAGAGGATTTGGATTTGTTTCCTTCCGTAACCAACAGgtact-tgactgtctaactctcagtccttgtgtatagattggcttttacttt---aaacactgatcgattgctgcaaatcttatttccttatgcag--------

upper sequence: GRMZM2G008611_T02 (Zea mays), 5'ss of exon 8
lower sequence: Vv11s0016g00700.t01 (Vitis vinifera), 5'ss of exon 7
AGATGCTAGTGTTATGTGGGACCAGAAAACAGGACGATCCAGAGGATTTGGTTTTGTTTCTTTCAGGAACCAGCAGgtagtgtcaccattttttaaaccctttgtgcattgttgccatgaacttttggagctgctgtttcatctcgttatgtcattattccttaacaggatgctca
||||||||| ||||||||||| |||||||| || || || || || ||||| |||||||||||| |||||||||||||| ||  |    |||   |     || ||  ||||| |  |  | ||||       ||  ||||| |  | ||    | |||  ||| |  | | |   
AGATGCTAGGGTTATGTGGGATCAGAAAACTGGGCGTTCAAGGGGTTTTGGGTTTGTTTCTTTCCGGAACCAGCAGgtaatgaaatggcttt---acttgattttgttttgttccttttcattttt------cctcattcatgttatgattctgtcatt--ttatcttgtttccag

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|32927422|gb|CF032234.1|CF032234
EST:     AAACAGGACGATCCAGAGGATTTGGTTTTGTTTCTTTCAGGAACCAGCAG                         GATGCTCAAAGTGCGATAAATGACTTGAATGGTGTGTTCTCTAGTTCCATG
genomic: AAACAGGACGATCCAGAGGATTTGGTTTTGTTTCTTTCAGGAACCAGCAGgtagtgtcac ... tccttaacagGATGCTCAAAGTGAGATAAATGACTTGAATGGTGTGTTCTCTAGTTCCATG
EST: gi|32940921|gb|CF045740.1|CF045740
EST:     AAACAGGACGATCCAGAGGATTTGGTTTTGTTTCTTTCAGGAACCAGCAG                         GATGCTCAAAGTGCGATAAATGACTTGAATGGTGTGTTCTCTAGTTCCATG
genomic: AAACAGGACGATCCAGAGGATTTGGTTTTGTTTCTTTCAGGAACCAGCAGgtagtgtcac ... tccttaacagGATGCTCAAAGTGAGATAAATGACTTGAATGGTGTGTTCTCTAGTTCCATG
EST: gi|32927656|gb|CF032468.1|CF032468
EST:     AAACAGGACGATCCAGAGGATTTGGTTTTGTTTCTTTCAGGAACCAGCAG                         GATGCTCAAAGTGCGATAAATGACTTGAATGGTGTGTTCTCTAGTTCCATG
genomic: AAACAGGACGATCCAGAGGATTTGGTTTTGTTTCTTTCAGGAACCAGCAGgtagtgtcac ... tccttaacagGATGCTCAAAGTGAGATAAATGACTTGAATGGTGTGTTCTCTAGTTCCATG
EST: gi|32927013|gb|CF031825.1|CF031825
EST:     AAACAGGACGATCCAGAGGATTTGGTTTTGTTTCTTTCAGGAACCAGCAG                         GATGCTCAAAGTGCGATAAATGACTTGAATGGTGTGTTCTCTAGTTCCATG
genomic: AAACAGGACGATCCAGAGGATTTGGTTTTGTTTCTTTCAGGAACCAGCAGgtagtgtcac ... tccttaacagGATGCTCAAAGTGAGATAAATGACTTGAATGGTGTGTTCTCTAGTTCCATG
EST: gi|32850873|gb|CD990554.1|CD990554
EST:     AAACAGGACGATCCAGAGGATTTGGTTTTGGTTCTTTCAGGAACCAGCAG                         GATGCTCAAAGTGCGATAAATGACTTGAATGGTGTGTTCTCTAATTCCATG
genomic: AAACAGGACGATCCAGAGGATTTGGTTTTGTTTCTTTCAGGAACCAGCAGgtagtgtcac ... tccttaacagGATGCTCAAAGTGAGATAAATGACTTGAATGGTGTGTTCTCTAGTTCCATG
EST: gi|32850928|gb|CD990609.1|CD990609
EST:     AAACAGGACGATCCAGAGGATTTGGTTTTGTTTCTTTCAGGAACCAGCAG                         GATGCTCAAAGTGCGATAAATGACTTGAATGGTGTGTTCTCTAGTTCCATG
genomic: AAACAGGACGATCCAGAGGATTTGGTTTTGTTTCTTTCAGGAACCAGCAGgtagtgtcac ... tccttaacagGATGCTCAAAGTGAGATAAATGACTTGAATGGTGTGTTCTCTAGTTCCATG
EST: gi|32927394|gb|CF032206.1|CF032206
EST:     AAACAGGACGATCCAGAGGATTTGGTTTTGTTTCTTTCAGGAACCAGCAG                         GATGCTCAAAGTGCGATAAATGACTTGAATGGTGTGTTCTCTAGTTCCATG
genomic: AAACAGGACGATCCAGAGGATTTGGTTTTGTTTCTTTCAGGAACCAGCAGgtagtgtcac ... tccttaacagGATGCTCAAAGTGAGATAAATGACTTGAATGGTGTGTTCTCTAGTTCCATG
EST: gi|32928054|gb|CF032866.1|CF032866
EST:     AAACAGGACGATCCAGAGGATTTGGTTTTGTTTCTTTCAGGAACCAGCAG                         GATGCTCAAAGTGCGATAAATGACTTGAATGGTGTGTTCTCTAGTTCCATG
genomic: AAACAGGACGATCCAGAGGATTTGGTTTTGTTTCTTTCAGGAACCAGCAGgtagtgtcac ... tccttaacagGATGCTCAAAGTGAGATAAATGACTTGAATGGTGTGTTCTCTAGTTCCATG
EST: gi|32928740|gb|CF033552.1|CF033552
EST:     AAACAGGACGATCCAGAGGATTTGGTTTTGTTTCTTTCAGGAACCAGCAG                         GATGCTCAAAGTGCGATAAATGACTTGAATGGTGTGTTCTCTAGTTCCATG
genomic: AAACAGGACGATCCAGAGGATTTGGTTTTGTTTCTTTCAGGAACCAGCAGgtagtgtcac ... tccttaacagGATGCTCAAAGTGAGATAAATGACTTGAATGGTGTGTTCTCTAGTTCCATG
EST: gi|33092403|gb|CF052397.1|CF052397
EST:     AAACAGGACGATCCAGAGGATTTGGTTTTGTTTCTTTCAGGAACCAGCAG                         GATGCTCAAAGTGCGATAAATGACTTGAATGGTGTGTTCTCTAGTTCCATG
genomic: AAACAGGACGATCCAGAGGATTTGGTTTTGTTTCTTTCAGGAACCAGCAGgtagtgtcac ... tccttaacagGATGCTCAAAGTGAGATAAATGACTTGAATGGTGTGTTCTCTAGTTCCATG
EST: gi|113801770|gb|DW924582.1|DW924582
EST:     CAGGACGATCCAGAGGATTTGGTTTTGTTTCTTTCAGGAACCAGCTAG                         GATGCTCAAAGTGACGATAAATGACTTGAATGGTGTGTTCTCTAGTTCCA
genomic: CAGGACGATCCAGAGGATTTGGTTTTGTTTCTTTCAGGAACCAGC-AGgtagtgtcac ... tccttaacagGATGCTCAAAGTGA-GATAAATGACTTGAATGGTGTGTTCTCTAGTTCCA
EST: gi|32846545|gb|CD986226.1|CD986226
EST:     AAACAGGACGATCCAGAGGATTTGGTTTTGTTTCTTTCAGGAACCAGCAG                         GATGCTCAAAGTGCGATAAATGACTTGAATGGTGTGTTCTCTAGTTCCATG
genomic: AAACAGGACGATCCAGAGGATTTGGTTTTGTTTCTTTCAGGAACCAGCAGgtagtgtcac ... tccttaacagGATGCTCAAAGTGAGATAAATGACTTGAATGGTGTGTTCTCTAGTTCCATG
EST: gi|211381738|gb|FL482095.1|FL482095
EST:     AAACAGGACGATCCAGAGGATTTGGTTTTGTTTCTTTCAGGAACCAGCAG                         GATGCTCAAAGTGCGATAAATGACTTGAATGGTGTGTTCTCTAGTTCCATG
genomic: AAACAGGACGATCCAGAGGATTTGGTTTTGTTTCTTTCAGGAACCAGCAGgtagtgtcac ... tccttaacagGATGCTCAAAGTGAGATAAATGACTTGAATGGTGTGTTCTCTAGTTCCATG
EST: gi|32928010|gb|CF032822.1|CF032822
EST:     AAACAGGACGATCCAGAGGATTTGGTTTTGTTTCTTTCAGGAACCAGCAG                         GATGCTCAAAGTGCGATAAATGACTTGAATGGTGTGTTCTCTAGTTCCATG
genomic: AAACAGGACGATCCAGAGGATTTGGTTTTGTTTCTTTCAGGAACCAGCAGgtagtgtcac ... tccttaacagGATGCTCAAAGTGAGATAAATGACTTGAATGGTGTGTTCTCTAGTTCCATG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGATGCTAGTGTTATGTGGGACCAGAAAACAGGACGATCCAGAGGATTTGGTTTTGTTTCTTTCAGGAACCAGCAGgtagtgtcaccattttttaaaccctttgtgcattgttgccatgaacttttggagctgctgtttcatctcgttatgtcattattccttaacaggatgctca

- - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - -  GAGGAT