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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACAAAATCCAGATGACGTTTTTGACACAATTCTTGGTCTTATTGTTCGTTTGGCAGAGCATGGACTGATACATTGTGACTTTAATGAGTTCAATATCATGgtatctcttccttttccttttcttgtttgtcttgattttataagttttaaatccttggtataagtgaaaattatctggataagatactatggaacaagac...

Basic information

species Zea mays
transcript GRMZM2G472991_T01
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G472991_T01 (Zea mays), 5'ss of exon 9
lower sequence: LOC_Os01g66520.1 (Oryza sativa), 5'ss of exon 7
ACAAAATCCAGATGACGTTTTTGACACAATTCTTGGTCTTATTGTTCGTTTGGCAGAGCATGGACTGATACATTGTGACTTTAATGAGTTCAATATCATGgtatctcttccttttccttttctt-gtttgtcttgattttataagttttaaatccttggtataagtgaaaattatctggataagatactatggaacaagac----------------------------------------------------------------
|||||||||||| || |||||||||||||||||||| ||| ||||||||||||| |||||||| |||||||||||||| ||||| |||||||||||||||||||  |||| | | |||||| |  |||    | || || |     |||   | | ||  |  ||| |||    | |  |      || ||||    ||                                                                  
ACAAAATCCAGACGATGTTTTTGACACAATTCTTGGCCTTGTTGTTCGTTTGGCGGAGCATGGGCTGATACATTGTGATTTTAACGAGTTCAATATCATGgtattgcttcttgtaccttttataagttcacatagaattcact--ctttggttgcctgcaaacagtcaaacaggtgtcaaggtagaacaatggttgtagttttctagattaaacttctgaataatgtcaccatattttttctttgtgtgtattgatgttttgcag

upper sequence: GRMZM2G472991_T01 (Zea mays), 5'ss of exon 9
lower sequence: GLYMA18G04910.1 (Glycine max), 5'ss of exon 7
ACAAAATCCAGATGACGTTTTTGACACAATTCTTGGTCTTATTGTTCGTTTGGCAGAGCATGGACTGATACATTGTGACTTTAATGAGTTCAATATCATGgtatctcttccttttccttttcttgtttgtcttgattttataagttttaaatccttggtataagtgaaaattatctggataagatactatggaacaagac-------------------
 |  ||||||||    ||||||||  ||||||||||||   | ||||| |||||||||||||| || || |||||||| || ||||| || || ||||||||||   ||    | ||        |   |   |   || ||| |||||  | | ||  || ||| |   |  |  |  |  | | |||    |||                       
-CTGAATCCAGAGACAGTTTTTGAGGCAATTCTTGGTCAGGTCGTTCGGTTGGCAGAGCATGGTCTCATTCATTGTGATTTCAATGAATTTAACATCATGGtatgctttaacatgccagcataaatgattaaaggaattctaatttttat-ttcatgaaatcagttattgt-gttggcttttgcttctagtttacactctgaattctattcattgtaga

upper sequence: GRMZM2G472991_T01 (Zea mays), 5'ss of exon 9
lower sequence: GLYMA11G33320.1 (Glycine max), 5'ss of exon 7
ACAAAATCCAGATGACGTTTTTGACACAATTCTTGGTCTTATTGTTCGTTTGGCAGAGCATGGACTGATACATTGTGACTTTAATGAGTTCAATATCATGgtat-ctcttccttttccttttcttgtttgtcttgattttata---agtttta---aatccttggtataagtgaaaatta--tctggataagatactatggaacaagac------
||| ||||||||    ||||||||  ||||||||||||   ||||||| |||||||| ||||| || || |||||||| || ||||| || || |||||||||| || |  | |  |    |  || ||      ||| || |   | ||| |   ||||  |  |     ||    ||   ||||| | | | |||      ||          
ACAGAATCCAGAGACAGTTTTTGAGGCAATTCTTGGTCAGGTTGTTCGGTTGGCAGAACATGGTCTCATTCATTGTGATTTCAATGAATTTAACATCATGgtatgctttaacatgccagcataatgattaaaggaattctaaatttaatttcatgaaatcagttattctgttggcttttgcttctggttcacacactgaattccattcattgtag

upper sequence: GRMZM2G472991_T01 (Zea mays), 5'ss of exon 9
lower sequence: AT3G51270.2 (Arabidopsis thaliana), 5'ss of exon 8
ACAAAATCCAGATGACGTTTTTGACACAATTCTTGGTCTTATTGTTCGTTTGGCAGAGCATGGACTGATACATTGTGACTTTAATGAGTTCAATATCATGgtatctcttccttttccttttcttgtttgtcttgattttataagttttaaat-ccttggtataagtgaaaattatctggat-aagatactatggaacaagac----------------------------------------------------------------------------------------------
||| || || ||     |||| || |  ||  ||||| || ||||||||||||| |||||||| || || ||||||||||| ||||| ||||| ||||||||      | |||     | ||| |||    |  |  || ||  | | |  | | ||| |  || |   |   || |   | ||| | |  |   | |  |                                                                                               
ACAGAACCCTGAGACAATTTTCGAGAAGATCATTGGTATTGTTGTTCGTTTGGCTGAGCATGGTCTAATTCATTGTGACTTCAATGAATTCAACATCATGgtgaga--tacttagatctatctagttgaattataccttctatttgtaagttactttgctgaaaatatcatgcatttatttgaagctgccttctcatataagttaattaatacttctgtaagcatgctagttttgtcctctgcctacttacaattttcattgacacatcctgtttatgtatgcatgtatgttatag

upper sequence: GRMZM2G472991_T01 (Zea mays), 5'ss of exon 9
lower sequence: Vv05s0094g01560.t01 (Vitis vinifera), 5'ss of exon 7
ACAAAATCCAGATGACGTTTTTGACACAATTCTTGGTCTTATTGTTCGTTTGGCAGAGCATGGACTGATACATTGTGACTTTAATGAGTTCAATATCATGgtatctcttccttttccttttcttgtttgtcttgattttataagttttaaatccttggtata-agtgaaaattatc--tggataagatactatggaacaagac
 |||||||| ||    |||||||| |||||| |||||||| |||||| | ||||||| ||||| || || ||||||||||| ||||| ||||| || |||||||   || |   | || |  |    || ||  | ||| |  |  ||   |   ||  ||| |||||   ||  |  | | |   |  ||| |  |      
GCAAAATCCTGACATAGTTTTTGAAACAATTATTGGTCTTGTTGTTCATCTGGCAGAACATGGCCTTATTCATTGTGACTTCAATGAATTCAACATTATGgtatgcatttcaagtgctgtgttgccatgcctcaagtttgttggcatt---tttctgtcatacagtgattttttgcctttgttggaaagctaagagagtcttt

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|33094905|gb|CF054899.1|CF054899
EST:     TGGCAGAGCATGGACTGATACATTGTGACTTTAATGAGTTCAATATCATG                         ATTGATGATGATGAAAAAATTACGGTTATTGATTTTCCACAGATGGTATCT
genomic: TGGCAGAGCATGGACTGATACATTGTGACTTTAATGAGTTCAATATCATGgtatctcttc ... tgtcatgcagATTGATGATGATGAAAAAATTACGGTTATTGATTTTCCACAGATGGTATCT
EST: gi|93016530|gb|EB642050.1|EB642050
EST:     GGCAGAGCATGGACTGATACATTGTGACTTTAATGAGTTTCA-TATCATG                         ATTGATGATGATGAAAAAATTACG
genomic: GGCAGAGCATGGACTGATACATTGTGACTTTAATGAGTT-CAATATCATGgtatctcttc ... tgtcatgcagATTGATGATGATGAAAAAATTACG
EST: gi|33095027|gb|CF055021.1|CF055021
EST:     TGGCAGAGCATGGACTGATACATTGTGACTTTAATGAGTTCAATATCATG                         ATTGATGATGATGAAAAAATTACGGTTATTGATTTTCCACAGATGGTATCT
genomic: TGGCAGAGCATGGACTGATACATTGTGACTTTAATGAGTTCAATATCATGgtatctcttc ... tgtcatgcagATTGATGATGATGAAAAAATTACGGTTATTGATTTTCCACAGATGGTATCT
EST: gi|26456479|gb|CA828062.1|CA828062
EST:     TGGCAGAGCATGGACTGATACATTGTGACTTTAATGAGTTCAATATCATG                         ATTGATGATGATGAAAAAATTACGGTTATTGATTTTCCACAGATGGTATCT
genomic: TGGCAGAGCATGGACTGATACATTGTGACTTTAATGAGTTCAATATCATGgtatctcttc ... tgtcatgcagATTGATGATGATGAAAAAATTACGGTTATTGATTTTCCACAGATGGTATCT
EST: gi|20301471|gb|BQ164414.1|BQ164414
EST:     TGGCAGAGCATGGACTGATACATTGTGACTTTAATGAGTTCAATATCATG                         ATTGATGATGATGAAAAAATTACGGTTATTGATTTTCCACAGATGGTATCT
genomic: TGGCAGAGCATGGACTGATACATTGTGACTTTAATGAGTTCAATATCATGgtatctcttc ... tgtcatgcagATTGATGATGATGAAAAAATTACGGTTATTGATTTTCCACAGATGGTATCT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACAAAATCCAGATGACGTTTTTGACACAATTCTTGGTCTTATTGTTCGTTTGGCAGAGCATGGACTGATACATTGTGACTTTAATGAGTTCAATATCATGgtatctcttccttttccttttcttgtttgtcttgattttataagttttaaatccttggtataagtgaaaattatctggataagatactatggaacaagac

- - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA