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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGGCATCTTACACTCCCAATCATACTCTGGGAAGAATGTAAATGGATTGTTGTTCCAGCTACCTTTATCAGTGCTGCATCGCTATTCTGCATTGAGGAAgtaagtttcttctacttgtcattaggctctggaagttcacatcctaaactgacactattgcactttcag

Basic information

species Zea mays
transcript GRMZM2G114469_T02
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G114469_T02 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os03g01570.2 (Oryza sativa), 5'ss of exon 3
GTGGCATCTTACACTCCCAATCATACTCTGGGAAGAATGTAAATGGATTGTTGTTCCAGCTACCTTTATCAGTGCTGCATCGCTATTCTGCATTGAGGAAgtaagtttcttctacttgtcattaggctctggaa---gttcacatcctaaactga-cactattgcactttcag------------------------------
||||||||| || || ||| | ||||||||||| |||||||||||||| || ||||||||||| |||||||||||||| || |||||||||||||||||||||||| ||    |||| |  ||   | |        | |  |||   ||||||  ||  ||||  | ||                                 
GTGGCATCTCACGCTTCCAGTGATACTCTGGGATGAATGTAAATGGATAGTCGTTCCAGCTACTTTTATCAGTGCTGCCTCTCTATTCTGCATTGAGGAAgtaagtctca---acttatttttcaaccccaagttgtgcttccatttaaaactgttcaaaattgtgccttggtagctaccagctgcaggcagcaattggccat

upper sequence: GRMZM2G114469_T02 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA03G01280.1 (Glycine max), 5'ss of exon 4
GTGGCATCTTACACTCCCAATCATACTCTGGGAAGAATGTAAATGGATTGTTGTTCCAGCTACCTTTATCAGTGCTGCATCGCTATTCTGCATTGAGGAAgtaagtttcttctacttgtcattaggctctgga--agttcacatcctaaactgacac-tattgcactttcag-----------------------------
||||||| | |||||||| |||||||| ||||| || ||  | |||||||| ||||| ||||||||||| |||||||| ||  | || |||||||| |||||| | | || || |||  | ||     |||||  | || |  |   ||| | |    |  || | |||                                
GTGGCATTTGACACTCCCTATCATACTTTGGGATGATTGCCATTGGATTGTGGTTCCTGCTACCTTTATTAGTGCTGCCTCTTTGTTTTGCATTGAAGAAgtatgatcct-ctcctttaccttgactcctggactatttaatgtatcaaaataagttgttctgtaatttattgatggatggattcttggaaggaaaaatat

upper sequence: GRMZM2G114469_T02 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA07G07830.1 (Glycine max), 5'ss of exon 3
GTGGCATCTTACACTCCCAATCATACTCTGGGAAGAATGTAAATGGATTGTTGTTCCAGCTACCTTTATCAGTGCTGCATCGCTATTCTGCATTGAGGAAgtaagtttcttctacttgtcattaggctctgga--agttcacatcctaaactgacac-tattgcactttcag-----------------------------
||||||| | |||||||| |||||||| ||||| || ||  | |||||||| ||||| ||||||||||| || || || ||  | || |||||||| |||||| | | || || |||  | |||    |||||  | || |  |   ||| | |    |  || | |||                                
GTGGCATTTGACACTCCCTATCATACTTTGGGATGATTGCCATTGGATTGTGGTTCCTGCTACCTTTATTAGCGCCGCCTCTTTGTTTTGCATTGAAGAAgtatgatcct-ctcctttaccttaactcctggactatttaatgtatcaaaataagttgttctgtaatttattgatggatggattctttgaaggaaaagtat

upper sequence: GRMZM2G114469_T02 (Zea mays), 5'ss of exon 3
lower sequence: AT3G61320.1 (Arabidopsis thaliana), 5'ss of exon 3
GTGGCATCTTACACTCCCAATCATACTCTGGGAAGAATGTAAATGGATTGTTGTTCCAGCTACCTTTATCAGTGCTGCATCGCTATTCTGCATTGAGGAAgtaagtt-----tcttctacttgtcattaggctctggaagttcacatcctaaactgacactattgcactttcag---------------
 |||||||| || ||||||||||| |||||||| |||||  | |||||||||||||| ||||| || || |||||||| || || |||||||| || ||||||  ||      || || ||    | |   |       | |   ||||| |||    |    | |  |||                  
TTGGCATCTAACTCTCCCAATCATTCTCTGGGATGAATGCCATTGGATTGTTGTTCCTGCTACTTTCATTAGTGCTGCCTCTCTGTTCTGCATAGAAGAAgtactttgtcctcctcctcctccatacttaccctcttttgcttgaatccttaaccattaaaccttctttttggattggaaactctgcag

upper sequence: GRMZM2G114469_T02 (Zea mays), 5'ss of exon 3
lower sequence: Vv15s0046g02870.t01 (Vitis vinifera), 5'ss of exon 3
GTGGCATCTTACACTCCCAATCATACTCTGGGAAGAATGTAAATGGATTGTTGTTCCAGCTACCTTTATCAGTGCTGCATCGCTATTCTGCATTGAGGAAgtaagtttcttctacttgtcattaggctctg-gaagttcacatcctaaactgacactattgcactttcag-------------------
 |||||||| || ||||| ||||| |||||||| || || || |||||||| ||||| ||||| || ||||||||||| || || ||||||||||| |||||   ||||||   ||   |  | | ||||  |   ||||| || |  |      |||     || | |                    
CTGGCATCTCACTCTCCCCATCATCCTCTGGGAGGACTGCAACTGGATTGTGGTTCCTGCTACTTTCATCAGTGCTGCTTCTCTCTTCTGCATTGAAGAAgtctctttctttctctcccctgtggactctctgctattcac-tcattcatactttctagcttcctctaatctccctagagcttttgcag

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|149105830|gb|EE291426.2|EE291426
EST:     TTGTTCCAGCTACCTTTATCAGTGCTGCATCGCTATTCTGCATTGAGGAA                         GTGGGTGTTTTAATCGAAGAGCCGTTCCCCATGCTAGCTCTTGATGCCCTG
genomic: TTGTTCCAGCTACCTTTATCAGTGCTGCATCGCTATTCTGCATTGAGGAAgtaagtttct ... gcactttcagGTGGGTGTTCTAATCGAAGAGCCGTTCCCCATGCTAGCTCTTGATGCCCTG
EST: gi|74241850|gb|DT649764.1|DT649764
EST:     TTGTTCCAGCTACCTTTATCAGTGCTGCATCGCTATTCTGCATTGAGGAA                         GTGGGTGTTTTAATCGAAGAGCCGTTCCCCATGCTAGTTCTTGATGCCCTG
genomic: TTGTTCCAGCTACCTTTATCAGTGCTGCATCGCTATTCTGCATTGAGGAAgtaagtttct ... gcactttcagGTGGGTGTTCTAATCGAAGAGCCGTTCCCCATGCTAGCTCTTGATGCCCTG
EST: gi|76013522|gb|DT940692.1|DT940692
EST:     TTGTTCCAGCTACCTTTATCAGTGCTGCATCGCTATTCTGCATTGAGGAA                         GTGGGTGTTCTAATCGAAGAGCCGTTCCCCATGCTAGCTCTTGATGCCCTG
genomic: TTGTTCCAGCTACCTTTATCAGTGCTGCATCGCTATTCTGCATTGAGGAAgtaagtttct ... gcactttcagGTGGGTGTTCTAATCGAAGAGCCGTTCCCCATGCTAGCTCTTGATGCCCTG
EST: gi|110219329|gb|EC901227.1|EC901227
EST:     TTGTTCCAGCTACCTTTATCAGTGCTGCATCGCTATTCTGCATTGAGGAA                         GTGGGTGTTTTAATCGAAGAGCCGTTCCCCATGCTAGCTCTTGATGCCCTG
genomic: TTGTTCCAGCTACCTTTATCAGTGCTGCATCGCTATTCTGCATTGAGGAAgtaagtttct ... gcactttcagGTGGGTGTTCTAATCGAAGAGCCGTTCCCCATGCTAGCTCTTGATGCCCTG
EST: gi|71330676|gb|DR802123.1|DR802123
EST:     TTGTTCCAGCTACCTTTATCAGTGCTGCATCGCTATTCTGCATTGAGGAA                         GTGGGTGTTCTAATCGAAGAGCCGTTCCCCATGCTAGCTCTTGATGCCCTG
genomic: TTGTTCCAGCTACCTTTATCAGTGCTGCATCGCTATTCTGCATTGAGGAAgtaagtttct ... gcactttcagGTGGGTGTTCTAATCGAAGAGCCGTTCCCCATGCTAGCTCTTGATGCCCTG
EST: gi|110190927|gb|EC872825.1|EC872825
EST:     TTGTTCCAGCTACCTTTATCAGTGCTGCATCGCTATTTTGCATTGAGGAA                         GTGGGTGTTTTAATCGAAGAGCCGTTCCCCATGCTAGCTCTTGATGCCCTG
genomic: TTGTTCCAGCTACCTTTATCAGTGCTGCATCGCTATTCTGCATTGAGGAAgtaagtttct ... gcactttcagGTGGGTGTTCTAATCGAAGAGCCGTTCCCCATGCTAGCTCTTGATGCCCTG
EST: gi|89247018|gb|DY618804.1|DY618804
EST:     TTGTTCCAGCTACCTTTATCAGTGCTGCATCGCTATTCTGCATTGAGGAA                         GTGGGTGTTCTAATCGAAGAGCCGTTCCCCATGCTAGCTCTTGATGCCCTG
genomic: TTGTTCCAGCTACCTTTATCAGTGCTGCATCGCTATTCTGCATTGAGGAAgtaagtttct ... gcactttcagGTGGGTGTTCTAATCGAAGAGCCGTTCCCCATGCTAGCTCTTGATGCCCTG
EST: gi|111193039|gb|EE291175.1|EE291175
EST:     TTGTTCCAGCTACCTTTATCAGTGCTGCATCGCTATTCTGCATTGAGGAA                         GTGGGTGTTCTAATCGAAGAGCCGTTCCCCATGCTAGCTCTTGATGCCCTG
genomic: TTGTTCCAGCTACCTTTATCAGTGCTGCATCGCTATTCTGCATTGAGGAAgtaagtttct ... gcactttcagGTGGGTGTTCTAATCGAAGAGCCGTTCCCCATGCTAGCTCTTGATGCCCTG
EST: gi|32796105|gb|CD948341.1|CD948341
EST:     TTGTTCCAGCTACCTTTATCAGTGCTGCATCGCTATTCTGCATTGAGGAA                         GTGGGTGTTCTAATCGAAGAGCCGTTCCCCATGCTAGCTCTTGATGCCCTG
genomic: TTGTTCCAGCTACCTTTATCAGTGCTGCATCGCTATTCTGCATTGAGGAAgtaagtttct ... gcactttcagGTGGGTGTTCTAATCGAAGAGCCGTTCCCCATGCTAGCTCTTGATGCCCTG
EST: gi|101394185|gb|EB819027.1|EB819027
EST:     TTGTTCCAGCTACCTTTATCAGTGCTGCATCGCTATTCTGCATTGAGGAA                         GTGGGTGTTCTAATCGAAGAGCCGTTCCCCATGCTAGCTCTTGATGCCCTG
genomic: TTGTTCCAGCTACCTTTATCAGTGCTGCATCGCTATTCTGCATTGAGGAAgtaagtttct ... gcactttcagGTGGGTGTTCTAATCGAAGAGCCGTTCCCCATGCTAGCTCTTGATGCCCTG
EST: gi|211189013|gb|FL472399.1|FL472399
EST:     CTGCATCGCTATTCTGCATCGAGGAA                         GTGGGTGTTCTAATCGAAGAGCCGTTCCCCATGCTAGCTCTTGATGCCCTG
genomic: CTGCATCGCTATTCTGCATTGAGGAAgtaagtttct ... gcactttcagGTGGGTGTTCTAATCGAAGAGCCGTTCCCCATGCTAGCTCTTGATGCCCTG
EST: gi|71316167|gb|DR794766.1|DR794766
EST:     TTGTTCCAGCTACCTTTATCAGTGCTGCATCGCTATTCTGCATTGAGGAA                         GTGGGTGTTCTAATCGAAGAGCCGTTCCCCATGCTAGCTCTTGATGCCCTG
genomic: TTGTTCCAGCTACCTTTATCAGTGCTGCATCGCTATTCTGCATTGAGGAAgtaagtttct ... gcactttcagGTGGGTGTTCTAATCGAAGAGCCGTTCCCCATGCTAGCTCTTGATGCCCTG
EST: gi|71763713|gb|DR961650.1|DR961650
EST:     TTGTTCCAGCTACCTTTATCAGTGCTGCATCGCTATTCTGCATTGAGGAA                         GTGGGTGTTCTAATCGAAGAGCCGTTCCCCATGCTAGCTCTTGATGCCCTG
genomic: TTGTTCCAGCTACCTTTATCAGTGCTGCATCGCTATTCTGCATTGAGGAAgtaagtttct ... gcactttcagGTGGGTGTTCTAATCGAAGAGCCGTTCCCCATGCTAGCTCTTGATGCCCTG
EST: gi|32801645|gb|CD953881.1|CD953881
EST:     TTGTTCCAGCTACCTTTATCAGTGCTGCATCGCTATTCTGCATTGAGGAA                         GTGGGTGTTCTAATCGAAGAGCCGTTCCCCATGCTAGCTCTTGATGCCCTG
genomic: TTGTTCCAGCTACCTTTATCAGTGCTGCATCGCTATTCTGCATTGAGGAAgtaagtttct ... gcactttcagGTGGGTGTTCTAATCGAAGAGCCGTTCCCCATGCTAGCTCTTGATGCCCTG
EST: gi|71759496|gb|DR957433.1|DR957433
EST:     CAGTGCTGCATCGCTATTCTGCATTGAGGAA                         GTGGGTGTTCTAATCGAAGAGCCGTTCCCCATGCTAGCTCTTGATGCCCTG
genomic: CAGTGCTGCATCGCTATTCTGCATTGAGGAAgtaagtttct ... gcactttcagGTGGGTGTTCTAATCGAAGAGCCGTTCCCCATGCTAGCTCTTGATGCCCTG
EST: gi|211540671|gb|FL444167.1|FL444167
EST:     TGCATCGCTATTCTGCATCGAGGAA                         GTGGGTGTTCTAATCGAAGAGCCGTTCCCCATGCTAGCTCTTGATGCCCTG
genomic: TGCATCGCTATTCTGCATTGAGGAAgtaagtttct ... gcactttcagGTGGGTGTTCTAATCGAAGAGCCGTTCCCCATGCTAGCTCTTGATGCCCTG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTGGCATCTTACACTCCCAATCATACTCTGGGAAGAATGTAAATGGATTGTTGTTCCAGCTACCTTTATCAGTGCTGCATCGCTATTCTGCATTGAGGAAgtaagtttcttctacttgtcattaggctctggaagttcacatcctaaactgacactattgcactttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC