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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TAAACTGAGCGATCGCTTCCCACAGCCTTATGCAAACGAGCAAGCAGCCCGGTTTGCTAATGGTGGTGCATACCCTCCGGACCTTAGTCTCATCACAAAGgtaattacagctaattttttgcagtgatctgttgtgatcttccattgcgtatggcttactgttcacaatgcaatcattcag

Basic information

species Zea mays
transcript GRMZM2G158479_T04
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G158479_T04 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os05g23620.1 (Oryza sativa), 5'ss of exon 5
TAAACTGAGCGATCGCTTCCCACAGCCTTATGCAAACGAGCAAGCAGCCCGGTTTGCTAATGGTGGTGCATACCCTCCGGACCTTAGTCTCATCACAAAGgtaattacagctaattt--tttgcagtgatctgttgtgatcttccattgcg----tatggcttactgttcacaatgcaatcattcag
|||  | || || || |||||||| || ||| |||| |||||||||||||| ||||| |||||||| |||||||| || || || ||||| ||||| |||||||| | |  | ||    || ||  ||   |||| | ||||||||         | |   ||||||||   | | |     |||||
TAAGTTAAGTGACCGGTTCCCACAACCATATCCAAATGAGCAAGCAGCCCGTTTTGCAAATGGTGGGGCATACCCACCAGATCTCAGTCTTATCACGAAGgtaatgatattttatgccattggcgttgcattgtt-taatcttccaccttcaagttgtaatttactgtttg-actccgtatgttcag

upper sequence: GRMZM2G158479_T04 (Zea mays), 5'ss of exon 4
lower sequence: Vv09s0002g05950.t01 (Vitis vinifera), 5'ss of exon 3
TAAACTGAGCGATCGCTTCCCACAGCCTTATGCAAACGAGCAAGCAGCCCGGTTTGCTAATGGTGGTGCATACCCTCCGGACCTTAGTCTCATCACAAAGgtaat-----tacagctaattttttg-cagtgatctgttgtgatcttccattgcgtatggcttactgttcacaatgcaatcattcag
 || || || ||||| || || |||||||||||||| || ||||||||  | ||||||||||| || ||||| ||||| || || ||||||||||| |||||| |     |       ||   |||  ||   |   | |   ||  ||  | |  ||  || ||| ||     |   |        
AAAGCTAAGTGATCGTTTTCCTCAGCCTTATGCAAATGAACAAGCAGCTAGATTTGCTAATGGAGGAGCATATCCTCCAGATCTAAGTCTCATCACCAAGgtattaattttgttatagatcccttgatagaagtgaatggctgtccacccctaca-ataactgactctttgtcctctcag-------
















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|31356708|gb|CD441065.1|CD441065
EST:     GGTTTGCTAATGGTGGTGCATACCCTCCGGACCTTAGTCTCATCACAAAG                         GCAAGGCACAATGGTCAGAACTATGTTTTCGCTCTTCTTACTGGATATCAT
genomic: GGTTTGCTAATGGTGGTGCATACCCTCCGGACCTTAGTCTCATCACAAAGgtaattacag ... aatcattcagGCAAGGCACAATGGTCAGAACTATGTTTTCGCTCTTCTTACTGGATATCAT
EST: gi|67028963|gb|CO457712.1|CO457712
EST:     GGTTTGCTAATGGTGGTGCATACCCTCCGGACCTTAGTCTCATCACAAAG                         GCAAGGCACAATGGTCAGAACTATGTTTTCGCTCTTCTTACTGGATATCAT
genomic: GGTTTGCTAATGGTGGTGCATACCCTCCGGACCTTAGTCTCATCACAAAGgtaattacag ... aatcattcagGCAAGGCACAATGGTCAGAACTATGTTTTCGCTCTTCTTACTGGATATCAT
EST: gi|16379087|gb|BI992745.1|BI992745
EST:     GGTTTGCTAATGGTGGTGCATACCCTCCGGACCTTAGTCTCATCACAAAG                         GCAAGGCACAATGGTCAGAACTATGTTTTCGCTCTTCTTACTGGATATCAT
genomic: GGTTTGCTAATGGTGGTGCATACCCTCCGGACCTTAGTCTCATCACAAAGgtaattacag ... aatcattcagGCAAGGCACAATGGTCAGAACTATGTTTTCGCTCTTCTTACTGGATATCAT
EST: gi|5055406|gb|AI734293.1|AI734293
EST:     GGTTTGCTAATGGTGGTGCATACCCTCCGGACCTTAGTCTCATCACAAAG                         GCAAGGCACAATGGTCAGAACTATGTTTTCGCTCTTCTTACTGGATATCAT
genomic: GGTTTGCTAATGGTGGTGCATACCCTCCGGACCTTAGTCTCATCACAAAGgtaattacag ... aatcattcagGCAAGGCACAATGGTCAGAACTATGTTTTCGCTCTTCTTACTGGATATCAT
EST: gi|15323508|gb|BI478611.1|BI478611
EST:     GGTTTGCTAATGGTGGTGCATACCCTCCGGACCTTAGTCTCATCACAAAG                         GCAAGGCACAATGGTCAGAACTATGTTTTCGCTCTTCTTACTGGATATCAT
genomic: GGTTTGCTAATGGTGGTGCATACCCTCCGGACCTTAGTCTCATCACAAAGgtaattacag ... aatcattcagGCAAGGCACAATGGTCAGAACTATGTTTTCGCTCTTCTTACTGGATATCAT
EST: gi|60338899|gb|DN205872.1|DN205872
EST:     GGTTTGCTAATGGTGGTGCATACCCTCCGGACCTTAGTCTCATCACAAAG                         GCAAGGCACAATGGTCAGAACTATGTTTTCGCTCTTCTTACTGGATATCAT
genomic: GGTTTGCTAATGGTGGTGCATACCCTCCGGACCTTAGTCTCATCACAAAGgtaattacag ... aatcattcagGCAAGGCACAATGGTCAGAACTATGTTTTCGCTCTTCTTACTGGATATCAT
EST: gi|211036752|gb|FL261404.1|FL261404
EST:     GGTTTGCTAATGGTGGTGCATACCCTCCGGACCTTAGTCTCATCACAAAG                         GCAAGGCACAATGGTCAGAACTATGTTTTCGCTCTTCTTACTGGATATCAT
genomic: GGTTTGCTAATGGTGGTGCATACCCTCCGGACCTTAGTCTCATCACAAAGgtaattacag ... aatcattcagGCAAGGCACAATGGTCAGAACTATGTTTTCGCTCTTCTTACTGGATATCAT
EST: gi|74245922|gb|DT653836.1|DT653836
EST:     GGTTTGCTAATGGTGGTGCATACCCTCCGGACCTTAGTCTCATCACAAAG                         GCAAGGCACAATGGTCAGAACTATGTTTTCGCTCTTCTTACTGGATATCAT
genomic: GGTTTGCTAATGGTGGTGCATACCCTCCGGACCTTAGTCTCATCACAAAGgtaattacag ... aatcattcagGCAAGGCACAATGGTCAGAACTATGTTTTCGCTCTTCTTACTGGATATCAT
EST: gi|16919521|gb|BM074230.1|BM074230
EST:     TAGTCTCATCACAAAG                         GCAAGGCACAATGGTCAGAACTATGGTTTTCGCTCTTCTAACTGGATATCA
genomic: TAGTCTCATCACAAAGgtaattacag ... aatcattcagGCAAGGCACAATGGTCAGAACTAT-GTTTTCGCTCTTCTTACTGGATATCA
EST: gi|15590213|gb|BI674829.1|BI674829
EST:     GGTTTGCTAATGGTGGTGCATACCCTCCGGACCTTAGTCTCATCACAAAG                         GCAAGGCACAATGGTCAGAACTATGTTTTCGCTCTTCTTACTGGATATCAT
genomic: GGTTTGCTAATGGTGGTGCATACCCTCCGGACCTTAGTCTCATCACAAAGgtaattacag ... aatcattcagGCAAGGCACAATGGTCAGAACTATGTTTTCGCTCTTCTTACTGGATATCAT
EST: gi|31356905|gb|CD441262.1|CD441262
EST:     GGTTTGCTAATGGTGGTGCATACCCTCCGGACCTTAGTCTCATCACAAAG                         GCAAGGCACAATGGTCAGAACTATGTTTTCGCTCTTCTTACTGGATATCAT
genomic: GGTTTGCTAATGGTGGTGCATACCCTCCGGACCTTAGTCTCATCACAAAGgtaattacag ... aatcattcagGCAAGGCACAATGGTCAGAACTATGTTTTCGCTCTTCTTACTGGATATCAT
EST: gi|60396397|gb|DN229266.1|DN229266
EST:     GGTTTGCTAATGGTGGTGCATACCCTCCGGACCTTAGTCTCATCACAAAG                         GCAAGGCACAATGGTCAGAACTATGTTTTCGCTCTTCTTACTGGATATCAT
genomic: GGTTTGCTAATGGTGGTGCATACCCTCCGGACCTTAGTCTCATCACAAAGgtaattacag ... aatcattcagGCAAGGCACAATGGTCAGAACTATGTTTTCGCTCTTCTTACTGGATATCAT
EST: gi|14243082|gb|BG840790.2|BG840790
EST:     GGTTTGCTAATGGTGGTGCATACCCTCCGGACCTTAGTCTCATCACAAAG                         GCAAGGCACAATGGTCAGAACTATGTTTTCGCTCTTCTTACTGGATATCAT
genomic: GGTTTGCTAATGGTGGTGCATACCCTCCGGACCTTAGTCTCATCACAAAGgtaattacag ... aatcattcagGCAAGGCACAATGGTCAGAACTATGTTTTCGCTCTTCTTACTGGATATCAT
EST: gi|149097934|gb|EE183875.2|EE183875
EST:     GGTTTGCTAATGGTGGTGCATACCCTCCGGACCTTAGTCTCATCACAAAG                         GCAAGGCACAATGGTCAGAACTATGTTTTCGCTCTTCTTACTGGATATCAT
genomic: GGTTTGCTAATGGTGGTGCATACCCTCCGGACCTTAGTCTCATCACAAAGgtaattacag ... aatcattcagGCAAGGCACAATGGTCAGAACTATGTTTTCGCTCTTCTTACTGGATATCAT
EST: gi|6012601|gb|AW062038.1|AW062038
EST:     GGTTTGCTAATGGTGGTGCATACCCTCCGGACCTTAGTCTCATCACAAAG                         GCAAGGCACAATGGTCAGAACTATGTTTTCGCTCTTCTTACTGGATATCAT
genomic: GGTTTGCTAATGGTGGTGCATACCCTCCGGACCTTAGTCTCATCACAAAGgtaattacag ... aatcattcagGCAAGGCACAATGGTCAGAACTATGTTTTCGCTCTTCTTACTGGATATCAT
EST: gi|31354314|gb|CD438671.1|CD438671
EST:     GGTTTGCTAATGGTGGTGCATACCCTCCGGACCTTAGTCTCATCACAAAG                         GCAAGGCACAATGGTCAGAACTATGTTTTCGCTCTTCTTACTGGATATCAT
genomic: GGTTTGCTAATGGTGGTGCATACCCTCCGGACCTTAGTCTCATCACAAAGgtaattacag ... aatcattcagGCAAGGCACAATGGTCAGAACTATGTTTTCGCTCTTCTTACTGGATATCAT
EST: gi|78075104|gb|DV503538.1|DV503538
EST:     GGTTTGCTAATGGTGGTGCATACCCTCCGGACCTTAGTCTCATCACAAAG                         GCAAGGCACAATGGTCAGAACTATGTTTTCGCTCTTCTTACTGGATATCAT
genomic: GGTTTGCTAATGGTGGTGCATACCCTCCGGACCTTAGTCTCATCACAAAGgtaattacag ... aatcattcagGCAAGGCACAATGGTCAGAACTATGTTTTCGCTCTTCTTACTGGATATCAT
EST: gi|40303643|gb|CK348030.1|CK348030
EST:     GGTTTGCTAATGGTGGTGCATACCCTCCGGACCTTAGTCTCATCACAAAG                         GCAAGGCACAATGGTCAGAACTATGTTTTCGCTCTTCTTACTGGATATCAT
genomic: GGTTTGCTAATGGTGGTGCATACCCTCCGGACCTTAGTCTCATCACAAAGgtaattacag ... aatcattcagGCAAGGCACAATGGTCAGAACTATGTTTTCGCTCTTCTTACTGGATATCAT
EST: gi|211323658|gb|FL286664.1|FL286664
EST:     GGTTTGCTAATGGTGGTGCATACC-TCCGGACCTTAGTCTCATCACAAAG                         GCAAGGCACAATGGTCAGAACTATGTTTTCGCTCTTCTTACTGGATATCAT
genomic: GGTTTGCTAATGGTGGTGCATACCCTCCGGACCTTAGTCTCATCACAAAGgtaattacag ... aatcattcagGCAAGGCACAATGGTCAGAACTATGTTTTCGCTCTTCTTACTGGATATCAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TAAACTGAGCGATCGCTTCCCACAGCCTTATGCAAACGAGCAAGCAGCCCGGTTTGCTAATGGTGGTGCATACCCTCCGGACCTTAGTCTCATCACAAAGgtaattacagctaattttttgcagtgatctgttgtgatcttccattgcgtatggcttactgttcacaatgcaatcattcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG