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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTCACCTATCTAGGATATGACTTCCTTGCCATCAAGACTTTGGTTAATCGGGGAGTTTTTGCTTCAGTTGGCCGTCAGATCGGTGTTGGAAAGGAGTCTGgtatgttgtgttcatattgtttgttctttgtttgtcatgtggctagcgcacatgaagttatttctaatatctctatgatatacag

Basic information

species Zea mays
transcript GRMZM2G472991_T01
intron # 6
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 6
lower sequence: LOC_Os01g66520.1 (Oryza sativa), 5'ss of exon 4
CTCACCTATCTAGGATATGACTTCCTTGCCATCAAGACTTTGGTTAATCGGGGAGTTTTTGCTTCAGTTGGCCGTCAGATCGGTGTTGGAAAGGAGTCTGgtatgttgtgttcatattgtttgttctttgtttg---tcatgtggctagcgcacatgaagt---------tatttctaatatctctatgatatacag
||||| ||||| || ||||| ||||| |||||||| || ||||||||||| ||||| |||||||||||||| || || || ||||||||||||||||| ||||  |  |||| ||  |||||  || |  |||    | ||||  | | |||| || |  |         | | |||||| | ||  | |  | |||
CTCACATATCTTGGGTATGATTTCCTCGCCATCAAAACCTTGGTTAATCGTGGAGTATTTGCTTCAGTTGGTCGGCAAATTGGTGTTGGAAAGGAGTCAGgtacatgctgttgatgatgttttctcatgttttacttttatgtcacaatcgcatatcagatgttctaacatttgtctaatctttcctttacctgcag

upper sequence: GRMZM2G472991_T01 (Zea mays), 5'ss of exon 6
lower sequence: Vv05s0094g01560.t01 (Vitis vinifera), 5'ss of exon 4
CTCACCTATCTAGGATATGACTTCCTTGCCATCAAGACTTTGGTTAATCGGGGAGTTTTTGCTTCAGTTGGCCGTCAGATCGGTGTTGGAAAGGAGTCTGgtatgttgtgtt-catattgtttgttctttgtttgtcatgtggctagcgcacatgaagttatttctaatatct-ctatgatatacag----------
|| || || || |||||||| || ||||| || |||||| |||||||||| ||||| ||||   | ||||| ||||| || ||||| || |||||||||||||  || | ||  |||||  || |  |||  |    |      | |      ||   | |  |   |||     |||| |||   |          
CTTACTTACCTTGGATATGATTTTCTTGCAATAAAGACTCTGGTTAATCGTGGAGTATTTGTAGCTGTTGGTCGTCAAATTGGTGTCGGGAAGGAGTCTGgtaatttttcttatatattcattttaatttcctgtaaaaaaattttgtttgtgtgttttcacattagatactgattatggtatttcgtttcttcaag
















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|211277358|gb|FL192926.1|FL192926
EST:     GGGAGTTTTTGCTTCAGTTGGCCGTCAGATCGGTGTTGGAAAGGAGTCTG                         ATATATTTGAGGTTGCCACAGAGGATGGTACAGTACTCGCCATGAAACTTC
genomic: GGGAGTTTTTGCTTCAGTTGGCCGTCAGATCGGTGTTGGAAAGGAGTCTGgtatgttgtg ... tgatatacagATATATTTGAGGTTGCCACAGAGGATGGTACAGTACTCGCCATGAAACTTC
EST: gi|20300018|gb|BQ162961.1|BQ162961
EST:     GGGAGTTTTTGCTTCAGTTGGCCGTCAGATCGGTGTTGGAAAGGAGTCTG                         ATATATTTGAGGTTGCCACAGAGGATGGTACAGTACTCGCCATGAAACTTC
genomic: GGGAGTTTTTGCTTCAGTTGGCCGTCAGATCGGTGTTGGAAAGGAGTCTGgtatgttgtg ... tgatatacagATATATTTGAGGTTGCCACAGAGGATGGTACAGTACTCGCCATGAAACTTC
EST: gi|71429251|gb|DR810301.1|DR810301
EST:     GGGAGTTTTTGCTTCAGTTGGCCGTCAGATCGGTGTTGGAAAGGAGTCTG                         ATATATTTGAGGTTGCCACAGAGGATGGTACAGTACTCGCCATGAAACTTC
genomic: GGGAGTTTTTGCTTCAGTTGGCCGTCAGATCGGTGTTGGAAAGGAGTCTGgtatgttgtg ... tgatatacagATATATTTGAGGTTGCCACAGAGGATGGTACAGTACTCGCCATGAAACTTC
EST: gi|93016530|gb|EB642050.1|EB642050
EST:     GGGAGTTTTTGCTTCAGTTGGCCGTCAGATCGGTGTTGGAAAGGAGTCTG                         ATATATTTGAGGTTGCCACAGAGGATGGTACAGTACTCGCCATGAAACTTC
genomic: GGGAGTTTTTGCTTCAGTTGGCCGTCAGATCGGTGTTGGAAAGGAGTCTGgtatgttgtg ... tgatatacagATATATTTGAGGTTGCCACAGAGGATGGTACAGTACTCGCCATGAAACTTC
EST: gi|91056420|gb|EB166838.1|EB166838
EST:     GGGAGTTTTTGCTTCAGTTGGCCGTCAGATCGGTGTTGGAAAGGAGTCTG                         ATATATTTGAGGTTGCCACAGAGGATGGTACAGTACTCGCCATGAAACTTC
genomic: GGGAGTTTTTGCTTCAGTTGGCCGTCAGATCGGTGTTGGAAAGGAGTCTGgtatgttgtg ... tgatatacagATATATTTGAGGTTGCCACAGAGGATGGTACAGTACTCGCCATGAAACTTC
EST: gi|89106284|gb|DY576501.1|DY576501
EST:     GGGAGTTTTTGCTTCAGTTGGCCGTCAGATCGGTGTTGGAAAGGAGTCTG                         ATATATTTGAGGTTGCCACAGAGGATGGTACAGTACTCGCCATGAAACTTC
genomic: GGGAGTTTTTGCTTCAGTTGGCCGTCAGATCGGTGTTGGAAAGGAGTCTGgtatgttgtg ... tgatatacagATATATTTGAGGTTGCCACAGAGGATGGTACAGTACTCGCCATGAAACTTC
EST: gi|78112924|gb|DV531318.1|DV531318
EST:     GGGAGTTTTTGCTTCAGTTGGCCGTCAGATCGGTGTTGGAAAGGAGTCTG                         ATATATTTGAGGTTGCCACAGAGGATGGTACAGTACTCGCCATGAAACTTC
genomic: GGGAGTTTTTGCTTCAGTTGGCCGTCAGATCGGTGTTGGAAAGGAGTCTGgtatgttgtg ... tgatatacagATATATTTGAGGTTGCCACAGAGGATGGTACAGTACTCGCCATGAAACTTC
EST: gi|20299997|gb|BQ162940.1|BQ162940
EST:     GGGAGTTTTTGCTTCAGTTGGCCGTCAGATCGGTGTTGGAAAGGAGTCTG                         ATATATTTGAGGTTGCC-CAGAGGATGGTACAGTACTCGCCATGAAACTTC
genomic: GGGAGTTTTTGCTTCAGTTGGCCGTCAGATCGGTGTTGGAAAGGAGTCTGgtatgttgtg ... tgatatacagATATATTTGAGGTTGCCACAGAGGATGGTACAGTACTCGCCATGAAACTTC
EST: gi|18384009|gb|BM417209.1|BM417209
EST:     GGGAGTTTTTGCTTCAGTTGGCCGTCAGATCGGTGTTGGAAAGGAGTCTG                         ATATATTTGAGGTTGCCACAGAGGATGGTACAGTACTCGCCATGAAACTTC
genomic: GGGAGTTTTTGCTTCAGTTGGCCGTCAGATCGGTGTTGGAAAGGAGTCTGgtatgttgtg ... tgatatacagATATATTTGAGGTTGCCACAGAGGATGGTACAGTACTCGCCATGAAACTTC
EST: gi|18383990|gb|BM417190.1|BM417190
EST:     GGGAGTTTTTGCTTCAGTTGGCCGTCAGATCGGTGTTGGAAAGGAGTCTG                         ATATATTTGAGGTTGCCACAGAGGATGGTACAGTACTCGCCATGAAACTTC
genomic: GGGAGTTTTTGCTTCAGTTGGCCGTCAGATCGGTGTTGGAAAGGAGTCTGgtatgttgtg ... tgatatacagATATATTTGAGGTTGCCACAGAGGATGGTACAGTACTCGCCATGAAACTTC
EST: gi|76014835|gb|DT942005.1|DT942005
EST:     GGGAGTTTTTGCTTCAGTTGGCCGTCAGATCGGTGTTGGAAAGGAGTCTG                         ATATATTTGAGGTTGCCACAGAGGATGGTACAGTACTCGCCATGAAACTTC
genomic: GGGAGTTTTTGCTTCAGTTGGCCGTCAGATCGGTGTTGGAAAGGAGTCTGgtatgttgtg ... tgatatacagATATATTTGAGGTTGCCACAGAGGATGGTACAGTACTCGCCATGAAACTTC
EST: gi|76014878|gb|DT942048.1|DT942048
EST:     GGGAGTTTTTGCTTCAGTTGGCCGTCAGATCGGTGTTGGAAAGGAGTCTG                         ATATATTTGAGGTTGCCACAGAGGATGGTACAGTACTCGCCATGAAACTTC
genomic: GGGAGTTTTTGCTTCAGTTGGCCGTCAGATCGGTGTTGGAAAGGAGTCTGgtatgttgtg ... tgatatacagATATATTTGAGGTTGCCACAGAGGATGGTACAGTACTCGCCATGAAACTTC
EST: gi|22489226|gb|BU049149.1|BU049149
EST:     GGGAGTTTTTGCTTCAGTTGGCCGTCAGATCGGTGTTGGAAAGGAGTCTG                         ATATATTTGAGGTTGCCACAGAGGATGGTACAGTACTCGCCATGAAACTTC
genomic: GGGAGTTTTTGCTTCAGTTGGCCGTCAGATCGGTGTTGGAAAGGAGTCTGgtatgttgtg ... tgatatacagATATATTTGAGGTTGCCACAGAGGATGGTACAGTACTCGCCATGAAACTTC
EST: gi|78120952|gb|DV539336.1|DV539336
EST:     GGGAGTTTTTGCTTCAGTTGGCCGTCAGATCGGTGTTGGAAAGGAGTCTG                         ATATATTTGAGGTTGCCACAGAGGATGGTACAGTACTCGCCATGAAACTTC
genomic: GGGAGTTTTTGCTTCAGTTGGCCGTCAGATCGGTGTTGGAAAGGAGTCTGgtatgttgtg ... tgatatacagATATATTTGAGGTTGCCACAGAGGATGGTACAGTACTCGCCATGAAACTTC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTCACCTATCTAGGATATGACTTCCTTGCCATCAAGACTTTGGTTAATCGGGGAGTTTTTGCTTCAGTTGGCCGTCAGATCGGTGTTGGAAAGGAGTCTGgtatgttgtgttcatattgtttgttctttgtttgtcatgtggctagcgcacatgaagttatttctaatatctctatgatatacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG