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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTCAGCGAGTACACGGTTGTCCATTCCGGATGTGCGGTGAAGGTTGGCCTGACCGTGCCAATGGACAGGGTGTGCCTGCTGAGCTGCGGTGTGTCTTCAGgtaaatcctgaggttcagagcttcagatatctgagagtagctgtgttagctcgtctgtttgtaggaacagtgccttagttaccttgcatggttgcacatttttgtggatctgatcatccctctttgttcatggttctatcgttaggactcggtgcag

Basic information

species Zea mays
transcript GRMZM2G149272_T02
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G149272_T02 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os02g42520.3 (Oryza sativa), 5'ss of exon 4
TTCAGCGAGTACACGGTTGTCCATTCCGGATGTGCGGTGAAGGTTGGCCTGACCGTGCCAATGGACAGGGTGTGCCTGCTGAGCTGCGGTGTGTCTTCAGgtaaatcctgagg-ttcaga--gcttcagatatctgagagtagct-----gtgtt-----agctcgtct---gtttgtaggaacagtgccttagttaccttgcatggttgcacatttttgtggatct-gatcatccctct--ttgttcatgg-ttctatcgttaggactcggtgcag-
|||||||||||||||||||| || ||||| || ||||||||||| ||||  |||||||| ||||||||| | |||||||||||||| ||||| ||| ||||| |||  | |||  |||||  || ||||   | | |   || ||     |  ||     ||||  |     ||||   |   |   |  |||| |    |   | |||   || || || | || |  | | |  ||||  |  ||||||  |||  || ||           |   
TTCAGCGAGTACACGGTTGTGCACTCCGGTTGCGCGGTGAAGGTCGGCCCAACCGTGCCGATGGACAGGATATGCCTGCTGAGCTGTGGTGTATCTGCAGgtgaattttaagggctcagatggcatcagtgtttttactttatcttccacgcctttctgtagcttatacttggtttactgatgctaagaattaggtgtgctatgttgttctgcacttctgcgcattttaaccgtgtctctgatcattcatgtcttcgttcatttctgtatttcactag
















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|78087348|gb|DV515741.1|DV515741
EST:     GACCGTGCCAATGGACAGGGTGTGCCTGCTGAGCTGCGGTGTGTCTTCAG                         G
genomic: GACCGTGCCAATGGACAGGGTGTGCCTGCTGAGCTGCGGTGTGTCTTCAGgtaaatcctg ... ctcggtgcag-
EST: gi|78087348|gb|DV515741.1|DV515741
EST:     GACCGTGCCAATGGACAGGGTGTGCCTGCTGAGCTGCGGTGTGTCTTCAG                         G
genomic: GACCGTGCCAATGGACAGGGTGTGCCTGCTGAGCTGCGGTGTGTCTTCAGgtaaatcctg ... ctcggtgcag-
EST: gi|78087348|gb|DV515741.1|DV515741
EST:     GACCGTGCCAATGGACAGGGTGTGCCTGCTGAGCTGCGGTGTGTCTTCAG                         G
genomic: GACCGTGCCAATGGACAGGGTGTGCCTGCTGAGCTGCGGTGTGTCTTCAGgtaaatcctg ... ctcggtgcag-
EST: gi|78087348|gb|DV515741.1|DV515741
EST:     GACCGTGCCAATGGACAGGGTGTGCCTGCTGAGCTGCGGTGTGTCTTCAG                         G
genomic: GACCGTGCCAATGGACAGGGTGTGCCTGCTGAGCTGCGGTGTGTCTTCAGgtaaatcctg ... ctcggtgcag-
EST: gi|91873431|gb|EB403388.1|EB403388
EST:     GACCGTGCCAATGGACAGGGTGTGCCTGCTGAGCTGCGGTGTGTCTTCAG                         G
genomic: GACCGTGCCAATGGACAGGGTGTGCCTGCTGAGCTGCGGTGTGTCTTCAGgtaaatcctg ... ctcggtgcag-
EST: gi|91873431|gb|EB403388.1|EB403388
EST:     GACCGTGCCAATGGACAGGGTGTGCCTGCTGAGCTGCGGTGTGTCTTCAG                         G
genomic: GACCGTGCCAATGGACAGGGTGTGCCTGCTGAGCTGCGGTGTGTCTTCAGgtaaatcctg ... ctcggtgcag-
EST: gi|91873431|gb|EB403388.1|EB403388
EST:     GACCGTGCCAATGGACAGGGTGTGCCTGCTGAGCTGCGGTGTGTCTTCAG                         G
genomic: GACCGTGCCAATGGACAGGGTGTGCCTGCTGAGCTGCGGTGTGTCTTCAGgtaaatcctg ... ctcggtgcag-
EST: gi|91873431|gb|EB403388.1|EB403388
EST:     GACCGTGCCAATGGACAGGGTGTGCCTGCTGAGCTGCGGTGTGTCTTCAG                         G
genomic: GACCGTGCCAATGGACAGGGTGTGCCTGCTGAGCTGCGGTGTGTCTTCAGgtaaatcctg ... ctcggtgcag-
EST: gi|71448196|gb|DR829246.1|DR829246
EST:     GACCGTGCCAATGGACAGGGTGTGCCTGCTGTGCTGCGGTGTGTCTTCAG                         G
genomic: GACCGTGCCAATGGACAGGGTGTGCCTGCTGAGCTGCGGTGTGTCTTCAGgtaaatcctg ... ctcggtgcag-
EST: gi|71448196|gb|DR829246.1|DR829246
EST:     GACCGTGCCAATGGACAGGGTGTGCCTGCTGTGCTGCGGTGTGTCTTCAG                         G
genomic: GACCGTGCCAATGGACAGGGTGTGCCTGCTGAGCTGCGGTGTGTCTTCAGgtaaatcctg ... ctcggtgcag-
EST: gi|71448196|gb|DR829246.1|DR829246
EST:     GACCGTGCCAATGGACAGGGTGTGCCTGCTGTGCTGCGGTGTGTCTTCAG                         G
genomic: GACCGTGCCAATGGACAGGGTGTGCCTGCTGAGCTGCGGTGTGTCTTCAGgtaaatcctg ... ctcggtgcag-
EST: gi|71448196|gb|DR829246.1|DR829246
EST:     GACCGTGCCAATGGACAGGGTGTGCCTGCTGTGCTGCGGTGTGTCTTCAG                         G
genomic: GACCGTGCCAATGGACAGGGTGTGCCTGCTGAGCTGCGGTGTGTCTTCAGgtaaatcctg ... ctcggtgcag-
EST: gi|71769715|gb|DR967652.1|DR967652
EST:     GACCGTGCCAATGGACAGGGTGTGCCTGCTGAGCTGCGGTGTGTCTTCAG                         G
genomic: GACCGTGCCAATGGACAGGGTGTGCCTGCTGAGCTGCGGTGTGTCTTCAGgtaaatcctg ... ctcggtgcag-
EST: gi|71769715|gb|DR967652.1|DR967652
EST:     GACCGTGCCAATGGACAGGGTGTGCCTGCTGAGCTGCGGTGTGTCTTCAG                         G
genomic: GACCGTGCCAATGGACAGGGTGTGCCTGCTGAGCTGCGGTGTGTCTTCAGgtaaatcctg ... ctcggtgcag-
EST: gi|71769715|gb|DR967652.1|DR967652
EST:     GACCGTGCCAATGGACAGGGTGTGCCTGCTGAGCTGCGGTGTGTCTTCAG                         G
genomic: GACCGTGCCAATGGACAGGGTGTGCCTGCTGAGCTGCGGTGTGTCTTCAGgtaaatcctg ... ctcggtgcag-
EST: gi|71769715|gb|DR967652.1|DR967652
EST:     GACCGTGCCAATGGACAGGGTGTGCCTGCTGAGCTGCGGTGTGTCTTCAG                         G
genomic: GACCGTGCCAATGGACAGGGTGTGCCTGCTGAGCTGCGGTGTGTCTTCAGgtaaatcctg ... ctcggtgcag-
EST: gi|76921975|gb|DV168787.1|DV168787
EST:     GACCGTGCCAATGGACAGGGTGTGCCTGCTGAGCTGCGGTGTGTCTTCAG                         G
genomic: GACCGTGCCAATGGACAGGGTGTGCCTGCTGAGCTGCGGTGTGTCTTCAGgtaaatcctg ... ctcggtgcag-
EST: gi|76921975|gb|DV168787.1|DV168787
EST:     GACCGTGCCAATGGACAGGGTGTGCCTGCTGAGCTGCGGTGTGTCTTCAG                         G
genomic: GACCGTGCCAATGGACAGGGTGTGCCTGCTGAGCTGCGGTGTGTCTTCAGgtaaatcctg ... ctcggtgcag-
EST: gi|76921975|gb|DV168787.1|DV168787
EST:     GACCGTGCCAATGGACAGGGTGTGCCTGCTGAGCTGCGGTGTGTCTTCAG                         G
genomic: GACCGTGCCAATGGACAGGGTGTGCCTGCTGAGCTGCGGTGTGTCTTCAGgtaaatcctg ... ctcggtgcag-
EST: gi|76921975|gb|DV168787.1|DV168787
EST:     GACCGTGCCAATGGACAGGGTGTGCCTGCTGAGCTGCGGTGTGTCTTCAG                         G
genomic: GACCGTGCCAATGGACAGGGTGTGCCTGCTGAGCTGCGGTGTGTCTTCAGgtaaatcctg ... ctcggtgcag-
EST: gi|14203856|gb|BG837533.1|BG837533
EST:     GGACAGGGTGTGCCTGCTGAGCTGCGGTGTGTCTGCAGGACTCGGTGCAG                         TCTGGAATGTAGCTAATGTATCAAAGGGCTCAAGTGTAGCTATATTTGGT
genomic: GGACAGGGTGTGCCTGCTGAGCTGCGGTGTG--T------CT---T-CAGgtaaatcctg ... ctcggtgcagTCTGGAATGTAGCTAATGTATCAAAGGGCTCAAGTGTAGCTATATTTGGT
EST: gi|71331903|gb|DR802837.1|DR802837
EST:     GACCGTGCCAATGGACAGGGTGTGCCTGCTGAGCTGCGGTGTGTCTTCAG                         G
genomic: GACCGTGCCAATGGACAGGGTGTGCCTGCTGAGCTGCGGTGTGTCTTCAGgtaaatcctg ... ctcggtgcag-
EST: gi|71331903|gb|DR802837.1|DR802837
EST:     GACCGTGCCAATGGACAGGGTGTGCCTGCTGAGCTGCGGTGTGTCTTCAG                         G
genomic: GACCGTGCCAATGGACAGGGTGTGCCTGCTGAGCTGCGGTGTGTCTTCAGgtaaatcctg ... ctcggtgcag-
EST: gi|71331903|gb|DR802837.1|DR802837
EST:     GACCGTGCCAATGGACAGGGTGTGCCTGCTGAGCTGCGGTGTGTCTTCAG                         G
genomic: GACCGTGCCAATGGACAGGGTGTGCCTGCTGAGCTGCGGTGTGTCTTCAGgtaaatcctg ... ctcggtgcag-
EST: gi|71331903|gb|DR802837.1|DR802837
EST:     GACCGTGCCAATGGACAGGGTGTGCCTGCTGAGCTGCGGTGTGTCTTCAG                         G
genomic: GACCGTGCCAATGGACAGGGTGTGCCTGCTGAGCTGCGGTGTGTCTTCAGgtaaatcctg ... ctcggtgcag-
EST: gi|148958260|gb|EC904476.2|EC904476
EST:     GACCGTGCCAATGGACAGGGTGTGCCTGCTGAGCTGCGGTGTGTCTTCAG                         G
genomic: GACCGTGCCAATGGACAGGGTGTGCCTGCTGAGCTGCGGTGTGTCTTCAGgtaaatcctg ... ctcggtgcag-
EST: gi|148958260|gb|EC904476.2|EC904476
EST:     GACCGTGCCAATGGACAGGGTGTGCCTGCTGAGCTGCGGTGTGTCTTCAG                         G
genomic: GACCGTGCCAATGGACAGGGTGTGCCTGCTGAGCTGCGGTGTGTCTTCAGgtaaatcctg ... ctcggtgcag-
EST: gi|148958260|gb|EC904476.2|EC904476
EST:     GACCGTGCCAATGGACAGGGTGTGCCTGCTGAGCTGCGGTGTGTCTTCAG                         G
genomic: GACCGTGCCAATGGACAGGGTGTGCCTGCTGAGCTGCGGTGTGTCTTCAGgtaaatcctg ... ctcggtgcag-
EST: gi|148958260|gb|EC904476.2|EC904476
EST:     GACCGTGCCAATGGACAGGGTGTGCCTGCTGAGCTGCGGTGTGTCTTCAG                         G
genomic: GACCGTGCCAATGGACAGGGTGTGCCTGCTGAGCTGCGGTGTGTCTTCAGgtaaatcctg ... ctcggtgcag-
EST: gi|71325644|gb|DR799509.1|DR799509
EST:     GACCGTGCCAATGGACAGGGTGTGCCTGCTGAGCTGCGGTGTGTCTTCAG                         G
genomic: GACCGTGCCAATGGACAGGGTGTGCCTGCTGAGCTGCGGTGTGTCTTCAGgtaaatcctg ... ctcggtgcag-
EST: gi|71325644|gb|DR799509.1|DR799509
EST:     GACCGTGCCAATGGACAGGGTGTGCCTGCTGAGCTGCGGTGTGTCTTCAG                         G
genomic: GACCGTGCCAATGGACAGGGTGTGCCTGCTGAGCTGCGGTGTGTCTTCAGgtaaatcctg ... ctcggtgcag-
EST: gi|71325644|gb|DR799509.1|DR799509
EST:     GACCGTGCCAATGGACAGGGTGTGCCTGCTGAGCTGCGGTGTGTCTTCAG                         G
genomic: GACCGTGCCAATGGACAGGGTGTGCCTGCTGAGCTGCGGTGTGTCTTCAGgtaaatcctg ... ctcggtgcag-
EST: gi|71325644|gb|DR799509.1|DR799509
EST:     GACCGTGCCAATGGACAGGGTGTGCCTGCTGAGCTGCGGTGTGTCTTCAG                         G
genomic: GACCGTGCCAATGGACAGGGTGTGCCTGCTGAGCTGCGGTGTGTCTTCAGgtaaatcctg ... ctcggtgcag-
EST: gi|71771533|gb|DR969470.1|DR969470
EST:     GACCGTGCCAATGGACAGGGTGTGCCTGCTGAGCTGCGGTGTGTCTTCAG                         TCTGGAATGTAGCTAATGTATCAAAGGGCTCAAGTGTAGCTATATTTGGTC
genomic: GACCGTGCCAATGGACAGGGTGTGCCTGCTGAGCTGCGGTGTGTCTTCAGgtaaatcctg ... ctcggtgcagTCTGGAATGTAGCTAATGTATCAAAGGGCTCAAGTGTAGCTATATTTGGTC
EST: gi|78087855|gb|DV516248.1|DV516248
EST:     GACCGTGCCAATGGACAGGGTGTGCCTGCTGAGCTGCGGTGTGTCTTCAG                         G
genomic: GACCGTGCCAATGGACAGGGTGTGCCTGCTGAGCTGCGGTGTGTCTTCAGgtaaatcctg ... ctcggtgcag-
EST: gi|78087855|gb|DV516248.1|DV516248
EST:     GACCGTGCCAATGGACAGGGTGTGCCTGCTGAGCTGCGGTGTGTCTTCAG                         G
genomic: GACCGTGCCAATGGACAGGGTGTGCCTGCTGAGCTGCGGTGTGTCTTCAGgtaaatcctg ... ctcggtgcag-
EST: gi|78087855|gb|DV516248.1|DV516248
EST:     GACCGTGCCAATGGACAGGGTGTGCCTGCTGAGCTGCGGTGTGTCTTCAG                         G
genomic: GACCGTGCCAATGGACAGGGTGTGCCTGCTGAGCTGCGGTGTGTCTTCAGgtaaatcctg ... ctcggtgcag-
EST: gi|78087855|gb|DV516248.1|DV516248
EST:     GACCGTGCCAATGGACAGGGTGTGCCTGCTGAGCTGCGGTGTGTCTTCAG                         G
genomic: GACCGTGCCAATGGACAGGGTGTGCCTGCTGAGCTGCGGTGTGTCTTCAGgtaaatcctg ... ctcggtgcag-
EST: gi|149083974|gb|EE173360.2|EE173360
EST:     GACCGTGCCAATGGACAGGGTGTGCCTGCTGAGCTGCGGTGTGTCTTCAG                         G
genomic: GACCGTGCCAATGGACAGGGTGTGCCTGCTGAGCTGCGGTGTGTCTTCAGgtaaatcctg ... ctcggtgcag-
EST: gi|149083974|gb|EE173360.2|EE173360
EST:     GACCGTGCCAATGGACAGGGTGTGCCTGCTGAGCTGCGGTGTGTCTTCAG                         G
genomic: GACCGTGCCAATGGACAGGGTGTGCCTGCTGAGCTGCGGTGTGTCTTCAGgtaaatcctg ... ctcggtgcag-
EST: gi|149083974|gb|EE173360.2|EE173360
EST:     GACCGTGCCAATGGACAGGGTGTGCCTGCTGAGCTGCGGTGTGTCTTCAG                         G
genomic: GACCGTGCCAATGGACAGGGTGTGCCTGCTGAGCTGCGGTGTGTCTTCAGgtaaatcctg ... ctcggtgcag-
EST: gi|149083974|gb|EE173360.2|EE173360
EST:     GACCGTGCCAATGGACAGGGTGTGCCTGCTGAGCTGCGGTGTGTCTTCAG                         G
genomic: GACCGTGCCAATGGACAGGGTGTGCCTGCTGAGCTGCGGTGTGTCTTCAGgtaaatcctg ... ctcggtgcag-
EST: gi|101382109|gb|EB813110.1|EB813110
EST:     GACCGTGCCAATGGACAGGGTGTGCCTGCTGAGCTGCGGTGTGTCTTCAG                         G
genomic: GACCGTGCCAATGGACAGGGTGTGCCTGCTGAGCTGCGGTGTGTCTTCAGgtaaatcctg ... ctcggtgcag-
EST: gi|101382109|gb|EB813110.1|EB813110
EST:     GACCGTGCCAATGGACAGGGTGTGCCTGCTGAGCTGCGGTGTGTCTTCAG                         G
genomic: GACCGTGCCAATGGACAGGGTGTGCCTGCTGAGCTGCGGTGTGTCTTCAGgtaaatcctg ... ctcggtgcag-
EST: gi|101382109|gb|EB813110.1|EB813110
EST:     GACCGTGCCAATGGACAGGGTGTGCCTGCTGAGCTGCGGTGTGTCTTCAG                         G
genomic: GACCGTGCCAATGGACAGGGTGTGCCTGCTGAGCTGCGGTGTGTCTTCAGgtaaatcctg ... ctcggtgcag-
EST: gi|101382109|gb|EB813110.1|EB813110
EST:     GACCGTGCCAATGGACAGGGTGTGCCTGCTGAGCTGCGGTGTGTCTTCAG                         G
genomic: GACCGTGCCAATGGACAGGGTGTGCCTGCTGAGCTGCGGTGTGTCTTCAGgtaaatcctg ... ctcggtgcag-
EST: gi|76016068|gb|DT943238.1|DT943238
EST:     GACCGTGCCAATGGACAGGGTGTGCCTGCTGAGCTGCGGTGTGTCTTCAG                         G
genomic: GACCGTGCCAATGGACAGGGTGTGCCTGCTGAGCTGCGGTGTGTCTTCAGgtaaatcctg ... ctcggtgcag-
EST: gi|76016068|gb|DT943238.1|DT943238
EST:     GACCGTGCCAATGGACAGGGTGTGCCTGCTGAGCTGCGGTGTGTCTTCAG                         G
genomic: GACCGTGCCAATGGACAGGGTGTGCCTGCTGAGCTGCGGTGTGTCTTCAGgtaaatcctg ... ctcggtgcag-
EST: gi|76016068|gb|DT943238.1|DT943238
EST:     GACCGTGCCAATGGACAGGGTGTGCCTGCTGAGCTGCGGTGTGTCTTCAG                         G
genomic: GACCGTGCCAATGGACAGGGTGTGCCTGCTGAGCTGCGGTGTGTCTTCAGgtaaatcctg ... ctcggtgcag-
EST: gi|76016068|gb|DT943238.1|DT943238
EST:     GACCGTGCCAATGGACAGGGTGTGCCTGCTGAGCTGCGGTGTGTCTTCAG                         G
genomic: GACCGTGCCAATGGACAGGGTGTGCCTGCTGAGCTGCGGTGTGTCTTCAGgtaaatcctg ... ctcggtgcag-

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTCAGCGAGTACACGGTTGTCCATTCCGGATGTGCGGTGAAGGTTGGCCTGACCGTGCCAATGGACAGGGTGTGCCTGCTGAGCTGCGGTGTGTCTTCAGgtaaatcctgaggttcagagcttcagatatctgagagtagctgtgttagctcgtctgtttgtaggaacagtgccttagttaccttgcatggttgcacatttttgtggatctgatcatccctctttgttcatggttctatcgttaggactcggtgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC