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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACTGTTGCAAAAAGCGTGGAGTTCGAGGATAGCGCGAAGAATGTTGGGGCGAATCTGGTGAAGCAAGTTGCTGATGCTACGAACAAAGCTGCAGGGGATGgtgggcaccagggcttcgtgaaatcactgttttttttcgtgaatcagcatctgaactacctgtcagctgctatacatcactacatgacccatcttaatct...

Basic information

species Zea mays
transcript GRMZM2G074790_T03
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G074790_T03 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os05g46290.1 (Oryza sativa), 5'ss of exon 3
ACTGTTGCAAAAAGCGTGGAGTTCGAGGATAGCGCGAAGAATGTTGGGGCGAATCTGGTGAAGCAAGTTGCTGATGCTACGAACAAAGCTGCAGGGGATGgtgggcaccagggcttcgtgaaatcactgttttttttcgtgaatcagcatctgaactacctgtcagct---gctat----acatcactacatgacccatcttaatct
|| |||||||||||| | ||||| ||||| || || ||||||||||| || || |||||||||||||||||||| ||||| || || |  ||||| ||||||  | ||| | |||    ||||| |||      || | |||     ||| |||||||  | |  | |   ||| |    | | ||    |  | ||   || || |
ACGGTTGCAAAAAGCATTGAGTTTGAGGACAGTGCTAAGAATGTTGGTGCAAACCTGGTGAAGCAAGTTGCTGAAGCTACTAATAAGGTCGCAGGAGATGgtaaggacc-gagctctaggaaattact------ttacttgagctgccatatgaactatatattcgattgagctttgagcatagcagattagcatcccgtttgattt
















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|149014572|gb|EE044215.2|EE044215
EST:     GAATCTGGTGAAGCAAGTTGCTGATGCTACGAACAAAGCTGCAGGGGATG                         GTACCACCTGTGCAACTGTGCTTACACAGGCAATTCTTACTGAAGGATGCA
genomic: GAATCTGGTGAAGCAAGTTGCTGATGCTACGAACAAAGCTGCAGGGGATGgtgggcacca ... ctgaaaacagGTACCACCTGTGCAACTGTGCTTACACAGGCAATTCTTACTGAAGGATGCA
EST: gi|71438972|gb|DR820022.1|DR820022
EST:     GAATCTGGTGAAGCAAGTTGCTGATGCTACGAACAAAGCTGCAGGGGATG                         GTACCACCTGTGCAACTGTGCTTACACAGGCAATTCTTACTGAAGGATGCA
genomic: GAATCTGGTGAAGCAAGTTGCTGATGCTACGAACAAAGCTGCAGGGGATGgtgggcacca ... ctgaaaacagGTACCACCTGTGCAACTGTGCTTACACAGGCAATTCTTACTGAAGGATGCA
EST: gi|18649393|gb|BM498212.1|BM498212
EST:     TGCTGATGCTACGAACAAAGCTGCAGGAGATG                         GTACCACCTGTGCAACTGTGCTTACACAGGCAATTCTTACTGAAGGATGC-
genomic: TGCTGATGCTACGAACAAAGCTGCAGGGGATGgtgggcacca ... ctgaaaacagGTACCACCTGTGCAACTGTGCTTACACAGGCAATTCTTACTGAAGGATGCA
EST: gi|211181733|gb|FL012624.1|FL012624
EST:     GAATCTGGTGAAGCAAGTTGCTGATGCTACGAACAAAGCTGCAGGGGATG                         GTACCACCTGTGCAACTGTGCTTACACAGGCAATTCTTACTGAAGGATGCA
genomic: GAATCTGGTGAAGCAAGTTGCTGATGCTACGAACAAAGCTGCAGGGGATGgtgggcacca ... ctgaaaacagGTACCACCTGTGCAACTGTGCTTACACAGGCAATTCTTACTGAAGGATGCA
EST: gi|28909718|gb|CB331067.1|CB331067
EST:     GAATCTGGTGAAGCAAGTTGCTGATGCTACGAACAAAGCTGCAGGGGATG                         GTACCACCTGTGCAACTGTGCTTACACAGGCAATTCTTACTGAAGGATGCA
genomic: GAATCTGGTGAAGCAAGTTGCTGATGCTACGAACAAAGCTGCAGGGGATGgtgggcacca ... ctgaaaacagGTACCACCTGTGCAACTGTGCTTACACAGGCAATTCTTACTGAAGGATGCA
EST: gi|149083932|gb|EE173310.2|EE173310
EST:     GAATCTGGTGAAGCAAGTTGCTGATGCTACGAACAAAGCTGCAGGGGATG                         GTACCACCTGTGCAACTGTGCTTACACAGGCAATTCTTACTGAAGGATGCA
genomic: GAATCTGGTGAAGCAAGTTGCTGATGCTACGAACAAAGCTGCAGGGGATGgtgggcacca ... ctgaaaacagGTACCACCTGTGCAACTGTGCTTACACAGGCAATTCTTACTGAAGGATGCA
EST: gi|149051769|gb|EE155894.2|EE155894
EST:     GAATCTGGTGAAGCAAGTTGCTGATGCTACGAACAAAGCTGCAGGGGATG                         GTACCACCTGTGCAACTGTGCTTACACAGGCAATTCTTACTGAAGGATGCA
genomic: GAATCTGGTGAAGCAAGTTGCTGATGCTACGAACAAAGCTGCAGGGGATGgtgggcacca ... ctgaaaacagGTACCACCTGTGCAACTGTGCTTACACAGGCAATTCTTACTGAAGGATGCA
EST: gi|148966460|gb|EE017469.2|EE017469
EST:     GAATCTGGTGAAGCAAGTTGCTGATGCTACGAACAAAGCTGCAGGGGATG                         GTACCACCTGTGCAACTGTGCTTACACAGGCAATTCTTACTGAAGGATGCA
genomic: GAATCTGGTGAAGCAAGTTGCTGATGCTACGAACAAAGCTGCAGGGGATGgtgggcacca ... ctgaaaacagGTACCACCTGTGCAACTGTGCTTACACAGGCAATTCTTACTGAAGGATGCA
EST: gi|78120143|gb|DV538527.1|DV538527
EST:     GAATCTGGTGAAGCAAGTTGCTGATGCTACGAACAAAGCTGCAGGGGATG                         GTACCACCTGTGCAACTGTGCTTACACAGGCAATTCTTACTGAAGGATGCA
genomic: GAATCTGGTGAAGCAAGTTGCTGATGCTACGAACAAAGCTGCAGGGGATGgtgggcacca ... ctgaaaacagGTACCACCTGTGCAACTGTGCTTACACAGGCAATTCTTACTGAAGGATGCA
EST: gi|78118616|gb|DV537000.1|DV537000
EST:     GAATCTGGTGAAGCAAGTTGCTGATGCTACGAACAAAGCTGCAGGGGATG                         GTACCACCTGTGCAACTGTGCTTACACAGGCAATTCTTACTGAAGGATGCA
genomic: GAATCTGGTGAAGCAAGTTGCTGATGCTACGAACAAAGCTGCAGGGGATGgtgggcacca ... ctgaaaacagGTACCACCTGTGCAACTGTGCTTACACAGGCAATTCTTACTGAAGGATGCA
EST: gi|18649617|gb|BM498436.1|BM498436
EST:     CTGATGCTACGAACAAAGCTGCAGGAGATG                         GTACCACCTGTGCAACTGTGCTTACACAGGCAATTCTTACTGAAGGATGC-
genomic: CTGATGCTACGAACAAAGCTGCAGGGGATGgtgggcacca ... ctgaaaacagGTACCACCTGTGCAACTGTGCTTACACAGGCAATTCTTACTGAAGGATGCA
EST: gi|148937683|gb|EC881881.2|EC881881
EST:     GAATCTGGTGAAGCAAGTTGCTGATGCTACGAACAAAGCTGCAGGGGATG                         GTACCACCTGTGCAACTGTGCTTACACAGGCAATTCTTACTGAAGGATGCA
genomic: GAATCTGGTGAAGCAAGTTGCTGATGCTACGAACAAAGCTGCAGGGGATGgtgggcacca ... ctgaaaacagGTACCACCTGTGCAACTGTGCTTACACAGGCAATTCTTACTGAAGGATGCA
EST: gi|31351656|gb|CD436013.1|CD436013
EST:     TAATCTGGTGAAGCAAGTTGCTGATGCTACGAACAAACCTGCAGGGGATG                         GTACCACCTGTGCAACTGTGCTTACACAGGCAATTCTTACTGAAGGATGCA
genomic: GAATCTGGTGAAGCAAGTTGCTGATGCTACGAACAAAGCTGCAGGGGATGgtgggcacca ... ctgaaaacagGTACCACCTGTGCAACTGTGCTTACACAGGCAATTCTTACTGAAGGATGCA
EST: gi|31350305|gb|CD434662.1|CD434662
EST:     GAATCTGGTGAAGCAAGTTGCTGATGCTACGAACAAAGCTGCAGGGGATG                         GTACCACCTGTGCAACTGTGCTTACACAGGCAATTCTTACTGAAGGATGCA
genomic: GAATCTGGTGAAGCAAGTTGCTGATGCTACGAACAAAGCTGCAGGGGATGgtgggcacca ... ctgaaaacagGTACCACCTGTGCAACTGTGCTTACACAGGCAATTCTTACTGAAGGATGCA
EST: gi|211181732|gb|FL012623.1|FL012623
EST:     GAATCTGGTGAAGCAAGTTGCTGATGCTACGAACAAAGCTGCAGGGGATG                         GTACCACCTGTGCAACTGTGCTTACACAGGCAATTCTTACTGAAGGATGCA
genomic: GAATCTGGTGAAGCAAGTTGCTGATGCTACGAACAAAGCTGCAGGGGATGgtgggcacca ... ctgaaaacagGTACCACCTGTGCAACTGTGCTTACACAGGCAATTCTTACTGAAGGATGCA
EST: gi|18648744|gb|BM497563.1|BM497563
EST:     AGTTGCTGATGCTACGAAC-AAGCTGCAGGAGATG                         GTACCACCTGTGCAACTGTGCTTACACAGGCAATTCTTACTGAAGGATGCA
genomic: AGTTGCTGATGCTACGAACAAAGCTGCAGGGGATGgtgggcacca ... ctgaaaacagGTACCACCTGTGCAACTGTGCTTACACAGGCAATTCTTACTGAAGGATGCA
EST: gi|67015320|gb|CO444069.1|CO444069
EST:     GAATCTGGTGAAGCAAGTTGCTGATGCTACGAACAAAGCTGCAGGGGATG                         GTACCACCTGTGCAACTGTGCTTACACAGGCAATTCTTACTGAAGGATGCA
genomic: GAATCTGGTGAAGCAAGTTGCTGATGCTACGAACAAAGCTGCAGGGGATGgtgggcacca ... ctgaaaacagGTACCACCTGTGCAACTGTGCTTACACAGGCAATTCTTACTGAAGGATGCA
EST: gi|74242338|gb|DT650252.1|DT650252
EST:     GAATCTGGTGAAGCAAGTTGCTGATGCTACGAACAAAGCTGCAGGGGATG                         GTACCACCTGTGCAACTGTGCTTACACAGGCAATTCTTACTGAAGGATGCA
genomic: GAATCTGGTGAAGCAAGTTGCTGATGCTACGAACAAAGCTGCAGGGGATGgtgggcacca ... ctgaaaacagGTACCACCTGTGCAACTGTGCTTACACAGGCAATTCTTACTGAAGGATGCA
EST: gi|149010196|gb|EE042014.2|EE042014
EST:     GAATCTGGTGAAGCAAGTTGCTGATGCTACGAACAAAGCTGCAGGGGATG                         GTACCACCTGTGCAACTGTGCTTACACAGGCAATTCTTACTGAAGGATGCA
genomic: GAATCTGGTGAAGCAAGTTGCTGATGCTACGAACAAAGCTGCAGGGGATGgtgggcacca ... ctgaaaacagGTACCACCTGTGCAACTGTGCTTACACAGGCAATTCTTACTGAAGGATGCA
EST: gi|31664231|gb|CD572956.1|CD572956
EST:     GAATCTGGTGAAGCAAGTTGCTGATGCTACGAACAAAGCTGCAGGGGATG                         GTACCACCTGTGCAACTGTGCTTACACAGGCAATTCTTACTGAAGGATGCA
genomic: GAATCTGGTGAAGCAAGTTGCTGATGCTACGAACAAAGCTGCAGGGGATGgtgggcacca ... ctgaaaacagGTACCACCTGTGCAACTGTGCTTACACAGGCAATTCTTACTGAAGGATGCA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACTGTTGCAAAAAGCGTGGAGTTCGAGGATAGCGCGAAGAATGTTGGGGCGAATCTGGTGAAGCAAGTTGCTGATGCTACGAACAAAGCTGCAGGGGATGgtgggcaccagggcttcgtgaaatcactgttttttttcgtgaatcagcatctgaactacctgtcagctgctatacatcactacatgacccatcttaatct

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG