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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tctgaagaccctgaaactccagtgattttcttgcttatttatgacatcaccagtaccctgtccatacagtaaaaatgttgctgaaatgattcgaacacagGCCTTTGTGAGCGAGTACGCTGTCTGGAGAAGTGACGCGGGTAGAGGCAGTCTTCTTGCTTCGTTGGCTGAAGCTGCTTTCCTCACTGGTCTGGAGAAGA

Basic information

species Zea mays
transcript GRMZM2G006130_T05
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G006130_T05 (Zea mays), 3'ss of exon 12
lower sequence: LOC_Os12g03470.3 (Oryza sativa), 3'ss of exon 13
--tctgaagaccctgaaactccagtgattttcttgcttatttatgacatcaccagtaccctgtccatacagtaaaaatgttgctgaaatgattcgaacacagGCCTTTGTGAGCGAGTACGCTGTCTGGAGAAGTGACGCGGGTAGAGGCAGTCTTCTTGCTTCGTTGGCTGAAGCTGCTTTCCTCACTGGTCTGGAGAAGA
   || |    | |  | ||  |  ||| | || || |||||||  | || |        || ||||  | || |  | ||  | | ||| || |    ||||| ||||| || || || ||||| ||||||||||| || |||||||| ||||| |||||||| ||||| |||||||||||||| ||||| ||||||||||
ttgcttattcacttctatctttacagatgtgct-gcctatttatctcttctcatccctattggccattaaatatatttcttcat-atatgttttggttgcagGCTTTTGTCAGTGAATATGCTGTTTGGAGAAGTGATGCAGGTAGAGGAAGTCTACTTGCTTCATTGGCAGAAGCTGCTTTCCTTACTGGACTGGAGAAGA

upper sequence: GRMZM2G006130_T05 (Zea mays), 3'ss of exon 12
lower sequence: LOC_Os11g03730.2 (Oryza sativa), 3'ss of exon 13
-----tctgaagaccctgaaactccagtgattttcttgcttatttatgacatcaccagtaccctgtccatacagtaaaaatgttgctgaaatgattcgaacacagGCCTTTGTGAGCGAGTACGCTGTCTGGAGAAGTGACGCGGGTAGAGGCAGTCTTCTTGCTTCGTTGGCTGAAGCTGCTTTCCTCACTGGTCTGGAGAAGA
     | ||| ||   | | |       |||  |||||     | ||  |||| |  |   | | | ||       |   |  | |  | ||| || |    ||||| ||||| || || || ||||| ||||||||||| || |||||||| ||||| |||||||| ||||| || || |||||||| ||||| ||||||||||
tcatgtgtgatgatgtttacatgttttggataatcttggaacctcattgcatctcttg---cttattcactt--ctatctttcttcatatatgttttggttgcagGCTTTTGTCAGTGAATATGCTGTTTGGAGAAGTGATGCAGGTAGAGGAAGTCTACTTGCTTCATTGGCAGAGGCAGCTTTCCTTACTGGACTGGAGAAGA
















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|32924623|gb|CF029435.1|CF029435
EST:     TGTTTAACATGAGGAGCACATTTGACAGAACATCTCGTAGTGGACCTAAG                         GCTTTTGTGAGCGAGT
genomic: TGTTTAACATGAGGAGCACATTTGACAGAACATCACGTAGTGGACCTAAGgtaagtctaa ... tcgaacacagGCCTTTGTGAGCGAGT
EST: gi|211495379|gb|FL350690.1|FL350690
EST:     TGTTTAACATGAGGAGCACATTTGACAGAACATCACGTAGTGGACCTAAG                         GCCTTTGTGAGCGAGTACGCTGTCTGGAGAAGTGACGCGGGTAGAGGCAGT
genomic: TGTTTAACATGAGGAGCACATTTGACAGAACATCACGTAGTGGACCTAAGgtaagtctaa ... tcgaacacagGCCTTTGTGAGCGAGTACGCTGTCTGGAGAAGTGACGCGGGTAGAGGCAGT
EST: gi|32924613|gb|CF029425.1|CF029425
EST:     TGTTTAACATGAGGAGCACATTTGACAGAACATCTCGTAGTGGACCTAAG                         GCTTTTGTGAGCGAGTA
genomic: TGTTTAACATGAGGAGCACATTTGACAGAACATCACGTAGTGGACCTAAGgtaagtctaa ... tcgaacacagGCCTTTGTGAGCGAGTA
EST: gi|211336372|gb|FL380531.1|FL380531
EST:     TGTTTAACATGAGGAGCACATTTGACAGAACATCACGTAGTGGACCTAAG                         GCCTTTGTGAGCGAGTACGCTGTCTGGAGAAGTGACGCGGGTAGAGGCAGT
genomic: TGTTTAACATGAGGAGCACATTTGACAGAACATCACGTAGTGGACCTAAGgtaagtctaa ... tcgaacacagGCCTTTGTGAGCGAGTACGCTGTCTGGAGAAGTGACGCGGGTAGAGGCAGT
EST: gi|32929966|gb|CF034778.1|CF034778
EST:     TGTTTAACATGAGGAGCACATTTGACAGAACATCTCGTAGTGGACCTAAG                         GCTTTTGTGAGCGAGT
genomic: TGTTTAACATGAGGAGCACATTTGACAGAACATCACGTAGTGGACCTAAGgtaagtctaa ... tcgaacacagGCCTTTGTGAGCGAGT
EST: gi|32929408|gb|CF034220.1|CF034220
EST:     TGTTTAACATGAGGAGCACATTTGACAGAACATCTCGTAGTGGACCTAAG                         GCTTTTGTGAGCGAGT
genomic: TGTTTAACATGAGGAGCACATTTGACAGAACATCACGTAGTGGACCTAAGgtaagtctaa ... tcgaacacagGCCTTTGTGAGCGAGT
EST: gi|211098336|gb|FL317177.1|FL317177
EST:     TGTTTAACATGAGGAGCACATTTGACAGAACATCACGTA--KKACCTAAG                         GCCTTTGTGAGCGAGTACGCTGTCTGGAGAAGTGACGCGGGTAGAGGCAGT
genomic: TGTTTAACATGAGGAGCACATTTGACAGAACATCACGTAGTGGACCTAAGgtaagtctaa ... tcgaacacagGCCTTTGTGAGCGAGTACGCTGTCTGGAGAAGTGACGCGGGTAGAGGCAGT
EST: gi|32924183|gb|CF028995.1|CF028995
EST:     TGTTTAACATGAGGAGCACATTTGACAGAACATCTCGTAGTGGACCTAAG                         GCTTTTGTGAGCGAGTA
genomic: TGTTTAACATGAGGAGCACATTTGACAGAACATCACGTAGTGGACCTAAGgtaagtctaa ... tcgaacacagGCCTTTGTGAGCGAGTA
EST: gi|32924017|gb|CF028829.1|CF028829
EST:     TGTTTAACATGAGGAGCACATTTGACAGAACATCTCGTAGTGGACCTAAG                         GCTTTTGTGAGCGAGT
genomic: TGTTTAACATGAGGAGCACATTTGACAGAACATCACGTAGTGGACCTAAGgtaagtctaa ... tcgaacacagGCCTTTGTGAGCGAGT
EST: gi|87151803|gb|DY396592.1|DY396592
EST:     TGTTTAACATGAGGAGCACATTTGACAGAACATCTCGTAGTGGACCTAAG                         GCCTTTGTGAGCGAGTACGCTGTCTGGAGAAGTGACGCGGGTAGAGGCAGT
genomic: TGTTTAACATGAGGAGCACATTTGACAGAACATCACGTAGTGGACCTAAGgtaagtctaa ... tcgaacacagGCCTTTGTGAGCGAGTACGCTGTCTGGAGAAGTGACGCGGGTAGAGGCAGT
EST: gi|32928349|gb|CF033161.1|CF033161
EST:     TGTTTAACATGAGGAGCACATTTGACAGAACATCTCGTAGTGGACCTAAG                         GCTTTTGTGAGCGAGTA
genomic: TGTTTAACATGAGGAGCACATTTGACAGAACATCACGTAGTGGACCTAAGgtaagtctaa ... tcgaacacagGCCTTTGTGAGCGAGTA
EST: gi|32923966|gb|CF028778.1|CF028778
EST:     TGTTTAACATGAGGAGCACATTTGACAGAACATCTCGTAGTGGACCTAAG                         GCTTTTGTGAGCGAGT
genomic: TGTTTAACATGAGGAGCACATTTGACAGAACATCACGTAGTGGACCTAAGgtaagtctaa ... tcgaacacagGCCTTTGTGAGCGAGT
EST: gi|20300152|gb|BQ163095.1|BQ163095
EST:     TGTTTAACATGAGGAGCACATTTGACAGAACATCTCGTAGTGGACCTAAG                         GCCTTTGTGAGCGAGTACGCTGTCTGGAGAAGTGACGCGGGTAGAGGCAGT
genomic: TGTTTAACATGAGGAGCACATTTGACAGAACATCACGTAGTGGACCTAAGgtaagtctaa ... tcgaacacagGCCTTTGTGAGCGAGTACGCTGTCTGGAGAAGTGACGCGGGTAGAGGCAGT
EST: gi|211378660|gb|FL357038.1|FL357038
EST:     TGTTTAACATGAGGAGCACATTTGACAGAACATCACGTAGTGGACCTAAG                         GCCTTTGTGAGCGAGTACGCTGTCTGGAGAAGTGACGCGGGTAGAGGCAGT
genomic: TGTTTAACATGAGGAGCACATTTGACAGAACATCACGTAGTGGACCTAAGgtaagtctaa ... tcgaacacagGCCTTTGTGAGCGAGTACGCTGTCTGGAGAAGTGACGCGGGTAGAGGCAGT
EST: gi|211258110|gb|FL346334.1|FL346334
EST:     TGTTTAACATGAGGAGCACATTTGACAGAACATCACGTAGTGGACCTAAG                         GCCTTTGTGAGCGAGTACGCTGTCTGGAGAAGTGACGCGGGTAGAGGCAGT
genomic: TGTTTAACATGAGGAGCACATTTGACAGAACATCACGTAGTGGACCTAAGgtaagtctaa ... tcgaacacagGCCTTTGTGAGCGAGTACGCTGTCTGGAGAAGTGACGCGGGTAGAGGCAGT
EST: gi|18654846|gb|BM499651.1|BM499651
EST:     TGTTTAACATGAGGAGCACATTTGACAGAACATCTCGTAGTGGACCTAAG                         GCCTTTGTGAGCGAGTACGCTGTCTGGAGAAGTGACGCGGGTAGAGGCAGT
genomic: TGTTTAACATGAGGAGCACATTTGACAGAACATCACGTAGTGGACCTAAGgtaagtctaa ... tcgaacacagGCCTTTGTGAGCGAGTACGCTGTCTGGAGAAGTGACGCGGGTAGAGGCAGT
EST: gi|211474807|gb|FL320108.1|FL320108
EST:     TGTTTAACATGAGGAGCACATNTGACAGAACATCACGTAGTGGACCTAAG                         GCCTTTGTGAGCGAGTACGCTGTCTGGAGAAGTGACGCGGGTAGAGGCAGT
genomic: TGTTTAACATGAGGAGCACATTTGACAGAACATCACGTAGTGGACCTAAGgtaagtctaa ... tcgaacacagGCCTTTGTGAGCGAGTACGCTGTCTGGAGAAGTGACGCGGGTAGAGGCAGT
EST: gi|32924051|gb|CF028863.1|CF028863
EST:     TGTTTAACATGAGGAGCACATTTGACAGAACATCTCGTAGTGGACCTAAG                         GCTTTTGTGAGCGAGT
genomic: TGTTTAACATGAGGAGCACATTTGACAGAACATCACGTAGTGGACCTAAGgtaagtctaa ... tcgaacacagGCCTTTGTGAGCGAGT
EST: gi|32923839|gb|CF028651.1|CF028651
EST:     TGTTTAACATGAGGAGCACATTTGACAGAACATCTCGTAGTGGACCTAAG                         GCTTTTGTGAGCGAGTAC
genomic: TGTTTAACATGAGGAGCACATTTGACAGAACATCACGTAGTGGACCTAAGgtaagtctaa ... tcgaacacagGCCTTTGTGAGCGAGTAC
EST: gi|21331549|gb|BQ486930.1|BQ486930
EST:     TGTTTAACATGAGGAGCACATTTGACAGAACATCTCGTAGTGGACCTAAG                         GCTTTTGTGAGCGAGTACGCTGTCTGGAGAAGTGACGCGGGTAGAGGCA
genomic: TGTTTAACATGAGGAGCACATTTGACAGAACATCACGTAGTGGACCTAAGgtaagtctaa ... tcgaacacagGCCTTTGTGAGCGAGTACGCTGTCTGGAGAAGTGACGCGGGTAGAGGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atcaccagtaccctgtccatacagtaaaaatgttgctgaaatgattcgaacacagGCCTTTGTGAGCGAGTACGCTGTCTGGAGAAGTGACGCGGGTAGAGGCAGTCTTCTTGCTTCGTTGGCTGAAGCTGCTTTCCTCACTGGTCTGGAGAAGA
                        taaaaatgtt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tctgaagaccctgaaactccagtgattttcttgcttatttatgacatcaccagtaccctgtccatacagtaaaaatgttgctgaaatgattcgaacacagGCCTTTGTGAGCGAGTACGCTGTCTGGAGAAGTGACGCGGGTAGAGGCAGTCTTCTTGCTTCGTTGGCTGAAGCTGCTTTCCTCACTGGTCTGGAGAAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA