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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATAGCAGTCTGTGCTGATGATCCTGAATATCGTCACTACAACGACATCAGTGAGCTGTCTCCTCATCGCCTGCAAGAGATCAAGCGGTTCTTTGAAGATTgtatcctgctcgattcatctattgttttctgactacacaatgctctagtatatttgggacgatcacatccacaggtttaagcttccttagcggtatcttctag

Basic information

species Zea mays
transcript GRMZM2G061928_T04
intron # 7
splice site 5'
intron type U12 (go to U12 genes for details)

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G061928_T02 (Zea mays), 5'ss of exon 7
lower sequence: LOC_Os04g59040.1 (Oryza sativa), 5'ss of exon 7
ATAGCAGTCTGTGCTGATGATCCTGAATATCGTCACTACAACGACATCAGTGAGCTGTCTCCTCATCGCCTGCAAGAGATCAAGCGGTTCTTTGAAGATTgtatcctgctcgattcatctattgttttctgactacacaatgc-tctagtatatttgggacgatcacatccacaggtttaagcttccttagcggtat-cttctag
|||||||| |||||||||||||||||||| ||||| ||||| ||||||||||||||||||||||| ||||| |||||||| || || ||||||||||| ||||||||  | |     | ||| ||||    | | || |   | | ||||||| |      | |||     |||  | | |   |||||| |  |||  || |||
ATAGCAGTATGTGCTGATGATCCTGAATACCGTCATTACAATGACATCAGTGAGCTGTCTCCTCACCGCCTCCAAGAGATTAAACGCTTCTTTGAAGACTgtatcctcatagtccgttttatggttta--aattgcatatcccatatagtatagt---attggtcatgcatacatctgttattgtccttaacaatatgtttttag
















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|211146692|gb|FK994974.1|FK994974
EST:     AGCTGTCTCCTCATCGCCTGCAAGAGATCAAGCGGTTCCTTTTGA-GATT                         ATCAGAGGAATGAGAATAAAGAGGTTGCTGTCGATGCAATCTTTGCCTGC
genomic: AGCTGTCTCCTCATCGCCTGCAAGAGATCAAGCGGTTC-TTT-GAAGATTgtatcctgct ... tatcttctagATAAGAAGAATGAGAATAAAGAGGTTGCTGTCGATGCATTCTT-GCCTGC
EST: gi|32825698|gb|CD965408.1|CD965408
EST:     TGAGCTGTCTCCTCATCGCCTGCAAGAGATCAAGCGGTTCTTTGAAGATT                         ATAAGAAGAATGAGAATAAAGAGGTTGCTGTCGATGCATTCTTGCCTGCGA
genomic: TGAGCTGTCTCCTCATCGCCTGCAAGAGATCAAGCGGTTCTTTGAAGATTgtatcctgct ... tatcttctagATAAGAAGAATGAGAATAAAGAGGTTGCTGTCGATGCATTCTTGCCTGCGA
EST: gi|211091461|gb|FK999164.1|FK999164
EST:     TGAGCTGTCTCCTCATCGCCTGCAAGAGATCAAGCGGTTCTTTGAAGATT                         ATAAGAAGAATGAGAATAAAGAGGTTGCTGTCGATGCATTCTTGCCTGCGA
genomic: TGAGCTGTCTCCTCATCGCCTGCAAGAGATCAAGCGGTTCTTTGAAGATTgtatcctgct ... tatcttctagATAAGAAGAATGAGAATAAAGAGGTTGCTGTCGATGCATTCTTGCCTGCGA
EST: gi|28930839|gb|CB334200.1|CB334200
EST:     TGAGCTGTCTCCTCATCGCCTGCAAGAGATCAAGCGGTT-TTTGAAGAT-                         ATAAGAAGAATGAGAATAAAGAGGGTGCTG
genomic: TGAGCTGTCTCCTCATCGCCTGCAAGAGATCAAGCGGTTCTTTGAAGATTgtatcctgct ... tatcttctagATAAGAAGAATGAGAATAAAGAGGTTGCTG
EST: gi|211091460|gb|FK999163.1|FK999163
EST:     TGAGCTGTCTCCTCATCGCCTGCAAGAGATCAAGCGGTTCTTTGAAGATT                         ATAAGAAGAATGAGAATAAAGAGGNTGCTGTCGATGCATTCTTGCCTGCGA
genomic: TGAGCTGTCTCCTCATCGCCTGCAAGAGATCAAGCGGTTCTTTGAAGATTgtatcctgct ... tatcttctagATAAGAAGAATGAGAATAAAGAGGTTGCTGTCGATGCATTCTTGCCTGCGA
EST: gi|74237956|gb|DT645870.1|DT645870
EST:     TGAGCTGTCTCCTCATCGCCTGCAAGAGATCAAGCGGTTCTTTGAAGATT                         ATAAGAAGAATGAGAATAAAGAGGTTGCTGTCGATGCATTCTTGCCTGCGA
genomic: TGAGCTGTCTCCTCATCGCCTGCAAGAGATCAAGCGGTTCTTTGAAGATTgtatcctgct ... tatcttctagATAAGAAGAATGAGAATAAAGAGGTTGCTGTCGATGCATTCTTGCCTGCGA
EST: gi|211270190|gb|FL112873.1|FL112873
EST:     TGAGCTGTCTCCTCATCGCCTGCAAGAGATCAAGCGGGTCTTTGAAGATT                         ATAAGAAGA-TGAGAATAAAGNAG-TTGCTGTCGATGCATTCTTGCCTG
genomic: TGAGCTGTCTCCTCATCGCCTGCAAGAGATCAAGCGGTTCTTTGAAGATTgtatcctgct ... tatcttctagATAAGAAGAATGAGAATAAAG-AGGTTGCTGTCGATGCATTCTTGCCTG
EST: gi|211148121|gb|FK994989.1|FK994989
EST:     TGAGCTGTCTCCTCATCGCCTGCAAGAGATCAAGCGGTTCTTTGAAGATT                         ATAAGAAGA-TGAGAATAAAGAGGTTGCTGTCGATGCATTCTTGCCTGCGA
genomic: TGAGCTGTCTCCTCATCGCCTGCAAGAGATCAAGCGGTTCTTTGAAGATTgtatcctgct ... tatcttctagATAAGAAGAATGAGAATAAAGAGGTTGCTGTCGATGCATTCTTGCCTGCGA
EST: gi|5901386|gb|AW042486.1|AW042486
EST:     TGAGCTGTCTCCTCATCGCCTGCAAGAGATCAAGCGGTTCTTTGAAGATT                         ATAAGAAGAATGAGAATAAAGAGGTTGCTGTCGATGCATTCTTGCCTGCG
genomic: TGAGCTGTCTCCTCATCGCCTGCAAGAGATCAAGCGGTTCTTTGAAGATTgtatcctgct ... tatcttctagATAAGAAGAATGAGAATAAAGAGGTTGCTGTCGATGCATTCTTGCCTGCG
EST: gi|32838675|gb|CD978353.1|CD978353
EST:     TGAGCTGTCTCCTCATCGCCTGCAAGAGATCAAGCGGTTCTTTGAAGATT                         ATAAGAAGAATGAGAATAAAGAGGTTGCTGTCGATGCATTCTTGCCTGCGA
genomic: TGAGCTGTCTCCTCATCGCCTGCAAGAGATCAAGCGGTTCTTTGAAGATTgtatcctgct ... tatcttctagATAAGAAGAATGAGAATAAAGAGGTTGCTGTCGATGCATTCTTGCCTGCGA
EST: gi|5325092|gb|AI783283.1|AI783283
EST:     TGAGCTGTCTCCTCATCGCCTGCAAGAGATCAAGCGGTTCTTTGAAGATT                         ATAAGAAGAATGAGAATAAAGAGGTTGCTGTCGATGCATTCTTGCCTGCGA
genomic: TGAGCTGTCTCCTCATCGCCTGCAAGAGATCAAGCGGTTCTTTGAAGATTgtatcctgct ... tatcttctagATAAGAAGAATGAGAATAAAGAGGTTGCTGTCGATGCATTCTTGCCTGCGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATAGCAGTCTGTGCTGATGATCCTGAATATCGTCACTACAACGACATCAGTGAGCTGTCTCCTCATCGCCTGCAAGAGATCAAGCGGTTCTTTGAAGATTgtatcctgctcgattcatctattgttttctgactacacaatgctctagtatatttgggacgatcacatccacaggtttaagcttccttagcggtatcttctag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA