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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCACAAAGGAAGGGTCAAAGAGGGGGTTGAGAAATCAAGAGACAGGTCAAGGAGCCGTAGTCCAAGGCCAAGgtgaagactttagttccttccacattatgtccagcattactttaaatcatcttttatggtaacccccctatatatacatatatgtgctctggtaagtaac...

Basic information

species Zea mays
transcript GRMZM2G110143_T03
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G110143_T03 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os08g37960.2 (Oryza sativa), 5'ss of exon 5
CCACAAAGGAAGGGTCAAAGAGGGGGTTGAGAAATCAAGAGACAGGTCAAGGAGCCGTAGTCCAAGGCCAAGgtgaagactttagttccttccacattatgtccagcattactttaaatcatcttt-tatggtaacccccctatatatacat---atatgtgctctggtaagtaac
 |  ||||||||| ||| ||| | ||||||||||||| | ||||||||||| |||||||| ||||||| |||||| | || ||| ||||||  || |||  |   ||||      || |  | ||| ||    ||      || || | | |   | || |   |  ||  |    
ACGAAAAGGAAGGATCATAGAAGAGGTTGAGAAATCACGGGACAGGTCAAGAAGCCGTAGCCCAAGGCGAAGgtgcataccttatttccttttactttactttt-gcatatagggaacttgtttttctaaaaaaaaataaataaatttccttcccaaatatttccatgttggc---
















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|32833902|gb|CD973580.1|CD973580
EST:     GGGGTTGAGAAATCAAGAGACAGGTCAAGGAGCCGTAGTCCAAGGCCAAG                         GCACAGAGACAGAGATGATAGAAGGCGAAGTCGCAGCAGGAGCAGGAGCAG
genomic: GGGGTTGAGAAATCAAGAGACAGGTCAAGGAGCCGTAGTCCAAGGCCAAGgtgaagactt ... ttttaactagGCACAGAGACAGAGATGATAGAAGGCGAAGTCGCAGCAGGAGCAGGAGCAG
EST: gi|8401368|gb|BE057002.1|BE057002
EST:     GGGGTTGAGAAATCAAGAGACAGGTCAAGGAGCCGTAGTCCAAGGCCAAG                         ACACAGAGACAGAGATGATAGAAGGCGAAGTCGCAGCAGGAGCAGGAGCAG
genomic: GGGGTTGAGAAATCAAGAGACAGGTCAAGGAGCCGTAGTCCAAGGCCAAGgtgaagactt ... ttttaactagGCACAGAGACAGAGATGATAGAAGGCGAAGTCGCAGCAGGAGCAGGAGCAG
EST: gi|32846542|gb|CD986223.1|CD986223
EST:     GGGGTTGAGAAATCAAGAGACAGGTCAAGGGGCCGTAGTCCAAGGCCAAG                         GCACAGAGACAGAGATGATAGAAGGCGAAGTCGCAGCAGGAGCAGGAGCAG
genomic: GGGGTTGAGAAATCAAGAGACAGGTCAAGGAGCCGTAGTCCAAGGCCAAGgtgaagactt ... ttttaactagGCACAGAGACAGAGATGATAGAAGGCGAAGTCGCAGCAGGAGCAGGAGCAG
EST: gi|149070638|gb|EE159049.2|EE159049
EST:     GGGGTTGAGAAATCAAGAGACAGGTCAAGGAGCCGTAGTCCAAGGCCAAG                         GCACAGAGACAGAGATGATAGAAGGCGAAGTCGCAGCAGGAGCAGGAGCAG
genomic: GGGGTTGAGAAATCAAGAGACAGGTCAAGGAGCCGTAGTCCAAGGCCAAGgtgaagactt ... ttttaactagGCACAGAGACAGAGATGATAGAAGGCGAAGTCGCAGCAGGAGCAGGAGCAG
EST: gi|33100333|gb|CF060293.1|CF060293
EST:     GGGGTTGAGAAATCAAGAGCCAGGTCAAGGAGCCGTAGTCCAAGGCCAAG                         GCACAGAGACAGAGATGATAGAAGGCGAAGTCGCAGCAGGAGCAGGAGCAG
genomic: GGGGTTGAGAAATCAAGAGACAGGTCAAGGAGCCGTAGTCCAAGGCCAAGgtgaagactt ... ttttaactagGCACAGAGACAGAGATGATAGAAGGCGAAGTCGCAGCAGGAGCAGGAGCAG
EST: gi|149107883|gb|EE292243.2|EE292243
EST:     GGGGTTGAGAAATCAAGAGACAGGTCAAGGAGCCGTAGTCCAAGGCCAAG                         GCACAGAGACAGAGATGATAGAAGGCGAAGTCGCAGCAGGAGCAGGAGCAG
genomic: GGGGTTGAGAAATCAAGAGACAGGTCAAGGAGCCGTAGTCCAAGGCCAAGgtgaagactt ... ttttaactagGCACAGAGACAGAGATGATAGAAGGCGAAGTCGCAGCAGGAGCAGGAGCAG
EST: gi|32835620|gb|CD975298.1|CD975298
EST:     GGGGTTGAGAAATCAAGAGACAGGTCAAGGAGCCGTAGTCCAAGGCCAAG                         GCACAGAGACAGAGATGATAGAAGGCGAAGTCGCAGCAGGAGCAGGAGCAG
genomic: GGGGTTGAGAAATCAAGAGACAGGTCAAGGAGCCGTAGTCCAAGGCCAAGgtgaagactt ... ttttaactagGCACAGAGACAGAGATGATAGAAGGCGAAGTCGCAGCAGGAGCAGGAGCAG

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
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---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCACAAAGGAAGGGTCAAAGAGGGGGTTGAGAAATCAAGAGACAGGTCAAGGAGCCGTAGTCCAAGGCCAAGgtgaagactttagttccttccacattatgtccagcattactttaaatcatcttttatggtaacccccctatatatacatatatgtgctctggtaagtaac

- - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - AAGGAG