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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAGCAGAAGTGTGTTCCCCTAGAGGACCTAGCTGCAGAGTTCAGGATGCGAACCCAGgtacttcaaaattacgtataagatgttcgaatgctgttatgaataataggattaacttcccatgccctattatttttaaatagaaattgtgataatgccc...

Basic information

species Zea mays
transcript GRMZM2G179429_T03
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G179429_T03 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os07g01320.1 (Oryza sativa), 5'ss of exon 6
AAGCAGAAGTGTGTTCCCCTAGAGGACCTAGCTGCAGAGTTCAGGATGCGAACCCAGgtacttcaaaattacgtataagatgttcgaa-------tgctgttatgaataataggattaacttcccatgccctattatttttaaatagaaattgtgataatgccc
|| |||||||||||||| ||||||||||| || ||||||||||||||| |||| |||||| || || |     |||| |   |  | |       | ||  |     ||| |  ||||||     |||| || | |  | |||    |  |    |        
AACCAGAAGTGTGTTCCTCTAGAGGACCTTGCCGCAGAGTTCAGGATGAGAACACAGgtaattaaagagcctttatatgccatagggactagtgttactactgctgctaacatcattaacactttatgcactctgagctataaggtcatgtcagaac-------
















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|88754687|gb|DY538828.1|DY538828
EST:     TGTTTCCCTAGAGGACCTAGCTGCAGAGTTCAGGATGCGAACCCAG                         GACTGTATCAATCGGATTGTTACTCTGGAAAGCATGGATAG
genomic: TGTTCCCCTAGAGGACCTAGCTGCAGAGTTCAGGATGCGAACCCAGgtacttcaaa ... tcatttgcagGACTGTATCAATCGGATTGTTACTCTGGAAAGCATGGGTAT
EST: gi|31364129|gb|CD448484.1|CD448484
EST:     AGTGTGTTCCCCTAGAGGACCTAGCTGCAGAGTTCAGGATGCGAACCCAG                         GACTGTATCAATCGGATTGTTACTCTGGAAAGCATGGATAG
genomic: AGTGTGTTCCCCTAGAGGACCTAGCTGCAGAGTTCAGGATGCGAACCCAGgtacttcaaa ... tcatttgcagGACTGTATCAATCGGATTGTTACTCTGGAAAGCATGGGTAT
EST: gi|60357983|gb|DN224956.1|DN224956
EST:     AGTGTGTTCCCCTAGAGGACCTAGCTGCAGAGTTCAGGATGCGAACCCAG                         GACTGTATCAATCGGATTGTTACTCTGGAAAGCATGGATAG
genomic: AGTGTGTTCCCCTAGAGGACCTAGCTGCAGAGTTCAGGATGCGAACCCAGgtacttcaaa ... tcatttgcagGACTGTATCAATCGGATTGTTACTCTGGAAAGCATGGGTAT
EST: gi|76014913|gb|DT942083.1|DT942083
EST:     AGTGTGTTCCCCTAGAGGACCTAGCTGCAGAGTTCAGGATGCGAACCCAG                         GACTGTATCAATCCGATTGTTACTC
genomic: AGTGTGTTCCCCTAGAGGACCTAGCTGCAGAGTTCAGGATGCGAACCCAGgtacttcaaa ... tcatttgcagGACTGTATCAATCGGATTGTTACTC
EST: gi|76014912|gb|DT942082.1|DT942082
EST:     AGTGTGTTCCCCTAGAGGACCTAGCTGCAGAGTTCAGGATGCGAACCCAG                         GACTGTATCAATCGGATTGTTACTCTGGAAAGCATGGATAG
genomic: AGTGTGTTCCCCTAGAGGACCTAGCTGCAGAGTTCAGGATGCGAACCCAGgtacttcaaa ... tcatttgcagGACTGTATCAATCGGATTGTTACTCTGGAAAGCATGGGTAT
EST: gi|32165071|gb|CD670389.1|CD670389
EST:     AGTGTGTTCCCCTAGAGGACCTAGCTGCAGAGTTCAGGATGCGAACCCAG                         GACTGTATCAATCGGATTGTTACTCTGGAAAGCATGGATAG
genomic: AGTGTGTTCCCCTAGAGGACCTAGCTGCAGAGTTCAGGATGCGAACCCAGgtacttcaaa ... tcatttgcagGACTGTATCAATCGGATTGTTACTCTGGAAAGCATGGGTAT
EST: gi|148956262|gb|EC902060.2|EC902060
EST:     GTGTGTTCCCCTAGAGGACCTAGCTGCAGAGTTCAGGATGCCGA-CCCAG                         GACTGTATCAATCGGATTGTTACTCTGGAAAGCATGG
genomic: GTGTGTTCCCCTAGAGGACCTAGCTGCAGAGTTCAGGATGC-GAACCCAGgtacttcaaa ... tcatttgcagGACTGTATCAATCGGATTGTTACTCTGGAAAGCATGG
EST: gi|91048409|gb|EB158827.1|EB158827
EST:     AGTGTGTTCCCCTAGAGGACCTAGCTGCAGAGTTCAGGATGCGAACCCAG                         GACTGTATCAATCGGATTGTTACTCTGGAAAGCATGGATAG
genomic: AGTGTGTTCCCCTAGAGGACCTAGCTGCAGAGTTCAGGATGCGAACCCAGgtacttcaaa ... tcatttgcagGACTGTATCAATCGGATTGTTACTCTGGAAAGCATGGGTAT
EST: gi|31364620|gb|CD448975.1|CD448975
EST:     AGTGTGTTCCCCTAGAGGACCTAGCTGCAGAGTTCAGGATGCGAACCCAG                         GACTGTATCAATCGGATTGTTACTCTGGAAAGCATGGATAG
genomic: AGTGTGTTCCCCTAGAGGACCTAGCTGCAGAGTTCAGGATGCGAACCCAGgtacttcaaa ... tcatttgcagGACTGTATCAATCGGATTGTTACTCTGGAAAGCATGGGTAT
EST: gi|211469382|gb|FL187167.1|FL187167
EST:     AGTGTGTTCCCCTAGAGGACCTAGCTGCAGAGTTCAGGATGCGAACCCAG                         GACTGTATCAATCGGATTGTTACTCTGGAAAGCATGGATAG
genomic: AGTGTGTTCCCCTAGAGGACCTAGCTGCAGAGTTCAGGATGCGAACCCAGgtacttcaaa ... tcatttgcagGACTGTATCAATCGGATTGTTACTCTGGAAAGCATGGGTAT
EST: gi|71307153|gb|DR789747.1|DR789747
EST:     AGTGTGTTCCCCTAGAGGACCTAGCTGCAGAGTTCAGGATGCGAACCCAG                         GACTGTATTCA-TCGGGAT-GTTACTCTGGAAAG
genomic: AGTGTGTTCCCCTAGAGGACCTAGCTGCAGAGTTCAGGATGCGAACCCAGgtacttcaaa ... tcatttgcagGACTGTAT-CAATCGG-ATTGTTACTCTGGAAAG
EST: gi|78112541|gb|DV530935.1|DV530935
EST:     AGTGTGTTCCCCTAGAGGACCTAGCTGCAGAGTTCAGGATGCGAACCCAG                         GACTGTATCAATCGGATTGTTACTCTGGAAAGCATGGATAG
genomic: AGTGTGTTCCCCTAGAGGACCTAGCTGCAGAGTTCAGGATGCGAACCCAGgtacttcaaa ... tcatttgcagGACTGTATCAATCGGATTGTTACTCTGGAAAGCATGGGTAT
EST: gi|211427421|gb|FL445183.1|FL445183
EST:     AGTGTGTTCCCCTAGATGACCTAGCTGCAGAGTTCAGGATGCGAACCCAG                         GACTGTATCAATCGGATTGTTACTCTGGAAAGCATGGATAG
genomic: AGTGTGTTCCCCTAGAGGACCTAGCTGCAGAGTTCAGGATGCGAACCCAGgtacttcaaa ... tcatttgcagGACTGTATCAATCGGATTGTTACTCTGGAAAGCATGGGTAT
EST: gi|148932548|gb|EC876363.2|EC876363
EST:     AGTGTGTTCCCCTAGAGGACCTAGCTGCAGAGTTCAGGATGCGAACCCAG                         GACTGTATCAATCGGATTGTTACTCTGGAAAGCATGGATAG
genomic: AGTGTGTTCCCCTAGAGGACCTAGCTGCAGAGTTCAGGATGCGAACCCAGgtacttcaaa ... tcatttgcagGACTGTATCAATCGGATTGTTACTCTGGAAAGCATGGGTAT
EST: gi|71773570|gb|DR971468.1|DR971468
EST:     AGTGTGTTCCCCTAGAGGACCTAGCTGCAGAGTTCAGGATGCGAACCCAG                         GACTGTATCAATCGGATTGTTACTCTGGAAAGCATGGATAG
genomic: AGTGTGTTCCCCTAGAGGACCTAGCTGCAGAGTTCAGGATGCGAACCCAGgtacttcaaa ... tcatttgcagGACTGTATCAATCGGATTGTTACTCTGGAAAGCATGGGTAT
EST: gi|71757661|gb|DR955598.1|DR955598
EST:     AGTGTGTTCCCCTAGAGGACCTAGCTGCAGAGTTCAGGATGCGAACCCAG                         GACTGTATCAATCGGATTGTTACTCTGGAAAGCATGG
genomic: AGTGTGTTCCCCTAGAGGACCTAGCTGCAGAGTTCAGGATGCGAACCCAGgtacttcaaa ... tcatttgcagGACTGTATCAATCGGATTGTTACTCTGGAAAGCATGG
EST: gi|94472565|gb|EB701523.1|EB701523
EST:     AGTGTGTTCCCCTAGAGGACCTAGCTGCAGAGTTCAGGATGCGAACCCAG                         GACTGTATCAATCGGATTGTTACTCTGGAAAGCATGGATAG
genomic: AGTGTGTTCCCCTAGAGGACCTAGCTGCAGAGTTCAGGATGCGAACCCAGgtacttcaaa ... tcatttgcagGACTGTATCAATCGGATTGTTACTCTGGAAAGCATGGGTAT
EST: gi|148958245|gb|EC904458.2|EC904458
EST:     AGTGTGTTCCCCTAGAGGACCTAGCTGCAGAGTTCAGGATGCGAACCCAG                         GACTGTATNCA-TCGGATTGTTACTCTGGAAAGCATGGATAG
genomic: AGTGTGTTCCCCTAGAGGACCTAGCTGCAGAGTTCAGGATGCGAACCCAGgtacttcaaa ... tcatttgcagGACTGTAT-CAATCGGATTGTTACTCTGGAAAGCATGGGTAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAGCAGAAGTGTGTTCCCCTAGAGGACCTAGCTGCAGAGTTCAGGATGCGAACCCAGgtacttcaaaattacgtataagatgttcgaatgctgttatgaataataggattaacttcccatgccctattatttttaaatagaaattgtgataatgccc

- - - - - - - - - - AGAGGA
- - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - -  CTGCAG
- - - - - - - - - - - - - - - - - - - - - AGGATG