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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCGGAGTGGGACATCCTCAGCAACGGAGGCCCGATGCAGGAGATGGCCAACATCGCCAAGGGGCAGGAGCACGGGAACTCGGTGTCCCTCCTCAGAGCCAgtgtgagtactactgctgctgccattctgttctgtttttttttttcaaatagcatgtctagagcagtgccaccgggaacgtgccacgttccgtgtcctgg...

Basic information

species Zea mays
transcript GRMZM2G026643_T01
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G026643_T01 (Zea mays), 5'ss of exon 8
lower sequence: LOC_Os02g45250.1 (Oryza sativa), 5'ss of exon 8
GCGGAGTGGGACATCCTCAGCAACGGAGGCCCGATGCAGGAGATGGCCAACATCGCCAAGGGGCAGGAGCACGGGAACTCGGTGTCCCTCCTCAGAGCCAgtgtgagtactactgctgctgccattctgttctgt-ttttttttttcaaatagcatgtcta---gagcagtgccaccgggaac-gtgccacgttccgtgtcctgg
  ||||||||||||||||||||| |||||||| |||||||||||| || | |||||||||||||||  | | ||||||||||| || |||||||| ||||||||||||| |  |||| |  | | |||| |||     ||| || |    |    || |||   |   ||| | || |   |  ||   ||||   ||    |  
--GGAGTGGGACATCCTCAGCAATGGAGGCCCCATGCAGGAGATGACCCAGATCGCCAAGGGGCAGCGGGATGGGAACTCGGTTTCACTCCTCAGGGCCAGTgtgagtatt--tgctaccccaaatctgctctaaacatttcttcttttgtgcggtgcctaactggatagtactactgtatatagtaaaacgtagagtaatttt-
















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|31910354|gb|CD651381.1|CD651381
EST:     CATCGCCAAGGGGCAGGAGCACGGGAACTCGGTGTCCCTCCTCAGAGCCA                         GCCATGAGTGCCAACCAGAGCAGCATGCTGATCCTCCAGGAGACTTGCACT
genomic: CATCGCCAAGGGGCAGGAGCACGGGAACTCGGTGTCCCTCCTCAGAGCCAgtgtgagtac ... ctcactgcagGCCATGAGTGCCAACCAGAGCAGCATGCTGATCCTCCAGGAGACTTGCACT
EST: gi|18660024|gb|BM500647.1|BM500647
EST:     CATCGCCAAGGGGCAGGAGCACGGGAACTCGGTGTCCCTCCTCAGAGCCA                         GTGCCATGAGTGCCAACCAGAGCAGCAT
genomic: CATCGCCAAGGGGCAGGAGCACGGGAACTCGGTGTCCCTCCTCAGAGCCAgtgtgagtac ... ctcactgcagG--CCATGAGTGCCAACCAGAGCAGCAT
EST: gi|88852796|gb|DY543020.1|DY543020
EST:     CATCGCCAAGGGGCAGGAGCACGGGAACTCGGTGTCCCTCCTCAGAGCCA                         GTGCCATGAGTGCCAACCAGAGCAGCATGCTGATCCTCCAGGAGACTTGCA
genomic: CATCGCCAAGGGGCAGGAGCACGGGAACTCGGTGTCCCTCCTCAGAGCCAgtgtgagtac ... ctcactgcagG--CCATGAGTGCCAACCAGAGCAGCATGCTGATCCTCCAGGAGACTTGCA
EST: gi|74244866|gb|DT652780.1|DT652780
EST:     CATCGCCAAGGGGCAGGAGCACGGGAACTCGGTGTCCCTCCTCAGAGCCA                         G
genomic: CATCGCCAAGGGGCAGGAGCACGGGAACTCGGTGTCCCTCCTCAGAGCCAgtgtgagtac ... ctcactgcag-
EST: gi|74244866|gb|DT652780.1|DT652780
EST:     CATCGCCAAGGGGCAGGAGCACGGGAACTCGGTGTCCCTCCTCAGAGCCA                         G
genomic: CATCGCCAAGGGGCAGGAGCACGGGAACTCGGTGTCCCTCCTCAGAGCCAgtgtgagtac ... ctcactgcag-
EST: gi|74244866|gb|DT652780.1|DT652780
EST:     CATCGCCAAGGGGCAGGAGCACGGGAACTCGGTGTCCCTCCTCAGAGCCA                         G
genomic: CATCGCCAAGGGGCAGGAGCACGGGAACTCGGTGTCCCTCCTCAGAGCCAgtgtgagtac ... ctcactgcag-
EST: gi|211462300|gb|FL096434.1|FL096434
EST:     CATCGCCAAGGGGCAGGAGCACGGGAACTCGGTGTCCCTCCTCAGAGCCA                         GTGCCATGAGTGCCAACCAGAGCAGCATGCTGATCCTCCAGGAGACTTGCA
genomic: CATCGCCAAGGGGCAGGAGCACGGGAACTCGGTGTCCCTCCTCAGAGCCAgtgtgagtac ... ctcactgcagG--CCATGAGTGCCAACCAGAGCAGCATGCTGATCCTCCAGGAGACTTGCA
EST: gi|76929403|gb|DV172000.1|DV172000
EST:     CATCGCCAAGGGGCAGGAGCACGGGAACTCGGTGTCCCTCCTCAGAGCCA                         GTGCCATGAGTGCCAACCAGAGCAGCATGCTGATCCTCCNAG-AGACTTGC
genomic: CATCGCCAAGGGGCAGGAGCACGGGAACTCGGTGTCCCTCCTCAGAGCCAgtgtgagtac ... ctcactgcagG--CCATGAGTGCCAACCAGAGCAGCATGCTGATCCTCC-AGGAGACTTGC
EST: gi|74245648|gb|DT653562.1|DT653562
EST:     CATCGCCAAGGGGCAGGAGCACGGGAACTCGGTGTCCCTCCTCAGAGCCA                         GTGCCATGAGTGCCAACCAGAGCAGCATGCTGATCCTCCAGGAGACTTGCA
genomic: CATCGCCAAGGGGCAGGAGCACGGGAACTCGGTGTCCCTCCTCAGAGCCAgtgtgagtac ... ctcactgcagG--CCATGAGTGCCAACCAGAGCAGCATGCTGATCCTCCAGGAGACTTGCA
EST: gi|71437534|gb|DR818584.1|DR818584
EST:     CATCGCCAAGGGGCAGGAGCACGGGAACTCGGTGTCCCTCCTCAGAGCCA                         GTGCCATGAGTGCCAACCAGAGCAGCATGCTGATCCTCCAGGAGACTTGCA
genomic: CATCGCCAAGGGGCAGGAGCACGGGAACTCGGTGTCCCTCCTCAGAGCCAgtgtgagtac ... ctcactgcagG--CCATGAGTGCCAACCAGAGCAGCATGCTGATCCTCCAGGAGACTTGCA
EST: gi|71299494|gb|DR785758.1|DR785758
EST:     GGGAACTCGGTGTCCCTCCTCAGAGCCA                         G
genomic: GGGAACTCGGTGTCCCTCCTCAGAGCCAgtgtgagtac ... ctcactgcag-
EST: gi|71299494|gb|DR785758.1|DR785758
EST:     GGGAACTCGGTGTCCCTCCTCAGAGCCA                         G
genomic: GGGAACTCGGTGTCCCTCCTCAGAGCCAgtgtgagtac ... ctcactgcag-
EST: gi|71299494|gb|DR785758.1|DR785758
EST:     GGGAACTCGGTGTCCCTCCTCAGAGCCA                         G
genomic: GGGAACTCGGTGTCCCTCCTCAGAGCCAgtgtgagtac ... ctcactgcag-
EST: gi|88852725|gb|DY542949.1|DY542949
EST:     CATCGCCAAGGGGCAGGAGCACGGGAACTCGGTGTCCCTCCTCAGAGCCA                         GTGCCATGAGTGCCAACCAGAGCAGCATGCTGATCCTCCAGGAGACTTGCA
genomic: CATCGCCAAGGGGCAGGAGCACGGGAACTCGGTGTCCCTCCTCAGAGCCAgtgtgagtac ... ctcactgcagG--CCATGAGTGCCAACCAGAGCAGCATGCTGATCCTCCAGGAGACTTGCA
EST: gi|211462299|gb|FL096433.1|FL096433
EST:     CATCGCCAAGGGGCAGGAGCACGGGAACTCGGTGTCC-TCCTCAGAGCCA                         GTGCCATGAGTGCCAACCAGAGCAGCATGCTGATCCTCCAGGAGACT
genomic: CATCGCCAAGGGGCAGGAGCACGGGAACTCGGTGTCCCTCCTCAGAGCCAgtgtgagtac ... ctcactgcagG--CCATGAGTGCCAACCAGAGCAGCATGCTGATCCTCCAGGAGACT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCGGAGTGGGACATCCTCAGCAACGGAGGCCCGATGCAGGAGATGGCCAACATCGCCAAGGGGCAGGAGCACGGGAACTCGGTGTCCCTCCTCAGAGCCAgtgtgagtactactgctgctgccattctgttctgtttttttttttcaaatagcatgtctagagcagtgccaccgggaacgtgccacgttccgtgtcctgg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTCCTC