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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGCGAAGAAGGACAGCAAGGTCGAGTCGAAGCAGAGCAAGGGGAACGCTCTCAACGAGATGCTCGAGCTCAGGAGCTGCTCCAGTTGTCTCTTCTTCGAGgtatggctcttctactatgcttccaccccatggtggaaatcttgttaccattgacatggtcttttttgcttacatttattacagttctgttaacattgaaagttttttccttcatgtattacag

Basic information

species Zea mays
transcript GRMZM2G168176_T01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G168176_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os02g37870.1 (Oryza sativa), 5'ss of exon 2
CGCGAAGAAGGACAGCAAGGTCGAGTCGAAGCAGAGCAAGGGGAACGCTCTCAACGAGATGCTCGAGCTCAGGAGCTGCTCCAGTTGTCTCTTCTTCGAGgtatggctcttctactatgcttccaccccatggtggaaatcttgttaccattgacatggtcttttttgcttacatttattacagttctgttaacattgaaagttttttccttcatgtattacag
||| |||||||||||||||||||||||||||||||||||||| || || ||||||||| ||||||||||||||| ||||||||| || ||||||||||||||||   | | |   ||| || | ||         ||  ||  ||| |    | | |  |||||  |||      | ||    |     || | |    |||          |||| | ||   
CGCCAAGAAGGACAGCAAGGTCGAGTCGAAGCAGAGCAAGGGCAATGCGCTCAACGAGCTGCTCGAGCTCAGGAACTGCTCCAGCTGCCTCTTCTTCGAGgtatatatttacacatatactgctac---------gatctcaagttgcttcaggcctcatctttgatgc----gctgatggttgcgtgcttgataggagaag----------catgcaatagg-
















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|101388447|gb|EB816210.1|EB816210
EST:     TCAACGAGATGCTCGAGCTCAGGAGCTGCTCCAGTTGTCTCTTCTTCGAG                         TGCCGAAAACAGAAGGATCTTTACCTTTGGATGGTGAAGTCTCCTGGAGGA
genomic: TCAACGAGATGCTCGAGCTCAGGAGCTGCTCCAGTTGTCTCTTCTTCGAGgtatggctct ... tgtattacagTGCCGAAAACAGAAGGATCTTTACCTTTGGATGGTGAAGTCTCCTGGAGGA
EST: gi|211512372|gb|FL212647.1|FL212647
EST:     TCAACGAGATGCTCGAGCTCAGGAGCTGCTCCAGTTGTCTCTTCTTCGAG                         TGCCGAAAACAGAAGGATCTTTACCTTTGGATGGTGAAGTCTCCTGGAGGA
genomic: TCAACGAGATGCTCGAGCTCAGGAGCTGCTCCAGTTGTCTCTTCTTCGAGgtatggctct ... tgtattacagTGCCGAAAACAGAAGGATCTTTACCTTTGGATGGTGAAGTCTCCTGGAGGA
EST: gi|148943696|gb|EC888763.2|EC888763
EST:     TCAACGAGATGCTCGAGCTCAGGAGCTGCTCCAGTTGTCTCTTCTTCGAG                         TGCCGAAAACAGAAGGATCTTTACCTTTGGATGGTGAAGTCTCCTGGAGGA
genomic: TCAACGAGATGCTCGAGCTCAGGAGCTGCTCCAGTTGTCTCTTCTTCGAGgtatggctct ... tgtattacagTGCCGAAAACAGAAGGATCTTTACCTTTGGATGGTGAAGTCTCCTGGAGGA
EST: gi|76289778|gb|DV029346.1|DV029346
EST:     TCAACGAGATGCTCGAGCTCAGGAGCTGCTCCAGTTGTCTCTTCTTCGAG                         TGCCGAAAACAGAAGGATCTTTACCTTTGGATGGTGAAGTCTCCTGGAGGA
genomic: TCAACGAGATGCTCGAGCTCAGGAGCTGCTCCAGTTGTCTCTTCTTCGAGgtatggctct ... tgtattacagTGCCGAAAACAGAAGGATCTTTACCTTTGGATGGTGAAGTCTCCTGGAGGA
EST: gi|76285403|gb|DV024971.1|DV024971
EST:     TCAACGAGATGCTCGAGCTCAGGAGCTGCTCCAGTTGTCTCTTCTTCGAG                         TGCCGAAAACAGAAGGATCTTTACCTTTGGATGGTGAAGTCTCCTGGAGGA
genomic: TCAACGAGATGCTCGAGCTCAGGAGCTGCTCCAGTTGTCTCTTCTTCGAGgtatggctct ... tgtattacagTGCCGAAAACAGAAGGATCTTTACCTTTGGATGGTGAAGTCTCCTGGAGGA
EST: gi|71325419|gb|DR799392.1|DR799392
EST:     TCAACGAGATGCTCGAGCTCAGGAGCTGCTCCAGTTGTCTCTTCTTCGAG                         TGCCGAAAACAGAAGGATCTTTACCTTTGGATGGTGAAGCCTCCTGGAGGA
genomic: TCAACGAGATGCTCGAGCTCAGGAGCTGCTCCAGTTGTCTCTTCTTCGAGgtatggctct ... tgtattacagTGCCGAAAACAGAAGGATCTTTACCTTTGGATGGTGAAGTCTCCTGGAGGA
EST: gi|71307148|gb|DR789745.1|DR789745
EST:     TCAACGAGATGCTCGAGCTCAGGAGCTGCTCCAGTTGTCTCTTCTTCGAG                         TGCCGAAAACAGAAGGATCTTTACCTTTGGATGGTGAAGTCTCCTGGAGGA
genomic: TCAACGAGATGCTCGAGCTCAGGAGCTGCTCCAGTTGTCTCTTCTTCGAGgtatggctct ... tgtattacagTGCCGAAAACAGAAGGATCTTTACCTTTGGATGGTGAAGTCTCCTGGAGGA
EST: gi|28930902|gb|CB334263.1|CB334263
EST:     TCAACGAGATGCTCGAGCTCAGGAGCTGCTCCAGTTGTCTCTTCTTCGAG                         TGCCGAAAACAGAAGGATCTTTACCTTTGGATGGTGAAGTCTCCTGGAGGA
genomic: TCAACGAGATGCTCGAGCTCAGGAGCTGCTCCAGTTGTCTCTTCTTCGAGgtatggctct ... tgtattacagTGCCGAAAACAGAAGGATCTTTACCTTTGGATGGTGAAGTCTCCTGGAGGA
EST: gi|78121527|gb|DV539911.1|DV539911
EST:     TCAACGAGATGCTCGAGCTCAGGAGCTGCTCCAGTTGTCTCTTCTTCGAG                         TGCCGAAAACAGAAGGATCTTTACCTTTGGATGGTGAAGTCTCCTGGAGGA
genomic: TCAACGAGATGCTCGAGCTCAGGAGCTGCTCCAGTTGTCTCTTCTTCGAGgtatggctct ... tgtattacagTGCCGAAAACAGAAGGATCTTTACCTTTGGATGGTGAAGTCTCCTGGAGGA
EST: gi|89759058|gb|DY688001.1|DY688001
EST:     TCAACGAGATGCTCGAGCTCAGGAGCTGCTCCAGTTGTCTCTTCTTCGAG                         TGCCGAAAACAGAAGGATCTTTACCTTTGGATGGTGAAGTCTCCTGGAGGA
genomic: TCAACGAGATGCTCGAGCTCAGGAGCTGCTCCAGTTGTCTCTTCTTCGAGgtatggctct ... tgtattacagTGCCGAAAACAGAAGGATCTTTACCTTTGGATGGTGAAGTCTCCTGGAGGA
EST: gi|6827088|gb|AW330731.1|AW330731
EST:     TCAACGAGATGCTCGAGCTCAGGAGCTGCTCCAGNTGTCTCTTCTTCGAG                         TGCCGAAAACAGAAGGATCTTTACCTTTGGATGGTGAAGTCTCCTGGAGGA
genomic: TCAACGAGATGCTCGAGCTCAGGAGCTGCTCCAGTTGTCTCTTCTTCGAGgtatggctct ... tgtattacagTGCCGAAAACAGAAGGATCTTTACCTTTGGATGGTGAAGTCTCCTGGAGGA
EST: gi|76283913|gb|DV023481.1|DV023481
EST:     TCAACGAGATGCTCGAGCTCAGGAGCTGCTCCAGTTGTCTCTTCTTCGAG                         TGCCGAAAACAGAAGGATCTTTACCTTTGGATGGTGAAGTCTCCTGGAGGA
genomic: TCAACGAGATGCTCGAGCTCAGGAGCTGCTCCAGTTGTCTCTTCTTCGAGgtatggctct ... tgtattacagTGCCGAAAACAGAAGGATCTTTACCTTTGGATGGTGAAGTCTCCTGGAGGA
EST: gi|78180563|gb|DV550891.1|DV550891
EST:     TCAACGAGATGCTCGAGCTCAGGAGCTGCTCCAGTTGTCTCTTCTTCGAG                         TGCCGAAAACAGAAGGATCTTTACCTTTGGATGGTGAAGTCTCCTGGAGGA
genomic: TCAACGAGATGCTCGAGCTCAGGAGCTGCTCCAGTTGTCTCTTCTTCGAGgtatggctct ... tgtattacagTGCCGAAAACAGAAGGATCTTTACCTTTGGATGGTGAAGTCTCCTGGAGGA
EST: gi|32945542|gb|CF050361.1|CF050361
EST:     TCAACGAGATGCTCGAGCTCAGGAGCTGCTCCAGTTGTCTCTTCTTCGAG                         TGCCGAAAACAGAAGGATCTTTACCTTTGGATGGTGAAGTCTCCTGGAGGA
genomic: TCAACGAGATGCTCGAGCTCAGGAGCTGCTCCAGTTGTCTCTTCTTCGAGgtatggctct ... tgtattacagTGCCGAAAACAGAAGGATCTTTACCTTTGGATGGTGAAGTCTCCTGGAGGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CGCGAAGAAGGACAGCAAGGTCGAGTCGAAGCAGAGCAAGGGGAACGCTCTCAACGAGATGCTCGAGCTCAGGAGCTGCTCCAGTTGTCTCTTCTTCGAGgtatggctcttctactatgcttccaccccatggtggaaatcttgttaccattgacatggtcttttttgcttacatttattacagttctgttaacattgaaagttttttccttcatgtattacag

- - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT