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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCGTCGCATGTTTCAATCCCACGGCGTTTGGTACCACGGCAAGAACATGCCTTCCTTTCCTGCTTGCTGCTAATGTGCTGGGATACATGGTTGGTTCTGGgtaaatacgtacgcttgtataaactcgatcgatcaataggatcccaagtatgcagttagttttggactgacgtacggtctgagtgttttcag

Basic information

species Zea mays
transcript GRMZM5G873519_T02
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G873519_T02 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os10g42780.6 (Oryza sativa), 5'ss of exon 3
GCGTCGCATGTTTCAATCCCACGGCGTTTGGTACCACGGCAAGAACATGCCTTCCTTTCCTGCTTGCTGCTAATGTGCTGGGATACATGGTTGGTTCTGGgtaaatacgtacgcttgtataaactcgatcgatcaataggatcccaagtatg-cagttagtt--ttggactgacgtacggtctgagtgttttcag------
  || || | | |    ||||| ||| |||||||||| |||| |||||||||||||||| |||||||| | | |||  | || |||||  |||||||  ||||  |||      || |||  ||||  ||  |      ||    ||  ||  |  || |||  ||   || |  |      | ||||     |       
CTGTTGCGTATGTTTCCCCCACTGCGCTTGGTACCACCGCAACAACATGCCTTCCTTTCTTGCTTGCTTCCACTGTTTTCGGTTACATCCTTGGTTCCCGgtac-tactccattttatatttactctctctttattcttgactttaaacataaccttttgttcattaacctcatctcaaaatttagtgcaaatatatgagt
















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|76285584|gb|DV025152.1|DV025152
EST:     CTTCCTTTCCTGCTTGCTGCTAATGTGCTGGGATACATGGTTGGTTCTGG                         GTTACCACCTGGCGTCAAGAAAGTGCTGCATCCGATCATCTCCTGCGCACT
genomic: CTTCCTTTCCTGCTTGCTGCTAATGTGCTGGGATACATGGTTGGTTCTGGgtaaatacgt ... gtgttttcagGTTACCACCTGGCGTCAAGAAAGTGCTGCATCCGATCATCTCCTGCGCACT
EST: gi|32851469|gb|CD991150.1|CD991150
EST:     TTCCTTTCCTGCTTGCTGCTAATGTGCTGGGATACCATGGTTGGTTCTGG                         GTTACCACCTGGCGTCAAGAAAGTGCTGCATCCGATCATCTCCTGCGCACT
genomic: TTCCTTTCCTGCTTGCTGCTAATGTGCTGGGATAC-ATGGTTGGTTCTGGgtaaatacgt ... gtgttttcagGTTACCACCTGGCGTCAAGAAAGTGCTGCATCCGATCATCTCCTGCGCACT
EST: gi|211315102|gb|FL381332.1|FL381332
EST:     CTTCCTTTCCTGCTTGCTGCTAATGTGCTGGGATACATGGTTGGTTCTGG                         GTTACCACCTGGCGTCAAGAAAGTGCTGCATCCGATCATCTCCTGCGCACT
genomic: CTTCCTTTCCTGCTTGCTGCTAATGTGCTGGGATACATGGTTGGTTCTGGgtaaatacgt ... gtgttttcagGTTACCACCTGGCGTCAAGAAAGTGCTGCATCCGATCATCTCCTGCGCACT
EST: gi|211200162|gb|FL429646.1|FL429646
EST:     CTTCCTTTCCTGCTTGCTGCTAATGTGCTGGGATACATGGTTGGTTCTGG                         GTTACCACCTGGCGTCAAGAAAGTGCTGCATCCGATCATCTCCTGCGCACT
genomic: CTTCCTTTCCTGCTTGCTGCTAATGTGCTGGGATACATGGTTGGTTCTGGgtaaatacgt ... gtgttttcagGTTACCACCTGGCGTCAAGAAAGTGCTGCATCCGATCATCTCCTGCGCACT
EST: gi|211231751|gb|FL386173.1|FL386173
EST:     CTTCCTTTCCTGCTTGCTGCTAATGTGCTGGGATACATGGTTGGTTCTGG                         GTTACCACCTGGCGTCAAGAAAGTGCTGCATCCGATCATCTCCTGCGCACT
genomic: CTTCCTTTCCTGCTTGCTGCTAATGTGCTGGGATACATGGTTGGTTCTGGgtaaatacgt ... gtgttttcagGTTACCACCTGGCGTCAAGAAAGTGCTGCATCCGATCATCTCCTGCGCACT
EST: gi|91875592|gb|EB405549.1|EB405549
EST:     CTTCCTTTCCTGCTTGCTGCTAATGTGCTGGGATACATGGTTGGTTCTGG                         GTTACCACCTGGCGTCAAGAAAGTGCTGCATCCGATCATCTCCTGCGCACT
genomic: CTTCCTTTCCTGCTTGCTGCTAATGTGCTGGGATACATGGTTGGTTCTGGgtaaatacgt ... gtgttttcagGTTACCACCTGGCGTCAAGAAAGTGCTGCATCCGATCATCTCCTGCGCACT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCGTCGCATGTTTCAATCCCACGGCGTTTGGTACCACGGCAAGAACATGCCTTCCTTTCCTGCTTGCTGCTAATGTGCTGGGATACATGGTTGGTTCTGGgtaaatacgtacgcttgtataaactcgatcgatcaataggatcccaagtatgcagttagttttggactgacgtacggtctgagtgttttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT