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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgcatctgtcgcctcttctctccacgcacctgcggcctaaccgtctgttgctgaccgtttctgtggttctctcagGCCCCGAAGAAGGATAAGGCCCCGCCGCCGTCGTCCAAGCCGGCCAAGTCCGGAGGCGGGAAGCAGAAGAAGAAGAAGTGGAGCAAGGGTAAGCAAAAGG

Basic information

species Zea mays
transcript GRMZM5G867518_T01
intron # 1
splice site 3'
intron type U2

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|71312092|gb|DR792572.1|DR792572
EST:     CCCTTCCTCTCCGTCGCTCGCCTCGCGCCTACGCCACCACCTCTGCCATG                         GCCCCGAAGAAGGATAAGGCCCCGCCGCCGTCGTCCAAGCCGGCCAAGTCC
genomic: CCCTTCCTCTCCGTCGCTCGCCTCGCGCCTACGCCACCACCTCTGCCATGgtgcatctgt ... gttctctcagGCCCCGAAGAAGGATAAGGCCCCGCCGCCGTCGTCCAAGCCGGCCAAGTCC
EST: gi|211278095|gb|FL004365.1|FL004365
EST:     CCCTTCCTCTCCGTCGCTCGCCTCGCGCCTACGCCACCACCTCTGCCATG                         GCCCCGAAGAAGGATAAGGCCCCGCCGCCGTCGTCCAAGCCGGCCAAGTCC
genomic: CCCTTCCTCTCCGTCGCTCGCCTCGCGCCTACGCCACCACCTCTGCCATGgtgcatctgt ... gttctctcagGCCCCGAAGAAGGATAAGGCCCCGCCGCCGTCGTCCAAGCCGGCCAAGTCC
EST: gi|211278102|gb|FL004372.1|FL004372
EST:     CCCTTCCTCTCCGTCGCTCGCCTCGCGCCTACGCCACCACCTCTGCCATG                         GNCCCGAAGAAGGATAAGGCCCCGCCGCCGTCGTCCAAGCCGG
genomic: CCCTTCCTCTCCGTCGCTCGCCTCGCGCCTACGCCACCACCTCTGCCATGgtgcatctgt ... gttctctcagGCCCCGAAGAAGGATAAGGCCCCGCCGCCGTCGTCCAAGCCGG
EST: gi|211278089|gb|FL004359.1|FL004359
EST:     CCCTTCCTCTCCGTCGCTCGCCTCGCGCCTACGCCACCACCTCTGCCATG                         GCCCCGAAGAAGGATAAGGCCCCGCCGCCGTCGTCCAAGCCGGCCAAGTCC
genomic: CCCTTCCTCTCCGTCGCTCGCCTCGCGCCTACGCCACCACCTCTGCCATGgtgcatctgt ... gttctctcagGCCCCGAAGAAGGATAAGGCCCCGCCGCCGTCGTCCAAGCCGGCCAAGTCC
EST: gi|211278103|gb|FL004373.1|FL004373
EST:     CCCTTCCTCTCCGTCGCTCGCCTCGCGCCTACGCCACCACCTCTGCCATG                         GCCCCGAAGAAGGATAAGGCCCCGCCGCCGTCGTCCAAGCCGGCCAAGTCC
genomic: CCCTTCCTCTCCGTCGCTCGCCTCGCGCCTACGCCACCACCTCTGCCATGgtgcatctgt ... gttctctcagGCCCCGAAGAAGGATAAGGCCCCGCCGCCGTCGTCCAAGCCGGCCAAGTCC
EST: gi|211209833|gb|FK949991.1|FK949991
EST:     CCCTTCCTCTCCGTCGCTCGCCTCGCGCCTACGCCACCACCTCTGCCATG                         GCCCCGAAGAAGGATAAGGCCCCGCCGCCGTCGTCCAAG
genomic: CCCTTCCTCTCCGTCGCTCGCCTCGCGCCTACGCCACCACCTCTGCCATGgtgcatctgt ... gttctctcagGCCCCGAAGAAGGATAAGGCCCCGCCGCCGTCGTCCAAG
EST: gi|148931044|gb|EC873634.2|EC873634
EST:     CCCTTCCTCTCCGTCGCTCGCCTCGCGCCTACGCCACCACCTCTGCCATG                         GCCCCGAAGAAGGATAAGGCCCCGCCGCCGTCGTCCAAGCCGGCCAAGTCC
genomic: CCCTTCCTCTCCGTCGCTCGCCTCGCGCCTACGCCACCACCTCTGCCATGgtgcatctgt ... gttctctcagGCCCCGAAGAAGGATAAGGCCCCGCCGCCGTCGTCCAAGCCGGCCAAGTCC
EST: gi|211281698|gb|FL004389.1|FL004389
EST:     CCCTTCCTCTCCGTCGCTCGCCTCGCGCCTACGCCACCACCTCTGCCATG                         GCCCCGAAGAAGGATAAGGCCCCGC-GCCGTCGTCCAAGCCGGCCAAGTCC
genomic: CCCTTCCTCTCCGTCGCTCGCCTCGCGCCTACGCCACCACCTCTGCCATGgtgcatctgt ... gttctctcagGCCCCGAAGAAGGATAAGGCCCCGCCGCCGTCGTCCAAGCCGGCCAAGTCC
EST: gi|32915222|gb|CF020034.1|CF020034
EST:     CCCTTCCTCTACGTCGCTCGCCTCGCGCCTGCGCCACCACCTCTGCCATG                         GCCCCGAAGAAGGATAAGGCCCCGCCGCCGTCGTCCAAGCCGGCCAAGTCC
genomic: CCCTTCCTCTCCGTCGCTCGCCTCGCGCCTACGCCACCACCTCTGCCATGgtgcatctgt ... gttctctcagGCCCCGAAGAAGGATAAGGCCCCGCCGCCGTCGTCCAAGCCGGCCAAGTCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tccacgcacctgcggcctaaccgtctgttgctgaccgtttctgtggttctctcagGCCCCGAAGAAGGATAAGGCCCCGCCGCCGTCGTCCAAGCCGGCCAAGTCCGGAGGCGGGAAGCAGAAGAAGAAGAAGTGGAGCAAGGGTAAGCAAAAGG
                            tgctgac  putative branch site (score: 2)
                                              ttctctc  putative PPT
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgcatctgtcgcctcttctctccacgcacctgcggcctaaccgtctgttgctgaccgtttctgtggttctctcagGCCCCGAAGAAGGATAAGGCCCCGCCGCCGTCGTCCAAGCCGGCCAAGTCCGGAGGCGGGAAGCAGAAGAAGAAGAAGTGGAGCAAGGGTAAGCAAAAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA