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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtgcaatagtttattatacacttgaccttttttttttcttgtgctctgctagttttatcaacatgagttaatgttccaattgaacatgtgtggctcaatgtacagAACCAAACAATGGAGAGCCAATCGCAATCAGCAACCTAAATTGTGTCAGCAGCTGGAGAAACTATACATTTCCAAAAAACTTACCAG

Basic information

species Zea mays
transcript GRMZM2G044317_T06
intron # 2
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|32164923|gb|CD670241.1|CD670241
EST:     TTTCAGTGAAAGCCAGAAAGTTCTGCGAGCCAAA                         AACCAAACAATGGAGAGCCAATCGCAATCAGCAACCTAAATTGTGTCAGCA
genomic: TTTCAGTGAAAGCCAGAAAGTTCTGCGAGCCAAAgtgagtgcaa ... caatgtacagAACCAAACAATGGAGAGCCAATCGCAATCAGCAACCTAAATTGTGTCAGCA
EST: gi|211298656|gb|FL153827.1|FL153827
EST:     ACCATCCAAATCAATATTTCAGTGAAAGCCAGAAAGTTCTGCGAGCCAAA                         AACCAAACAATGGAGAGCCAATCGCAATCAGCAACCTAAATTGTGTCAGCA
genomic: ACCATCCAAATCAATATTTCAGTGAAAGCCAGAAAGTTCTGCGAGCCAAAgtgagtgcaa ... caatgtacagAACCAAACAATGGAGAGCCAATCGCAATCAGCAACCTAAATTGTGTCAGCA
EST: gi|60351451|gb|DN218424.1|DN218424
EST:     ACCATCCAAATCAATATTTCAGTGAAAGCCAGAAAGTTCTGCGAGCCAAA                         AACCAAACAATGGAGAGCCAATCGCAATCAGCAACCTAAATTGTGTCAGCA
genomic: ACCATCCAAATCAATATTTCAGTGAAAGCCAGAAAGTTCTGCGAGCCAAAgtgagtgcaa ... caatgtacagAACCAAACAATGGAGAGCCAATCGCAATCAGCAACCTAAATTGTGTCAGCA
EST: gi|18383633|gb|BM416833.1|BM416833
EST:     TTTCAGTGAAAGCCAGAAAGTTCTGCGAGCCAAA                         ANCCAANCAATGGAGAGCCAATCGCAATCAGCAACCTAAATTGTGTCAGCA
genomic: TTTCAGTGAAAGCCAGAAAGTTCTGCGAGCCAAAgtgagtgcaa ... caatgtacagAACCAAACAATGGAGAGCCAATCGCAATCAGCAACCTAAATTGTGTCAGCA
EST: gi|32164924|gb|CD670242.1|CD670242
EST:     CCATCCAAATCAATATTTCANG-GAAAGCCAGAAAGTTCTGCGAGCCAAA                         AACCAAACAATGGAGAGCCAATCGCAATCAGCAACCTAAATTGTGTCAGCA
genomic: CCATCCAAATCAATATTTCA-GTGAAAGCCAGAAAGTTCTGCGAGCCAAAgtgagtgcaa ... caatgtacagAACCAAACAATGGAGAGCCAATCGCAATCAGCAACCTAAATTGTGTCAGCA
EST: gi|74238130|gb|DT646044.1|DT646044
EST:     CCCATCCAAATCAATATTTCAGTGAAAGCCAGAAAGTTCTGCGAGCCAAA                         AACCAAACAATGGAGAGCCAATCGCAATCAGCAACCTAAATTGTGTCAGCA
genomic: ACCATCCAAATCAATATTTCAGTGAAAGCCAGAAAGTTCTGCGAGCCAAAgtgagtgcaa ... caatgtacagAACCAAACAATGGAGAGCCAATCGCAATCAGCAACCTAAATTGTGTCAGCA
EST: gi|60354600|gb|DN221573.1|DN221573
EST:     AAATCAATATTTCAGTGAAAGCCAGAAAGTTTTGCGAGCCAAA                         AACCAAACAATGGAGAGCCAATCGCAATCAGCAACCTAAATTGTGTCAGCA
genomic: AAATCAATATTTCAGTGAAAGCCAGAAAGTTCTGCGAGCCAAAgtgagtgcaa ... caatgtacagAACCAAACAATGGAGAGCCAATCGCAATCAGCAACCTAAATTGTGTCAGCA
EST: gi|78021198|gb|DV489585.1|DV489585
EST:     ACCATCCAAATCAATATTTCAGTGAAAGCCAGAAAGTTCTGCGAGCCAAA                         AACCAAACAATGGAGAGCCAATCGCAATCAGCAACCTAAATTGTGTCAGCA
genomic: ACCATCCAAATCAATATTTCAGTGAAAGCCAGAAAGTTCTGCGAGCCAAAgtgagtgcaa ... caatgtacagAACCAAACAATGGAGAGCCAATCGCAATCAGCAACCTAAATTGTGTCAGCA
EST: gi|32832353|gb|CD972031.1|CD972031
EST:     ACCATCCAAATCAATATTTCAGCGAAAGCCAGAAAGTTCTGCGAGCCAAA                         AACCAAACAATGGAGAGCCAATCGCAATCAGCAACCTAAATTGTGTCAGCA
genomic: ACCATCCAAATCAATATTTCAGTGAAAGCCAGAAAGTTCTGCGAGCCAAAgtgagtgcaa ... caatgtacagAACCAAACAATGGAGAGCCAATCGCAATCAGCAACCTAAATTGTGTCAGCA
EST: gi|32833600|gb|CD973278.1|CD973278
EST:     ACCATCCAAATCAATATTTCAGCGAAAGCCAGAAAGTTCTGCGAGCCAAA                         AACCAAACAATGGAGAGCCAATCGCAATCAGCAACCTAAATTGTGTCAGCA
genomic: ACCATCCAAATCAATATTTCAGTGAAAGCCAGAAAGTTCTGCGAGCCAAAgtgagtgcaa ... caatgtacagAACCAAACAATGGAGAGCCAATCGCAATCAGCAACCTAAATTGTGTCAGCA
EST: gi|32834800|gb|CD974478.1|CD974478
EST:     ACCATCCAAATCAATATTTCAGCGAAAGCCAGAAAGTTCTGCGAGCCAAA                         AACCAAACAATGGAGAGCCAATCGCAATCAGCAACCTAAATTGTGTCAGCA
genomic: ACCATCCAAATCAATATTTCAGTGAAAGCCAGAAAGTTCTGCGAGCCAAAgtgagtgcaa ... caatgtacagAACCAAACAATGGAGAGCCAATCGCAATCAGCAACCTAAATTGTGTCAGCA
EST: gi|78088857|gb|DV517250.1|DV517250
EST:     ACCATCCAAATCAATATTTCAGTGAAAGCCAGAAAGTTCTGCGAGCCAAA                         AACCAAACAATGGAGAGCCAATCGCAATCAGCAACCTAAATTGTGTCAGCA
genomic: ACCATCCAAATCAATATTTCAGTGAAAGCCAGAAAGTTCTGCGAGCCAAAgtgagtgcaa ... caatgtacagAACCAAACAATGGAGAGCCAATCGCAATCAGCAACCTAAATTGTGTCAGCA
EST: gi|211096944|gb|FL476439.1|FL476439
EST:     ACCATCCAAATCAATATTTCAGTGAAAGCCAGAAAGTTCTGCGAGCCAAA                         AACCAAACAATGGAGAGCCAATCGCAATCAGCAACCTAAATTGTGTCAGCA
genomic: ACCATCCAAATCAATATTTCAGTGAAAGCCAGAAAGTTCTGCGAGCCAAAgtgagtgcaa ... caatgtacagAACCAAACAATGGAGAGCCAATCGCAATCAGCAACCTAAATTGTGTCAGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agttttatcaacatgagttaatgttccaattgaacatgtgtggctcaatgtacagAACCAAACAATGGAGAGCCAATCGCAATCAGCAACCTAAATTGTGTCAGCAGCTGGAGAAACTATACATTTCCAAAAAACTTACCAG
               agttaat  putative branch site (score: 4)
                 ttaatgtt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtgcaatagtttattatacacttgaccttttttttttcttgtgctctgctagttttatcaacatgagttaatgttccaattgaacatgtgtggctcaatgtacagAACCAAACAATGGAGAGCCAATCGCAATCAGCAACCTAAATTGTGTCAGCAGCTGGAGAAACTATACATTTCCAAAAAACTTACCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA