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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgaaaagaaactatgtgcttgtagatgtggttcactgcttacctatgtcattgttattagtgggctgtattcagctctaagcttgaagaatctcctacagGAAAATGATAGAGGGAAGCAACCAATGAAAGGCCAATCTCTAGTGGATGCTGCTTACCGAAAGGCAAAATCATTGAAGGCAGCCAGCAAACGGGCCCCTG

Basic information

species Zea mays
transcript GRMZM2G420865_T02
intron # 18
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|211343050|gb|FL472500.1|FL472500
EST:     TGGAGGCCCAGCGTGAGATGTTGGAAGATGAGGATGGCGAGAAAACAAAG                         GAAAATGATAGAGGGAAGCAACCAATGAAAGGCCAATCTCTAGTGGATGCT
genomic: TGGAGGCCCAGCGTGAGATGTTGGAAGATGAGGATGACGAGAAAACAAAGgttcagttct ... tctcctacagGAAAATGATAGAGGGAAGCAACCAATGAAAGGCCAATCTCTAGTGGATGCT
EST: gi|78090028|gb|DV518402.1|DV518402
EST:     TGGAGGCCCAGCGTGAGATGTTGGAAGATGAGGATGACGAGAAAACAAAG                         GAAAATGATAGAGGGAAGCAACCAATGAAAGGCCAATCTTTAGTGGATGCT
genomic: TGGAGGCCCAGCGTGAGATGTTGGAAGATGAGGATGACGAGAAAACAAAGgttcagttct ... tctcctacagGAAAATGATAGAGGGAAGCAACCAATGAAAGGCCAATCTCTAGTGGATGCT
EST: gi|211343049|gb|FL472499.1|FL472499
EST:     GGCCCAGCGTGAGATGTTGGAAGATGAGGATGGCGAGAAAACAAAG                         GAAAATGATAGAGGGAAGCAACCAATGAAAGGCCAATCTYTAGTGGATGCT
genomic: GGCCCAGCGTGAGATGTTGGAAGATGAGGATGACGAGAAAACAAAGgttcagttct ... tctcctacagGAAAATGATAGAGGGAAGCAACCAATGAAAGGCCAATCTCTAGTGGATGCT
EST: gi|37373944|gb|CF623297.1|CF623297
EST:     TGGAGGCCCAGCGTGAGATGTTGGAAGATGAGGATGACGAGAAAACAAAG                         GAAAATGATAGAGGGAAGCAACCAATGAAAGGCCAATCTCTAGTGGATGCT
genomic: TGGAGGCCCAGCGTGAGATGTTGGAAGATGAGGATGACGAGAAAACAAAGgttcagttct ... tctcctacagGAAAATGATAGAGGGAAGCAACCAATGAAAGGCCAATCTCTAGTGGATGCT
EST: gi|60396007|gb|DN228877.1|DN228877
EST:     TGGAGGCCCAGCGTGAGATGTTGGAAGATGAGGATGACGAGAAAACAAAG                         GAAAATGATAGAGGGAAGCAACCAATGAAAGGCCAATCTCTAGTGGATGCT
genomic: TGGAGGCCCAGCGTGAGATGTTGGAAGATGAGGATGACGAGAAAACAAAGgttcagttct ... tctcctacagGAAAATGATAGAGGGAAGCAACCAATGAAAGGCCAATCTCTAGTGGATGCT
EST: gi|32857031|gb|CD996712.1|CD996712
EST:     GAGGATGACNAG-AAACAGAG                         GGGAATGATAGAGGGAAGCAACCAATGAAAGGCCAATCTCTAGTGGATGCT
genomic: GAGGATGACGAGAAAACAAAGgttcagttct ... tctcctacagGAAAATGATAGAGGGAAGCAACCAATGAAAGGCCAATCTCTAGTGGATGCT
EST: gi|37398106|gb|CF636362.1|CF636362
EST:     TGGAGGCCCAGCGTGAGATGTTGGAAGATGAGGATGACGAGAAAACAAAG                         GAAAATGATAGAGGGAAGCAACCAATGAAAGGCCAATCTCTAGTGGATGCT
genomic: TGGAGGCCCAGCGTGAGATGTTGGAAGATGAGGATGACGAGAAAACAAAGgttcagttct ... tctcctacagGAAAATGATAGAGGGAAGCAACCAATGAAAGGCCAATCTCTAGTGGATGCT
EST: gi|40337352|gb|CK371422.1|CK371422
EST:     TGGAGGCCCAGCGTGAGATGTTGGAAGATGAGGATGACGAGAAAACAAAG                         GAAAATGATAGAGGGAAGCAACCAATGAAAGGCCAATCTCTAGTGGATGCT
genomic: TGGAGGCCCAGCGTGAGATGTTGGAAGATGAGGATGACGAGAAAACAAAGgttcagttct ... tctcctacagGAAAATGATAGAGGGAAGCAACCAATGAAAGGCCAATCTCTAGTGGATGCT
EST: gi|166622732|gb|EG172521.1|EG172521
EST:     GACGAGAAAACAAAG                         GAAAATGATAGAGGGAAGCAACCAATGAAAGGCCAATCTCTAGTGGATGCT
genomic: GACGAGAAAACAAAGgttcagttct ... tctcctacagGAAAATGATAGAGGGAAGCAACCAATGAAAGGCCAATCTCTAGTGGATGCT
EST: gi|67016515|gb|CO445264.1|CO445264
EST:     GATGAC-ATAAAACAAA-                         GAAAATGATAGAGGGAAGCAACCAATGAAAGGCCAATCTCTAGTGGATGCT
genomic: GATGACGAGAAAACAAAGgttcagttct ... tctcctacagGAAAATGATAGAGGGAAGCAACCAATGAAAGGCCAATCTCTAGTGGATGCT
EST: gi|60344195|gb|DN211168.1|DN211168
EST:     TGGAGGCCCAGCGTGAGATGTTGGAAGATGAGGATGACGAGAAAACAAAG                         GAAAATGATAGAGGGAAGCAACCAATGAAAGGCCAATCTCTAGTGGATGCT
genomic: TGGAGGCCCAGCGTGAGATGTTGGAAGATGAGGATGACGAGAAAACAAAGgttcagttct ... tctcctacagGAAAATGATAGAGGGAAGCAACCAATGAAAGGCCAATCTCTAGTGGATGCT
EST: gi|60341880|gb|DN208853.1|DN208853
EST:     TGGAGGCCCAGCGTGAGATGTTGGAAGATGAGGATGACGAGAAAACAAAG                         GAAAATGATAGAGGGAAGCAACCAATGAAAGGCCAATCTCTAGTGGATGCT
genomic: TGGAGGCCCAGCGTGAGATGTTGGAAGATGAGGATGACGAGAAAACAAAGgttcagttct ... tctcctacagGAAAATGATAGAGGGAAGCAACCAATGAAAGGCCAATCTCTAGTGGATGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtcattgttattagtgggctgtattcagctctaagcttgaagaatctcctacagGAAAATGATAGAGGGAAGCAACCAATGAAAGGCCAATCTCTAGTGGATGCTGCTTACCGAAAGGCAAAATCATTGAAGGCAGCCAGCAAACGGGCCCCTG
                                             tctcctac  CT-rich tract
     ttgttatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgaaaagaaactatgtgcttgtagatgtggttcactgcttacctatgtcattgttattagtgggctgtattcagctctaagcttgaagaatctcctacagGAAAATGATAGAGGGAAGCAACCAATGAAAGGCCAATCTCTAGTGGATGCTGCTTACCGAAAGGCAAAATCATTGAAGGCAGCCAGCAAACGGGCCCCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- -aaagaaa
- - - - - - - -tgcttgt
- - - - - - - - - - - - - - - - - -tgcttac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgggctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttcagct