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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aattaatatggtgggagtaatcataatgcctactaagttataaataccttttatcttttatctgttacattctaatgtgatcatggcataactatggcagGTAACTGCCGTCAAAGTTGCATTGTCCTCTGGTAGCCAGGGTCAGAAATTAGATTCAGTTCTAGCAAAACCTTTGAAGACTCAAGCTTTTGCTTCTCCTG

Basic information

species Zea mays
transcript GRMZM5G825854_T02
intron # 22
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G825854_T01 (Zea mays), 3'ss of exon 22
lower sequence: LOC_Os08g34970.1 (Oryza sativa), 3'ss of exon 22
aattaatatggtgggagtaatcataatgcctactaagttataaataccttttatcttttatctgttacattctaatg----tgatcatggcataactatggcagGTAACTGCCGTCAAAGTTGCATTGTCCTCTGGTAGCCAGGGTCAGAAATTAGATTCAGTTCTAGCAAAACCTTTGAAGACTCAAGCTTTTGCTTCTCCTG
 |||   |   |   ||  || || |  ||| |    |  ||      |   | |    |  |  |  |||||||||    ||| ||||   |  ||  | |||||||| || |||||||||| | ||||||| |||||||||||||||||||| ||||| ||||| || |||||  | ||||||||||| |||||||||||||
gatttcgaaaatttcag--attatga-acctgcattctagtattcttttcaaaaccgaaaagtagtttattctaatggagatgaacatgat-tgtctgggccagGTAACGGCTGTCAAAGTTGTACTGTCCTCGGGTAGCCAGGGTCAGAAATTGGATTCTGTTCTGGCTAAACCCCTTAAGACTCAAGCATTTGCTTCTCCTG
















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|37383203|gb|CF628592.1|CF628592
EST:     TGTCCATAACTAAATTAGTAGTTGACCCAATGCTTTCTTTTGTTACTAAG                         GTAACTGCCGTCAAAGTTGCATTGTCCTCTGGTAGCCAGGGTCAGAAATTA
genomic: TGTCCATAACTAAATTAGTAGTTGACCCAATGCTTTCTTTTGTTACTAAGgtagcaatat ... actatggcagGTAACTGCCGTCAAAGTTGCATTGTCCTCTGGTAGCCAGGGTCAGAAATTA
EST: gi|37389357|gb|CF631898.1|CF631898
EST:     GCTTTCTTTTGTTACTAAG                         GTAACTGCCGTCAAAGTTGCATTGTCCTCTGGTAGCCAGGGTCAGAAATTA
genomic: GCTTTCTTTTGTTACTAAGgtagcaatat ... actatggcagGTAACTGCCGTCAAAGTTGCATTGTCCTCTGGTAGCCAGGGTCAGAAATTA
EST: gi|32832225|gb|CD971903.1|CD971903
EST:     TGTCCATAACTAAATTAGTAGTTGACCCAATGCTTTCTTTTGTTACTAAG                         GTAACTGCCGTCAAAGTTGCATTGCCCTCTGGTAGCCAGGGTCAGAAATTA
genomic: TGTCCATAACTAAATTAGTAGTTGACCCAATGCTTTCTTTTGTTACTAAGgtagcaatat ... actatggcagGTAACTGCCGTCAAAGTTGCATTGTCCTCTGGTAGCCAGGGTCAGAAATTA
EST: gi|86468964|gb|DY235334.1|DY235334
EST:     TGTCCATAACTAAATTAGTAGTTGACCCAATGCTTTCTTTTGTTACTAAG                         GTAACTGCCGTCAAAGTTGCATTGTCCTCTGGTAGCCAGGGTCAGAAATTA
genomic: TGTCCATAACTAAATTAGTAGTTGACCCAATGCTTTCTTTTGTTACTAAGgtagcaatat ... actatggcagGTAACTGCCGTCAAAGTTGCATTGTCCTCTGGTAGCCAGGGTCAGAAATTA
EST: gi|93281266|gb|EB673530.1|EB673530
EST:     TGTCCATAACTAAATTAGTAGTTGACCCAATGCTTTCTTTTGTTATTAAG                         GTAACTGCCGTCAAAGTTGCATTGTCCTCTGGTAGCCAGGGTCAGAAATTA
genomic: TGTCCATAACTAAATTAGTAGTTGACCCAATGCTTTCTTTTGTTACTAAGgtagcaatat ... actatggcagGTAACTGCCGTCAAAGTTGCATTGTCCTCTGGTAGCCAGGGTCAGAAATTA
EST: gi|60348401|gb|DN215374.1|DN215374
EST:     TGTCCATAACTAAATTAGTAGTTGACCCAATGCTTTCTTTTGTTACTAAG                         GTAACTGCCGTCAAAGTTGCATTGTCCTCTGGTAGCCAGGGTCAGAAATTA
genomic: TGTCCATAACTAAATTAGTAGTTGACCCAATGCTTTCTTTTGTTACTAAGgtagcaatat ... actatggcagGTAACTGCCGTCAAAGTTGCATTGTCCTCTGGTAGCCAGGGTCAGAAATTA
EST: gi|32929996|gb|CF034808.1|CF034808
EST:     TGTCCATAACTAAATTAGTAGTTGACCCAATGCTTTCTTTTGTTACTAAG                         GTAACTGCCGTCAAAGTTGCATTGTCCTCTGGTAGCCAGGGTCAGAAATTA
genomic: TGTCCATAACTAAATTAGTAGTTGACCCAATGCTTTCTTTTGTTACTAAGgtagcaatat ... actatggcagGTAACTGCCGTCAAAGTTGCATTGTCCTCTGGTAGCCAGGGTCAGAAATTA
EST: gi|6102001|gb|AW126471.1|AW126471
EST:     TGTCCATAACTAAATTAGTAGCTGACCCAATGCTTTCTTTTGTTACTAAG                         GTAACTGCCGTCAAAGTTGCATTGTCCTCTGGTAGCCAGGGTCAGAAATTA
genomic: TGTCCATAACTAAATTAGTAGTTGACCCAATGCTTTCTTTTGTTACTAAGgtagcaatat ... actatggcagGTAACTGCCGTCAAAGTTGCATTGTCCTCTGGTAGCCAGGGTCAGAAATTA
EST: gi|32931787|gb|CF036599.1|CF036599
EST:     TGTCTATAACTAAATTAGTAGTTGACCCAATGCTTTCTTTTGTTACTAAG                         GTAACTGCCGTCAAAGTTGCATTGTCCTCTGGTAGCCAGGGTCAGA
genomic: TGTCCATAACTAAATTAGTAGTTGACCCAATGCTTTCTTTTGTTACTAAGgtagcaatat ... actatggcagGTAACTGCCGTCAAAGTTGCATTGTCCTCTGGTAGCCAGGGTCAGA
EST: gi|60348441|gb|DN215414.1|DN215414
EST:     TGTCCATAACTAAATTAGTAGTTGACCCAATGCTTTCTTTTGTTACTAAG                         GTAACTGCCGTCAAAGTTGCATTGTCCTCTGGTAGCCAGGGTCAGAAATTA
genomic: TGTCCATAACTAAATTAGTAGTTGACCCAATGCTTTCTTTTGTTACTAAGgtagcaatat ... actatggcagGTAACTGCCGTCAAAGTTGCATTGTCCTCTGGTAGCCAGGGTCAGAAATTA
EST: gi|60341619|gb|DN208592.1|DN208592
EST:     TGTCCATAACTAAATTAGTAGTTGACCCAATGCTTTCTTTTGTTACTAAG                         GTAACTGCCGTCAAAGTTGCATTGTCCTCTGGTAGCCAGGGTCAGAAATTA
genomic: TGTCCATAACTAAATTAGTAGTTGACCCAATGCTTTCTTTTGTTACTAAGgtagcaatat ... actatggcagGTAACTGCCGTCAAAGTTGCATTGTCCTCTGGTAGCCAGGGTCAGAAATTA
EST: gi|149104240|gb|EE289676.2|EE289676
EST:     TGTCCATAACTAAATTAGTAGTTGACCCAATGCTTTCTTTTGTTACTAAG                         GTAACTGCCGTCAAAGTTGCATTGTCCTCTGGTAGCCAGGGTCAGAAATTA
genomic: TGTCCATAACTAAATTAGTAGTTGACCCAATGCTTTCTTTTGTTACTAAGgtagcaatat ... actatggcagGTAACTGCCGTCAAAGTTGCATTGTCCTCTGGTAGCCAGGGTCAGAAATTA
EST: gi|211362787|gb|FL472151.1|FL472151
EST:     TGTCCATAACTAAATTAGTAGTTGACCCAATGCTTTCTTTTGTTACTAAG                         GTAACTGCCGTCAAAGTTGCATTGTCCTCTGGTAGCCAGGGTCAGAAATTA
genomic: TGTCCATAACTAAATTAGTAGTTGACCCAATGCTTTCTTTTGTTACTAAGgtagcaatat ... actatggcagGTAACTGCCGTCAAAGTTGCATTGTCCTCTGGTAGCCAGGGTCAGAAATTA
EST: gi|148953559|gb|EC898910.2|EC898910
EST:     CCAATGCTTTCTTTTGTTACTAAG                         GTAACTGCCGTCAAAGTTGCATTGTCCTTTGGTAGCCAGGGTCAGAAATTA
genomic: CCAATGCTTTCTTTTGTTACTAAGgtagcaatat ... actatggcagGTAACTGCCGTCAAAGTTGCATTGTCCTCTGGTAGCCAGGGTCAGAAATTA
EST: gi|211224223|gb|FK968322.1|FK968322
EST:     AATGCTTTCTTTTGTTACTAAG                         GTAACTGCCGTCAAAGTTGCATTGTCCTCTGGTAGCCAGGGTCAGAAATTA
genomic: AATGCTTTCTTTTGTTACTAAGgtagcaatat ... actatggcagGTAACTGCCGTCAAAGTTGCATTGTCCTCTGGTAGCCAGGGTCAGAAATTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

accttttatcttttatctgttacattctaatgtgatcatggcataactatggcagGTAACTGCCGTCAAAGTTGCATTGTCCTCTGGTAGCCAGGGTCAGAAATTAGATTCAGTTCTAGCAAAACCTTTGAAGACTCAAGCTTTTGCTTCTCCTG
     ttatcttttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aattaatatggtgggagtaatcataatgcctactaagttataaataccttttatcttttatctgttacattctaatgtgatcatggcataactatggcagGTAACTGCCGTCAAAGTTGCATTGTCCTCTGGTAGCCAGGGTCAGAAATTAGATTCAGTTCTAGCAAAACCTTTGAAGACTCAAGCTTTTGCTTCTCCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT