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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acttctgttcatgagtacatgttttctacctcttcatgtctgtttctatcatactttgctcttgaaatgtcttattaacttggctatgctcattgttcagCGGATGCAAAAGCTGATAAAGATGACACTAAGAGTCTCA

Basic information

species Zea mays
transcript GRMZM2G484880_T01
intron # 4
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|13178287|gb|BG349545.1|BG349545
EST:     AACAATGAAGTCTGGACGGTCAACACAGCATAAACCAAAAGTCTCCAATG                         CGGATGCAAAAGCTGATAAAGATGACACTAAGAGTCTCAT
genomic: AACAATGAAGTCTGGACGGTCAACACAGCATAAACCAAAAGTCTCCAATGgttagcttgc ... cattgttcagCGGATGCAAAAGCTGATAAAGATGACACTAAGAGTCTCAT
EST: gi|32866885|gb|CF006567.1|CF006567
EST:     AACAATGAAGTCTGGACGGTCAACACAGCATAAACCAAAAGTCTCCAATG                         CGGATGCAAAAGCTGATAAAGATGACACTAAGAGTCTCA
genomic: AACAATGAAGTCTGGACGGTCAACACAGCATAAACCAAAAGTCTCCAATGgttagcttgc ... cattgttcagCGGATGCAAAAGCTGATAAAGATGACACTAAGAGTCTCA
EST: gi|32865668|gb|CF005350.1|CF005350
EST:     AACAATGAAGTCTGGACGGTCAACACAGCATAAACCAAAAGTCTCCAATG                         CGGATGCAAAAGCTGATAAAGATGACACTAAGAGTCTCA
genomic: AACAATGAAGTCTGGACGGTCAACACAGCATAAACCAAAAGTCTCCAATGgttagcttgc ... cattgttcagCGGATGCAAAAGCTGATAAAGATGACACTAAGAGTCTCA
EST: gi|31997934|gb|CD661839.1|CD661839
EST:     AACAATGAAGTCTGGACGGTCAACACAGCATAAACCAAAAGTCTCCAATG                         CGGATGCAAAAGCTGATAAAGATGACACTAAGAGTCTCA
genomic: AACAATGAAGTCTGGACGGTCAACACAGCATAAACCAAAAGTCTCCAATGgttagcttgc ... cattgttcagCGGATGCAAAAGCTGATAAAGATGACACTAAGAGTCTCA
EST: gi|93284203|gb|EB676467.1|EB676467
EST:     AACAATGAAGTCTGGACGGTCAACACAGCATAAACCCAAAGTCTCCAATG                         CGGATGCAAAAGCTGATAAAGATGACACTAAAAGTCTCA
genomic: AACAATGAAGTCTGGACGGTCAACACAGCATAAACCAAAAGTCTCCAATGgttagcttgc ... cattgttcagCGGATGCAAAAGCTGATAAAGATGACACTAAGAGTCTCA
EST: gi|71434326|gb|DR815376.1|DR815376
EST:     AACAATGAAGTCTGGACGGTCAACACAGCATAAACCAAAAGTCTCCAATG                         CGGATGCAAAAGCTGATAAAGATGACACTAAGAGTCTCA
genomic: AACAATGAAGTCTGGACGGTCAACACAGCATAAACCAAAAGTCTCCAATGgttagcttgc ... cattgttcagCGGATGCAAAAGCTGATAAAGATGACACTAAGAGTCTCA
EST: gi|6031476|gb|AW076378.1|AW076378
EST:     AACAATGAAGTCTGGACGGTCAACACAGCATAAACCAAAAGTCTCCAATG                         CGGATGCAAAAGCTGATAAAGATGACACTAAGAGTCTCA
genomic: AACAATGAAGTCTGGACGGTCAACACAGCATAAACCAAAAGTCTCCAATGgttagcttgc ... cattgttcagCGGATGCAAAAGCTGATAAAGATGACACTAAGAGTCTCA
EST: gi|211058547|gb|FK994412.1|FK994412
EST:     AACAATGAAGTCTGGACGGTCAACACAGCATAAACCAAAAGTCTCCAATG                         CGGATGCAAAAGCTGATAAAGATGACACTAAGAGTCTCA
genomic: AACAATGAAGTCTGGACGGTCAACACAGCATAAACCAAAAGTCTCCAATGgttagcttgc ... cattgttcagCGGATGCAAAAGCTGATAAAGATGACACTAAGAGTCTCA
EST: gi|32855367|gb|CD995048.1|CD995048
EST:     AACAATGAAGTCTGGACGGTCAACACAGCATAAACCAAAAGTCTCCAATG                         CGGATGCAAAAGCTGATAAAGATGACACTAAGAGTCTCA
genomic: AACAATGAAGTCTGGACGGTCAACACAGCATAAACCAAAAGTCTCCAATGgttagcttgc ... cattgttcagCGGATGCAAAAGCTGATAAAGATGACACTAAGAGTCTCA
EST: gi|32913308|gb|CF018120.1|CF018120
EST:     AACAATGAAGTCTGGACGGTCAACACAGCATAAACCAAAAGTCTCCAATG                         CGGATGCAAAAGCTGATAAAGATGACACTAAGAGTCTCA
genomic: AACAATGAAGTCTGGACGGTCAACACAGCATAAACCAAAAGTCTCCAATGgttagcttgc ... cattgttcagCGGATGCAAAAGCTGATAAAGATGACACTAAGAGTCTCA
EST: gi|76912438|gb|DV164732.1|DV164732
EST:     AACAATGAAGTCTGGACGGTCAACACAGCATAAACCAAAAGTCTCCAATG                         CGGATGCAAAAGCTGATAAAGATGACACTAAGAGTCTCA
genomic: AACAATGAAGTCTGGACGGTCAACACAGCATAAACCAAAAGTCTCCAATGgttagcttgc ... cattgttcagCGGATGCAAAAGCTGATAAAGATGACACTAAGAGTCTCA
EST: gi|26456042|gb|CA827625.1|CA827625
EST:     AACAATGAAGTCTGGACGGTCAACACAGCATAAACCAAAAGTCTCCAATG                         CGGATGCAAAAGCTGATAAAGATGACACTAAGAGTCTCA
genomic: AACAATGAAGTCTGGACGGTCAACACAGCATAAACCAAAAGTCTCCAATGgttagcttgc ... cattgttcagCGGATGCAAAAGCTGATAAAGATGACACTAAGAGTCTCA
EST: gi|71331879|gb|DR802817.1|DR802817
EST:     AACAATGAAGTCTGGACGGTCAACACAGCATAAACCAAAAGTCTCCAATG                         CGGATGCAAAAGCTGATAAAGATGACACTAAGAGTCTCA
genomic: AACAATGAAGTCTGGACGGTCAACACAGCATAAACCAAAAGTCTCCAATGgttagcttgc ... cattgttcagCGGATGCAAAAGCTGATAAAGATGACACTAAGAGTCTCA
EST: gi|71438521|gb|DR819571.1|DR819571
EST:     AACAATGAAGTCTGGACGGTCAACACAGCATAAACCAAAAGTCTCCAATG                         CGGATGCAAAAGCTGATAAAGATGACACTAAGAGTCTCATTTCA
genomic: AACAATGAAGTCTGGACGGTCAACACAGCATAAACCAAAAGTCTCCAATGgttagcttgc ... cattgttcagCGGATGCAAAAGCTGATAAAGATGACACTAAGAG--TC---TCA
EST: gi|211058548|gb|FK994413.1|FK994413
EST:     ACAATGAAGTCTGGACGGGTCA-CACAGCATAAACCCAAAGTCTCCAATG                         CGGATGCAAAAGCTGA
genomic: ACAATGAAGTCTGGACGG-TCAACACAGCATAAACCAAAAGTCTCCAATGgttagcttgc ... cattgttcagCGGATGCAAAAGCTGA
EST: gi|211058545|gb|FK994410.1|FK994410
EST:     AACAATGAAGTCTGGACGGTCAACACAGCATAAACCAAAAGTCTCCAATG                         CGGATGCAAAAGCTGATAAAGATGACACTAAGAGTCTCA
genomic: AACAATGAAGTCTGGACGGTCAACACAGCATAAACCAAAAGTCTCCAATGgttagcttgc ... cattgttcagCGGATGCAAAAGCTGATAAAGATGACACTAAGAGTCTCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctatcatactttgctcttgaaatgtcttattaacttggctatgctcattgttcagCGGATGCAAAAGCTGATAAAGATGACACTAAGAGTCTCA
                           tattaac  putative branch site (score: 1)
                   aaatgtcttattaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
acttctgttcatgagtacatgttttctacctcttcatgtctgtttctatcatactttgctcttgaaatgtcttattaacttggctatgctcattgttcagCGGATGCAAAAGCTGATAAAGATGACACTAAGAGTCTCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG