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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGTTGAAGAGAGGATTGCAGCTGCAGACAGGAGAAAGATTGAGGGCAATGCATATTTCAAAGAAAAGAAGCTTGAGGAGGCCATGCAGCAATATGAAATGgttagtagcatgctatactttggacattattgtagttatcagcatattctgatttcagtcgacctgttctcttctacag

Basic information

species Zea mays
transcript GRMZM2G133624_T01
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G133624_T01 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os12g05090.1 (Oryza sativa), 5'ss of exon 5
AGTTGAAGAGAGGATTGCAGCTGCAGACAGGAGAAAGATTGAGGGCAATGCATATTTCAAAGAAAAGAAGCTTGAGGAGGCCATGCAGCAATATGAAATGgttagtagcatgctatactttggacatta-ttgtagttatcagcatattctgatttcagtcgacctgttctcttctacag
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AGTGGAAGAAAGGATTGAAGCAGCAGACAGGAGGAAGATTGAAGGCAATGAATATTTCAAAGAAAAGAAGTTCGAGGAGGCTATGCAGCAATATGAAATGgttagttgtctactg-atgtcattcttcagctattgtaagatgctcaatcataatccc-cctagctgttcttctttacag
















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|29130064|gb|CB380768.1|CB380768
EST:     CATGCAGCAATATGAAATG                         GCGATTGCATACATGGGAGATGATTTCATGTTTCAATTATTTGGAAAGTAC
genomic: CATGCAGCAATATGAAATGgttagtagca ... tcttctacagGCGATTGCATACATGGGAGATGATTTCATGTTTCAATTATTTGGAAAGTAC
EST: gi|60357904|gb|DN224877.1|DN224877
EST:     CATATTTCAAAGAAAAGAAGCTTGAGGAGGCCATGCAGCAATATGAAATG                         GCGATTGCATACATGGGAGATGATTTCATGTTTCAATTATTTGGAAAGTAC
genomic: CATATTTCAAAGAAAAGAAGCTTGAGGAGGCCATGCAGCAATATGAAATGgttagtagca ... tcttctacagGCGATTGCATACATGGGAGATGATTTCATGTTTCAATTATTTGGAAAGTAC
EST: gi|78108737|gb|DV527154.1|DV527154
EST:     AAAGAAAAGAAGCTTGAGGAGGCCATGCAGCAATATGAAATG                         GCGATTGCATACATGGGAGATGATTTCATGTTTCAATTATTTGGAAAGTAC
genomic: AAAGAAAAGAAGCTTGAGGAGGCCATGCAGCAATATGAAATGgttagtagca ... tcttctacagGCGATTGCATACATGGGAGATGATTTCATGTTTCAATTATTTGGAAAGTAC
EST: gi|71765927|gb|DR963864.1|DR963864
EST:     CATATTTCAAAGAAAAGAAGCTTGAGGAGGCCATGCAGCAATATGAAATG                         GCGATTGCATACATGGGAGATGATTTCATGTTTTCA-TTATTTTGGAA-GT
genomic: CATATTTCAAAGAAAAGAAGCTTGAGGAGGCCATGCAGCAATATGAAATGgttagtagca ... tcttctacagGCGATTGCATACATGGGAGATGATTTCATGTTT-CAATTATTT-GGAAAGT
EST: gi|71299220|gb|DR785608.1|DR785608
EST:     CATATTTCAAAGAAAAGAAGCTTGAGGAGGCCATGCAGCAATATGAAATG                         GCGATTGCATACATGGGAGATGATTTCATGTTTCAATTATTTGGAAAGTAC
genomic: CATATTTCAAAGAAAAGAAGCTTGAGGAGGCCATGCAGCAATATGAAATGgttagtagca ... tcttctacagGCGATTGCATACATGGGAGATGATTTCATGTTTCAATTATTTGGAAAGTAC
EST: gi|71438300|gb|DR819350.1|DR819350
EST:     CATATTTCAAAGAAAAGAAGCTTGAGGAGGCCATGCAGCAATATGAAATG                         GCGATTGCATACATGGGAGATGATTTCATGTTTCAATTATTTGGAAAGTAC
genomic: CATATTTCAAAGAAAAGAAGCTTGAGGAGGCCATGCAGCAATATGAAATGgttagtagca ... tcttctacagGCGATTGCATACATGGGAGATGATTTCATGTTTCAATTATTTGGAAAGTAC
EST: gi|71768316|gb|DR966253.1|DR966253
EST:     CATATTTCAAAGAAAAGAAGCTTGAGGAGGCCATGCAGCAATATGAAATG                         GCGATTGCATACATGGGAGATGATTTCATGTTTCAATTATTTGGAAAGTAC
genomic: CATATTTCAAAGAAAAGAAGCTTGAGGAGGCCATGCAGCAATATGAAATGgttagtagca ... tcttctacagGCGATTGCATACATGGGAGATGATTTCATGTTTCAATTATTTGGAAAGTAC
EST: gi|71756680|gb|DR954617.1|DR954617
EST:     ATATTTCAAAGAAAAGAAGC-TGNAGGAGGCCATGCAGCAATATGAAATG                         GCGATTGCATACATGGGAGATGATTTCATGTTTCAATTATTTGGAAAGTAC
genomic: ATATTTCAAAGAAAAGAAGCTTG-AGGAGGCCATGCAGCAATATGAAATGgttagtagca ... tcttctacagGCGATTGCATACATGGGAGATGATTTCATGTTTCAATTATTTGGAAAGTAC
EST: gi|78089641|gb|DV518015.1|DV518015
EST:     CATATTTCAAAGAAAAGAAGCTTGAGGAGGCCATGCAGCAATATGAAATG                         GCGATTGCATACATGGGAGATGATTTCATGTTTCAATTATTTGGAAAGTAC
genomic: CATATTTCAAAGAAAAGAAGCTTGAGGAGGCCATGCAGCAATATGAAATGgttagtagca ... tcttctacagGCGATTGCATACATGGGAGATGATTTCATGTTTCAATTATTTGGAAAGTAC
EST: gi|33104053|gb|CF064013.1|CF064013
EST:     CATATTTCAAAGAAAAGAAGCTTGAGGAGGCCATGCAGCAATATGAAATG                         GCGATTGCATACATGGGAGATGATTTCATGTTTCAATTATTTGGAAAGTAC
genomic: CATATTTCAAAGAAAAGAAGCTTGAGGAGGCCATGCAGCAATATGAAATGgttagtagca ... tcttctacagGCGATTGCATACATGGGAGATGATTTCATGTTTCAATTATTTGGAAAGTAC
EST: gi|71435312|gb|DR816362.1|DR816362
EST:     CATATTTCAAAGAAAAGAAGCTTGAGGAGGCCATGCAGCAATATGAAATG                         GCGATTGCATACATGGGAGATGATTTCATGTTTCAATTATTTGGAAAGTAC
genomic: CATATTTCAAAGAAAAGAAGCTTGAGGAGGCCATGCAGCAATATGAAATGgttagtagca ... tcttctacagGCGATTGCATACATGGGAGATGATTTCATGTTTCAATTATTTGGAAAGTAC
EST: gi|76021435|gb|DT948605.1|DT948605
EST:     CATATTTCAAAGAAAAGAAGCTTGAGGAGGCCATGCAGCAATATGAAATG                         GCGATTGCATACATGGGAGATGATTTCATGTTTCAATTATTTGGAAAGTAC
genomic: CATATTTCAAAGAAAAGAAGCTTGAGGAGGCCATGCAGCAATATGAAATGgttagtagca ... tcttctacagGCGATTGCATACATGGGAGATGATTTCATGTTTCAATTATTTGGAAAGTAC
EST: gi|149015212|gb|EE044997.2|EE044997
EST:     CATATTTCAAAGAAAAGAAGCTTGAGGAGGCCATGCAGCAATATGAAATG                         GCGATTGCATACATGGGAGATGATTTCATGGTTCAATTATTTGGAAAGTAC
genomic: CATATTTCAAAGAAAAGAAGCTTGAGGAGGCCATGCAGCAATATGAAATGgttagtagca ... tcttctacagGCGATTGCATACATGGGAGATGATTTCATGTTTCAATTATTTGGAAAGTAC
EST: gi|6526795|gb|AW216068.1|AW216068
EST:     GAGGAGGCCATGCAGCAATATGAAATG                         GCGATTGCATACATGGGAGATGATTTCATGTTTCAATTATTTGGAAAGTAC
genomic: GAGGAGGCCATGCAGCAATATGAAATGgttagtagca ... tcttctacagGCGATTGCATACATGGGAGATGATTTCATGTTTCAATTATTTGGAAAGTAC
EST: gi|71299221|gb|DR785609.1|DR785609
EST:     CATATTTCAAAGAAAAGAAGCTTGAGGAGGCCATGCAGCAATATGAAATG                         GCGATTGCATACATGGGAGATGATTTCATGTTTCAATTATTTGGAAAGTAC
genomic: CATATTTCAAAGAAAAGAAGCTTGAGGAGGCCATGCAGCAATATGAAATGgttagtagca ... tcttctacagGCGATTGCATACATGGGAGATGATTTCATGTTTCAATTATTTGGAAAGTAC
EST: gi|149076434|gb|EE165057.2|EE165057
EST:     CATATTTCAAAGAAAAGAAGCTTGAGGAGGCCATGCAGCAATATGAAATG                         GCGATTGCATACATGGGAGATGATTTCATGTTTTCA-TTATTTGGAAAGTA
genomic: CATATTTCAAAGAAAAGAAGCTTGAGGAGGCCATGCAGCAATATGAAATGgttagtagca ... tcttctacagGCGATTGCATACATGGGAGATGATTTCATGTTT-CAATTATTTGGAAAGTA
EST: gi|76021436|gb|DT948606.1|DT948606
EST:     CATATTTCAAAGAAAAGAAGCTTGAGGAGGCCATGCAGCAATATGAAATG                         GCGATTGCATACATGGGAGATGATTTCATGTTTCAATTATTTGGAAAGTAC
genomic: CATATTTCAAAGAAAAGAAGCTTGAGGAGGCCATGCAGCAATATGAAATGgttagtagca ... tcttctacagGCGATTGCATACATGGGAGATGATTTCATGTTTCAATTATTTGGAAAGTAC
EST: gi|71321226|gb|DR797322.1|DR797322
EST:     CATATTTCAAAGATAAGAAGCTTGAGGAGGCCATGCAGCAATATGAAATG                         GCGATTGCATACATGGGAGATGATTTCATGTTTCAATTATTTGGAAAGTAC
genomic: CATATTTCAAAGAAAAGAAGCTTGAGGAGGCCATGCAGCAATATGAAATGgttagtagca ... tcttctacagGCGATTGCATACATGGGAGATGATTTCATGTTTCAATTATTTGGAAAGTAC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGTTGAAGAGAGGATTGCAGCTGCAGACAGGAGAAAGATTGAGGGCAATGCATATTTCAAAGAAAAGAAGCTTGAGGAGGCCATGCAGCAATATGAAATGgttagtagcatgctatactttggacattattgtagttatcagcatattctgatttcagtcgacctgttctcttctacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG