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RefSeq Gene
 

RefSeq Gene DUX4

RefSeq: NM_033178.4   Status: Reviewed
Description: Homo sapiens double homeobox 4 (DUX4), mRNA.
CDS: 5' complete
OMIM: 606009
Entrez Gene: 22947
PubMed on Gene: DUX4
PubMed on Product: double homeobox protein 4
GeneCards: DUX4
AceView: DUX4
Stanford SOURCE: NM_033178

Summary of DUX4

This gene is located within a D4Z4 repeat array in the subtelomeric region of chromosome 4q. The D4Z4 repeat is polymorphic in length; a similar D4Z4 repeat array has been identified on chromosome 10. Each D4Z4 repeat unit has an open reading frame (named DUX4) that encodes two homeoboxes; the repeat-array and ORF is conserved in other mammals. There is no evidence for transcription of this gene from standard cDNA libraries, however, RT-PCR and in vitro expression experiments indicate that the ORF is transcribed. The encoded protein has been reported to function as a transcriptional activator of paired-like homeodomain transcription factor 1 (PITX1; GeneID 5307). Contraction of the microsatellite repeat causes autosomal dominant facioscapulohumeral muscular dystrophy (FSHD). [provided by RefSeq, May 2013]. Sequence Note: This RefSeq record was created from genomic sequence data because no transcript data was available for the full length of the gene. The extent of this protein is supported by similar human proteins. Publication Note: This RefSeq record includes a subset of the publications that are available for this gene. Please see the Gene record to access additional publications.


mRNA/Genomic Alignments

The alignment you clicked on is first in the table below.
BROWSER | SIZE IDENTITY CHROMOSOME  STRAND    START     END              QUERY      START  END  TOTAL
-----------------------------------------------------------------------------------------------------
browser |  1380  100.0%  Un_gl000228     +    112508    113887             NM_033178     1  1380  1380
browser |  1380  100.0%  Un_gl000228     +     76142     77521             NM_033178     1  1380  1380
browser |  1380  100.0%  Un_gl000228     +     99284    100663             NM_033178     1  1380  1380
browser |  1380  100.0%  Un_gl000228     +     72836     74215             NM_033178     1  1380  1380
browser |  1380   99.8%         10     + 135487177 135491849             NM_033178     1  1380  1380
browser |  1380   99.8%         10     + 135480558 135485241             NM_033178     1  1380  1380
browser |  1380  100.0%          4     + 191012063 191013442             NM_033178     1  1380  1380
browser |  1380  100.0%          4     + 191008763 191010142             NM_033178     1  1380  1380
browser |  1380  100.0%          4     + 191005470 191006849             NM_033178     1  1380  1380
browser |  1380  100.0%          4     + 190998876 191000255             NM_033178     1  1380  1380
browser |  1380  100.0%          4     + 190995583 190996962             NM_033178     1  1380  1380
browser |  1380  100.0%          4     + 190992290 190993669             NM_033178     1  1380  1380
browser |  1380  100.0%  Un_gl000228     +     86060     87439             NM_033178     1  1380  1380
browser |  1380   99.8%         10     + 135493786 135498458             NM_033178     1  1380  1380
browser |  1380  100.0%  Un_gl000228     +     82754     84133             NM_033178     1  1380  1380
browser |  1380  100.0%  Un_gl000228     +     79448     80827             NM_033178     1  1380  1380
browser |  1380  100.0%  Un_gl000228     +    102590    103969             NM_033178     1  1380  1380
browser |  1380  100.0%  Un_gl000228     +    105896    107275             NM_033178     1  1380  1380
browser |  1380  100.0%  Un_gl000228     +    109202    110581             NM_033178     1  1380  1380

View details of parts of alignment within browser window
.

Position: chrUn_gl000228:72836-74215
Genomic Size: 1380
Strand: +
Gene Symbol: DUX4
CDS Start: complete
CDS End: complete

Position: chrUn_gl000228:79448-80827
Genomic Size: 1380
Strand: +
Gene Symbol: DUX4
CDS Start: complete
CDS End: complete

Position: chr4:191012063-191013442
Band: 4q35.2
Genomic Size: 1380
Strand: +
Gene Symbol: DUX4
CDS Start: complete
CDS End: complete

Position: chrUn_gl000228:112508-113887
Genomic Size: 1380
Strand: +
Gene Symbol: DUX4
CDS Start: complete
CDS End: complete

Position: chrUn_gl000228:109202-110581
Genomic Size: 1380
Strand: +
Gene Symbol: DUX4
CDS Start: complete
CDS End: complete

Position: chrUn_gl000228:105896-107275
Genomic Size: 1380
Strand: +
Gene Symbol: DUX4
CDS Start: complete
CDS End: complete

Position: chrUn_gl000228:82754-84133
Genomic Size: 1380
Strand: +
Gene Symbol: DUX4
CDS Start: complete
CDS End: complete

Position: chrUn_gl000228:102590-103969
Genomic Size: 1380
Strand: +
Gene Symbol: DUX4
CDS Start: complete
CDS End: complete

Position: chrUn_gl000228:99284-100663
Genomic Size: 1380
Strand: +
Gene Symbol: DUX4
CDS Start: complete
CDS End: complete

Position: chrUn_gl000228:86060-87439
Genomic Size: 1380
Strand: +
Gene Symbol: DUX4
CDS Start: complete
CDS End: complete

Position: chrUn_gl000228:76142-77521
Genomic Size: 1380
Strand: +
Gene Symbol: DUX4
CDS Start: complete
CDS End: complete

Position: chr4:191008763-191010142
Band: 4q35.2
Genomic Size: 1380
Strand: +
Gene Symbol: DUX4
CDS Start: complete
CDS End: complete

Position: chr4:191005470-191006849
Band: 4q35.2
Genomic Size: 1380
Strand: +
Gene Symbol: DUX4
CDS Start: complete
CDS End: complete

Position: chr4:190998876-191000255
Band: 4q35.2
Genomic Size: 1380
Strand: +
Gene Symbol: DUX4
CDS Start: complete
CDS End: complete

Position: chr10:135480558-135485241
Band: 10q26.3
Genomic Size: 4684
Strand: +
Gene Symbol: DUX4
CDS Start: complete
CDS End: complete

Position: chr10:135487177-135491849
Band: 10q26.3
Genomic Size: 4673
Strand: +
Gene Symbol: DUX4
CDS Start: complete
CDS End: complete

Position: chr10:135493786-135498458
Band: 10q26.3
Genomic Size: 4673
Strand: +
Gene Symbol: DUX4
CDS Start: complete
CDS End: complete

Position: chr4:190992290-190993669
Band: 4q35.2
Genomic Size: 1380
Strand: +
Gene Symbol: DUX4
CDS Start: complete
CDS End: complete

Position: chr4:190995583-190996962
Band: 4q35.2
Genomic Size: 1380
Strand: +
Gene Symbol: DUX4
CDS Start: complete
CDS End: complete

Links to sequence:

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Data last updated: 2013-05-15

Description

The RefSeq Genes track shows known human protein-coding and non-protein-coding genes taken from the NCBI RNA reference sequences collection (RefSeq). The data underlying this track are updated daily.

Display Conventions and Configuration

This track follows the display conventions for gene prediction tracks. The color shading indicates the level of review the RefSeq record has undergone: predicted (light), provisional (medium), reviewed (dark).

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  • Codon coloring: This track contains an optional codon coloring feature that allows users to quickly validate and compare gene predictions. To display codon colors, select the genomic codons option from the Color track by codons pull-down menu. For more information about this feature, go to the Coloring Gene Predictions and Annotations by Codon page.
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Methods

RefSeq RNAs were aligned against the human genome using blat; those with an alignment of less than 15% were discarded. When a single RNA aligned in multiple places, the alignment having the highest base identity was identified. Only alignments having a base identity level within 0.1% of the best and at least 96% base identity with the genomic sequence were kept.

Credits

This track was produced at UCSC from RNA sequence data generated by scientists worldwide and curated by the NCBI RefSeq project.

References

Kent WJ. BLAT - the BLAST-like alignment tool. Genome Res. 2002 Apr;12(4):656-64.

Pruitt KD, Tatusova T, Maglott DR. NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res. 2005 Jan 1;33(Database issue):D501-4.