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RefSeq Gene
 

RefSeq Gene HCG9

RefSeq: NR_028032.1   Status: Validated
CDS: 3' complete
Entrez Gene: 10255
PubMed on Gene: HCG9
GeneCards: HCG9
AceView: HCG9
Stanford SOURCE: NR_028032

Summary of HCG9

This gene lies within the MHC class I region on chromosome 6p21.3. This gene is believed to be non-coding, but its function has not been determined. [provided by RefSeq, Jul 2009]. ##Evidence-Data-START## Transcript exon combination :: X95289.1 [ECO:0000332] ##Evidence-Data-END##


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 |   650  100.0%          6     +  29942892  29946177             NR_028032     1   650   670
browser |   650  100.0%  6_cox_hap2     +   1454595   1457881             NR_028032     1   650   670
browser |   650  100.0%  6_dbb_hap3     +   1236226   1239512             NR_028032     1   650   670
browser |   645   99.1%  6_mann_hap4     +   1241473   1244756             NR_028032     1   650   670
browser |   650   99.4%  6_mcf_hap5     +   1324753   1328039             NR_028032     1   650   670
browser |   650   99.3%  6_qbl_hap6     +   1235684   1238972             NR_028032     1   650   670
browser |   645   99.1%  6_ssto_hap7     +   1272216   1275499             NR_028032     1   650   670

Position: chr6:29942892-29946177
Band: 6p22.1
Genomic Size: 3286
Strand: +
Gene Symbol: HCG9

Position: chr6_cox_hap2:1454595-1457881
Genomic Size: 3287
Strand: +
Gene Symbol: HCG9

Position: chr6_dbb_hap3:1236226-1239512
Genomic Size: 3287
Strand: +
Gene Symbol: HCG9

Position: chr6_mann_hap4:1241473-1244756
Genomic Size: 3284
Strand: +
Gene Symbol: HCG9

Position: chr6_mcf_hap5:1324753-1328039
Genomic Size: 3287
Strand: +
Gene Symbol: HCG9

Position: chr6_qbl_hap6:1235684-1238972
Genomic Size: 3289
Strand: +
Gene Symbol: HCG9

Position: chr6_ssto_hap7:1272216-1275499
Genomic Size: 3284
Strand: +
Gene Symbol: HCG9

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).

The item labels and display colors of features within this track can be configured through the controls at the top of the track description page. This page is accessed via the small button to the left of the track's graphical display or through the link on the track's control menu.

  • Label: By default, items are labeled by gene name. Click the appropriate Label option to display the accession name instead of the gene name, show both the gene and accession names, or turn off the label completely.
  • 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.
  • Hide non-coding genes: By default, both the protein-coding and non-protein-coding genes are displayed. If you wish to see only the coding genes, click this box.

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.