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RefSeq Gene
 

RefSeq Gene HCG17

RefSeq: NR_052012.1   Status: Validated
Entrez Gene: 414778
PubMed on Gene: HCG17
GeneCards: HCG17
AceView: HCG17
Stanford SOURCE: NR_052012

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 |   732  100.0%  6_ssto_hap7     -   1532221   1623886             NR_052012     1   732   746
browser |   732   99.9%          6     -  30201816  30293911             NR_052012     1   732   746
browser |   616   99.7%  6_apd_hap1     -   1442004   1605540             NR_052012     1   732   746
browser |   732  100.0%  6_cox_hap2     -   1713911   1805917             NR_052012     1   732   746
browser |   732   99.9%  6_dbb_hap3     -   1495494   1587559             NR_052012     1   732   746
browser |   732   99.8%  6_mann_hap4     -   1550304   1641979             NR_052012     1   732   746
browser |   732   99.9%  6_qbl_hap6     -   1494731   1586805             NR_052012     1   732   746

Position: chr6:30201816-30293911
Band: 6p22.1
Genomic Size: 92096
Strand: -
Gene Symbol: HCG17

Position: chr6_apd_hap1:1442004-1605540
Genomic Size: 163537
Strand: -
Gene Symbol: HCG17

Position: chr6_cox_hap2:1713911-1805917
Genomic Size: 92007
Strand: -
Gene Symbol: HCG17

Position: chr6_dbb_hap3:1495494-1587559
Genomic Size: 92066
Strand: -
Gene Symbol: HCG17

Position: chr6_mann_hap4:1550304-1641979
Genomic Size: 91676
Strand: -
Gene Symbol: HCG17

Position: chr6_qbl_hap6:1494731-1586805
Genomic Size: 92075
Strand: -
Gene Symbol: HCG17

Position: chr6_ssto_hap7:1532221-1623886
Genomic Size: 91666
Strand: -
Gene Symbol: HCG17

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.