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RefSeq Gene
 

RefSeq Gene OR2J3

RefSeq: NM_001005216.3   Status: Validated
CDS: completeness unknown
OMIM: 615016
Entrez Gene: 442186
PubMed on Gene: OR2J3
PubMed on Product: olfactory receptor 2J3
GeneCards: OR2J3
AceView: OR2J3
Stanford SOURCE: NM_001005216

Summary of OR2J3

Olfactory receptors interact with odorant molecules in the nose, to initiate a neuronal response that triggers the perception of a smell. The olfactory receptor proteins are members of a large family of G-protein-coupled receptors (GPCR) arising from single coding-exon genes. Olfactory receptors share a 7-transmembrane domain structure with many neurotransmitter and hormone receptors and are responsible for the recognition and G protein-mediated transduction of odorant signals. The olfactory receptor gene family is the largest in the genome. The nomenclature assigned to the olfactory receptor genes and proteins for this organism is independent of other organisms. [provided by RefSeq, Jul 2008]. Sequence Note: This RefSeq was created from transcript and genomic sequence data to make the sequence consistent with the reference genome assembly. The genomic coordinates used for the transcript record were based on alignments.


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 |   936  100.0%          6     +  29079668  29080603          NM_001005216     1   936   936
browser |   936   99.8%  6_apd_hap1     +    383105    384040          NM_001005216     1   936   936
browser |   936   99.8%  6_cox_hap2     +    598545    599480          NM_001005216     1   936   936
browser |   936   99.8%  6_dbb_hap3     +    383078    384013          NM_001005216     1   936   936
browser |   936   99.8%  6_mann_hap4     +    383070    384005          NM_001005216     1   936   936
browser |   932   98.2%  6_mcf_hap5     +    383215    445883          NM_001005216     1   932   936
browser |   936   99.8%  6_qbl_hap6     +    383072    384007          NM_001005216     1   936   936
browser |   936   99.8%  6_ssto_hap7     +    420553    421488          NM_001005216     1   936   936

Position: chr6_dbb_hap3:383078-384013
Genomic Size: 936
Strand: +
Gene Symbol: OR2J3
CDS Start: complete
CDS End: complete

Position: chr6_cox_hap2:598545-599480
Genomic Size: 936
Strand: +
Gene Symbol: OR2J3
CDS Start: complete
CDS End: complete

Position: chr6_ssto_hap7:420553-421488
Genomic Size: 936
Strand: +
Gene Symbol: OR2J3
CDS Start: complete
CDS End: complete

Position: chr6_mcf_hap5:383215-445883
Genomic Size: 62669
Strand: +
Gene Symbol: OR2J3
CDS Start: complete
CDS End: not complete

Position: chr6_mann_hap4:383070-384005
Genomic Size: 936
Strand: +
Gene Symbol: OR2J3
CDS Start: complete
CDS End: complete

Position: chr6:29079668-29080603
Band: 6p22.1
Genomic Size: 936
Strand: +
Gene Symbol: OR2J3
CDS Start: complete
CDS End: complete

Position: chr6_qbl_hap6:383072-384007
Genomic Size: 936
Strand: +
Gene Symbol: OR2J3
CDS Start: complete
CDS End: complete

Position: chr6_apd_hap1:383105-384040
Genomic Size: 936
Strand: +
Gene Symbol: OR2J3
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).

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.