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RefSeq Gene
 

RefSeq Gene C4B_2

RefSeq: NM_001242823.2   Status: Reviewed
CDS: completeness unknown
Entrez Gene: 100293534
PubMed on Gene: C4B_2
PubMed on Product: complement C4-B-like preproprotein
GeneCards: C4B_2
AceView: C4B_2
Stanford SOURCE: NM_001242823

Summary of C4B_2

This gene encodes the basic form of complement factor 4, part of the classical activation pathway. The protein is expressed as a single chain precursor which is proteolytically cleaved into a trimer of alpha, beta, and gamma chains prior to secretion. The trimer provides a surface for interaction between the antigen-antibody complex and other complement components. The alpha chain may be cleaved to release C4 anaphylatoxin, a mediator of local inflammation. Deficiency of this protein is associated with systemic lupus erythematosus. This gene localizes to the major histocompatibility complex (MHC) class III region on chromosome 6. Varying haplotypes of this gene cluster exist, such that individuals may have 1, 2, or 3 copies of this gene. In addition, this gene exists as a long form and a short form due to the presence or absence of a 6.4 kb endogenous HERV-K retrovirus in intron 9. This GeneID and its associated RefSeq record represent a second copy of C4B found on ALT_REF_LOCI_7. [provided by RefSeq, Jul 2011]. Sequence Note: The RefSeq transcript and protein were derived from genomic sequence to make the sequence consistent with the reference genome assembly. The genomic coordinates used for the transcript record were based on alignments. ##Evidence-Data-START## Transcript exon combination :: BC063289.1, AB209989.1 [ECO:0000332] RNAseq introns :: single sample supports all introns ERS025081, ERS025082 [ECO:0000348] ##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 |  5427   99.8%          6     +  31949834  31970458          NM_001242823     1  5427  5427
browser |  5427  100.0%          6     +  31982572  32003195          NM_001242823     1  5427  5427
browser |  5427  100.0%  6_cox_hap2     +   3459590   3473846          NM_001242823     1  5427  5427
browser |  5427   99.8%  6_dbb_hap3     +   3235415   3256040          NM_001242823     1  5427  5427
browser |  5427  100.0%  6_dbb_hap3     +   3268155   3282411          NM_001242823     1  5427  5427
browser |  5427   99.8%  6_mcf_hap5     +   3362416   3383040          NM_001242823     1  5427  5427
browser |  5427   99.8%  6_qbl_hap6     +   3243624   3264249          NM_001242823     1  5427  5427
browser |  5427  100.0%  6_ssto_hap7     +   3282544   3303168          NM_001242823     1  5427  5427
browser |  5427  100.0%  6_ssto_hap7     +   3315282   3335906          NM_001242823     1  5427  5427

Position: chr6_ssto_hap7:3282544-3303168
Genomic Size: 20625
Strand: +
Gene Symbol: C4B_2
CDS Start: complete
CDS End: complete

Position: chr6_ssto_hap7:3315282-3335906
Genomic Size: 20625
Strand: +
Gene Symbol: C4B_2
CDS Start: complete
CDS End: complete

Position: chr6_qbl_hap6:3243624-3264249
Genomic Size: 20626
Strand: +
Gene Symbol: C4B_2
CDS Start: complete
CDS End: complete

Position: chr6_cox_hap2:3459590-3473846
Genomic Size: 14257
Strand: +
Gene Symbol: C4B_2
CDS Start: complete
CDS End: complete

Position: chr6:31949834-31970458
Band: 6p21.33
Genomic Size: 20625
Strand: +
Gene Symbol: C4B_2
CDS Start: complete
CDS End: complete

Position: chr6:31982572-32003195
Band: 6p21.33
Genomic Size: 20624
Strand: +
Gene Symbol: C4B_2
CDS Start: complete
CDS End: complete

Position: chr6_dbb_hap3:3268155-3282411
Genomic Size: 14257
Strand: +
Gene Symbol: C4B_2
CDS Start: complete
CDS End: complete

Position: chr6_mcf_hap5:3362416-3383040
Genomic Size: 20625
Strand: +
Gene Symbol: C4B_2
CDS Start: complete
CDS End: complete

Position: chr6_dbb_hap3:3235415-3256040
Genomic Size: 20626
Strand: +
Gene Symbol: C4B_2
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.
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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.