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CYB5D2 cytochrome b5 domain containing 2 [ Homo sapiens (human) ]

Gene ID: 124936, updated on 5-Mar-2024

Summary

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Official Symbol
CYB5D2provided by HGNC
Official Full Name
cytochrome b5 domain containing 2provided by HGNC
Primary source
HGNC:HGNC:28471
See related
Ensembl:ENSG00000167740 AllianceGenome:HGNC:28471
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Summary
Predicted to enable heme binding activity. Predicted to be involved in nervous system development. Predicted to act upstream of or within positive regulation of neuron differentiation. Predicted to be located in extracellular region. Predicted to be active in endomembrane system and membrane. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in testis (RPKM 7.4), kidney (RPKM 6.3) and 25 other tissues See more
Orthologs
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Genomic context

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Location:
17p13.2
Exon count:
6
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (4143168..4157701)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (4032352..4046939)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (4046462..4060995)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene zinc finger ZZ-type and EF-hand domain containing 1 Neighboring gene RNA, 5S ribosomal pseudogene 434 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11532 Neighboring gene small nucleolar RNA U13 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11533 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11534 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:4046085-4046636 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:4046637-4047189 Neighboring gene uncharacterized LOC124903898 Neighboring gene ReSE screen-validated silencer GRCh37_chr17:4072633-4072788 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:4079793-4080294 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:4080295-4080794 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr17:4081807-4083006 Neighboring gene ankyrin repeat and FYVE domain containing 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:4089981-4090980 Neighboring gene stem-loop binding protein pseudogene Neighboring gene MPRA-validated peak2695 silencer Neighboring gene RYK pseudogene 1

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. CYB5D2 displays tumor suppression activities towards cervical cancer. Xie Y, et al. Biochim Biophys Acta, 2016 Apr. PMID 26692170
  2. Neuferricin, a novel extracellular heme-binding protein, promotes neurogenesis. Kimura I, et al. J Neurochem, 2010 Mar. PMID 19968755
  3. Genetic predictors of risk and resilience in psychiatric disorders: a cross-disorder genome-wide association study of functional impairment in major depressive disorder, bipolar disorder, and schizophrenia. McGrath LM, et al. Am J Med Genet B Neuropsychiatr Genet, 2013 Dec. PMID 24039173, Free PMC Article
  4. Systematic interactome mapping of acute lymphoblastic leukemia cancer gene products reveals EXT-1 tumor suppressor as a Notch1 and FBWX7 common interactor. Daakour S, et al. BMC Cancer, 2016 May 26. PMID 27229929, Free PMC Article
  5. Interactome Analysis of Human Phospholipase D and Phosphatidic Acid-Associated Protein Network. Kattan RE, et al. Mol Cell Proteomics, 2022 Feb. PMID 35007762, Free PMC Article

See all (15) citations in PubMed

GeneRIFs: Gene References Into Functions

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
Genetic predictors of risk and resilience in psychiatric disorders: a cross-disorder genome-wide association study of functional impairment in major depressive disorder, bipolar disorder, and schizophrenia.
EBI GWAS Catalog

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • MGC32124

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables heme binding IEA
Inferred from Electronic Annotation
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in neuron differentiation IEA
Inferred from Electronic Annotation
more info
  
involved_in positive regulation of neuron differentiation IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
is_active_in endomembrane system IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in extracellular region IEA
Inferred from Electronic Annotation
more info
  
is_active_in membrane IBA
Inferred from Biological aspect of Ancestor
more info
  

General protein information

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Preferred Names
neuferricin
Names
cytochrome b5 domain-containing protein 2

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

  1. NM_001254755.2 → NP_001241684.1  neuferricin isoform 2

    See identical proteins and their annotated locations for NP_001241684.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR, lacks a portion of the 5' coding region, and initiates translation at a downstream start codon, compared to variant 1. Variants 2 and 3 encode the same isoform (2), which has a shorter N-terminus, compared to isoform 1.
    Source sequence(s)
    AC087292, BM681125, CK821986, EB386356
    Consensus CDS
    CCDS58501.1
    UniProtKB/Swiss-Prot
    Q8WUJ1
    Related
    ENSP00000458903.1, ENST00000575251.5

  2. NM_001254756.1 → NP_001241685.1  neuferricin isoform 2

    See identical proteins and their annotated locations for NP_001241685.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) differs in the 5' UTR, lacks a portion of the 5' coding region, and initiates translation at a downstream start codon, compared to variant 1. Variants 2 and 3 encode the same isoform (2), which has a shorter N-terminus, compared to isoform 1.
    Source sequence(s)
    AC087292, BM681125, CB112805, CB129650
    Consensus CDS
    CCDS58501.1
    UniProtKB/Swiss-Prot
    Q8WUJ1
    Related
    ENSP00000458352.2, ENST00000577075.6

  3. NM_144611.4 → NP_653212.1  neuferricin isoform 1 precursor

    See identical proteins and their annotated locations for NP_653212.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longer isoform (1).
    Source sequence(s)
    AC087292
    Consensus CDS
    CCDS11044.1
    UniProtKB/Swiss-Prot
    B2R7R6, D3DTJ9, I3L1K2, Q8WUJ1
    Related
    ENSP00000301391.4, ENST00000301391.8
    Conserved Domains (1) summary
    pfam00173
    Location:40 → 100
    Cyt-b5; Cytochrome b5-like Heme/Steroid binding domain

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000017.11 Reference GRCh38.p14 Primary Assembly

    Range
    4143168..4157701
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047435333.1 → XP_047291289.1  neuferricin isoform X2

  2. XM_006721447.4 → XP_006721510.2  neuferricin isoform X1

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060941.1 Alternate T2T-CHM13v2.0

    Range
    4032352..4046939
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054315042.1 → XP_054171017.1  neuferricin isoform X2

  2. XM_054315041.1 → XP_054171016.1  neuferricin isoform X1

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q8WUJ1.1 GenPept UniProtKB/Swiss-Prot:Q8WUJ1

Gene LinkOut

The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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