U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

Links from GEO Profiles

    • Showing Current items.

    Zbed5 zinc finger BED-type containing 5 [ Mus musculus (house mouse) ]

    Gene ID: 71970, updated on 12-May-2024

    Summary

    Go to the top of the page Help
    Official Symbol
    Zbed5provided by MGI
    Official Full Name
    zinc finger BED-type containing 5provided by MGI
    Primary source
    MGI:MGI:1919220
    See related
    Ensembl:ENSMUSG00000034173 AllianceGenome:MGI:1919220
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Mus musculus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
    Also known as
    Scand3; Chchd2l; 2410018M08Rik
    Summary
    Located in mitochondrion. Orthologous to several human genes including ZBED5 (zinc finger BED-type containing 5). [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Ubiquitous expression in adrenal adult (RPKM 344.6), duodenum adult (RPKM 276.2) and 28 other tissues See more
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    Go to the top of the page Help
    See Zbed5 in Genome Data Viewer
    Location:
    5 G1.3; 5 68.26 cM
    Exon count:
    6
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 5 NC_000071.7 (129924564..129937350)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 5 NC_000071.6 (129895723..129908509)

    Chromosome 5 - NC_000071.7Genomic Context describing neighboring genes Neighboring gene sulfatase modifying factor 2 Neighboring gene phosphorylase kinase gamma 1 Neighboring gene STARR-positive B cell enhancer ABC_E125 Neighboring gene coiled-coil-helix-coiled-coil-helix domain containing 2 Neighboring gene STARR-positive B cell enhancer ABC_E2766 Neighboring gene STARR-seq mESC enhancer starr_14464 Neighboring gene nuclear protein transcriptional regulator 2 Neighboring gene STARR-positive B cell enhancer ABC_E1308 Neighboring gene vitamin K epoxide reductase complex, subunit 1-like 1 Neighboring gene STARR-seq mESC enhancer starr_14467 Neighboring gene STARR-seq mESC enhancer starr_14468 Neighboring gene glucuronidase, beta

    Genomic regions, transcripts, and products

    Go to the top of the page Help

    Go to nucleotide: Graphics FASTA GenBank

    Expression

    Go to the top of the page Help
    • Project title: Mouse ENCODE transcriptome data
    • Description: RNA profiling data sets generated by the Mouse ENCODE project.
    • BioProject: PRJNA66167
    • Publication: PMID 25409824
    • Analysis date: n/a

    Bibliography

    Go to the top of the pageHelp

    Related articles in PubMed

    1. New TFII-I family target genes involved in embryonic development. Makeyev AV, et al. Biochem Biophys Res Commun, 2009 Sep 4. PMID 19527686, Free PMC Article
    2. Mapping the NPHP-JBTS-MKS protein network reveals ciliopathy disease genes and pathways. Sang L, et al. Cell, 2011 May 13. PMID 21565611, Free PMC Article
    3. High-throughput discovery of novel developmental phenotypes. Dickinson ME, et al. Nature, 2016 Sep 22. PMID 27626380, Free PMC Article
    4. A mitochondrial protein compendium elucidates complex I disease biology. Pagliarini DJ, et al. Cell, 2008 Jul 11. PMID 18614015, Free PMC Article
    5. Large-scale gene trapping in C57BL/6N mouse embryonic stem cells. Hansen GM, et al. Genome Res, 2008 Oct. PMID 18799693, Free PMC Article

    See all (17) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Scand3 is down-regulated during mouse embryonic stem cell differentiation.
      Title: New TFII-I family target genes involved in embryonic development.
    Submit: New GeneRIF Correction

    Variation

    Go to the top of the page Help

    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)
    • Endonuclease-mediated (1) 
    • Targeted (2) 

    Interactions

    Go to the top of the page Help
    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Go to the top of the page Help

    Markers

    Homology

    Gene Ontology Provided by MGI

    Function Evidence Code Pubs
    enables molecular_function ND
    No biological Data available
    more info
    		  
    Process Evidence Code Pubs
    involved_in biological_process ND
    No biological Data available
    more info
    		  
    Component Evidence Code Pubs
    located_in mitochondrion HDA PubMed 

    General protein information

    Go to the top of the page Help
    Preferred Names
    SCAN domain containing 3
    Names
    ZSCAN domain containing 3
    coiled-coil-helix-coiled-coil-helix domain containing 2-like

    NCBI Reference Sequences (RefSeq)

    Go to the top of the page Help

    NEW Try the new Transcript table

    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_001359408.1 → NP_001346337.1  SCAN domain containing 3 isoform 2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR and coding sequence compared to variant 1. The resulting isoform (2) is shorter at the N-terminus compared to isoform 1.
      Source sequence(s)
      AC164071
      Conserved Domains (3) summary
      pfam05699
      Location:650 → 715
      Dimer_Tnp_hAT; hAT family C-terminal dimerization region
      pfam06747
      Location:95 → 126
      CHCH; CHCH domain
      pfam14291
      Location:291 → 386
      DUF4371; Domain of unknown function (DUF4371)

    2. NM_183088.2 → NP_898911.2  SCAN domain containing 3 isoform 1

      See identical proteins and their annotated locations for NP_898911.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) encodes the longer isoform (1).
      Source sequence(s)
      AC164071, AK010551
      Consensus CDS
      CCDS39292.1
      UniProtKB/TrEMBL
      B2RPU8
      Related
      ENSMUSP00000044533.8, ENSMUST00000041466.14
      Conserved Domains (3) summary
      pfam05699
      Location:671 → 736
      Dimer_Tnp_hAT; hAT family C-terminal dimerization region
      pfam06747
      Location:116 → 147
      CHCH; CHCH domain
      pfam14291
      Location:335 → 407
      DUF4371; Domain of unknown function (DUF4371)

    RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

    Reference GRCm39 C57BL/6J

    Genomic

    1. NC_000071.7 Reference GRCm39 C57BL/6J

      Range
      129924564..129937350
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017321106.2 → XP_017176595.1  SCAN domain containing 3 isoform X2

      Conserved Domains (1) summary
      pfam06747
      Location:95 → 126
      CHCH; CHCH domain

    2. XM_017321105.3 → XP_017176594.1  SCAN domain containing 3 isoform X1

      Conserved Domains (3) summary
      pfam05699
      Location:650 → 715
      Dimer_Tnp_hAT; hAT family C-terminal dimerization region
      pfam06747
      Location:95 → 126
      CHCH; CHCH domain
      pfam14291
      Location:291 → 386
      DUF4371; Domain of unknown function (DUF4371)

    RNA

    1. XR_004942567.1 RNA Sequence

    Nucleotide Protein Strain
    Heading Accession and Version

    Gene LinkOut

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

    Chemical Information
    Molecular Biology Databases
    Research Materials
    Tools
    Miscellaneous