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Dph3 diphthamine biosynthesis 3 [ Mus musculus (house mouse) ]

Gene ID: 105638, updated on 5-Mar-2024

Summary

Official Symbol
Dph3provided by MGI
Official Full Name
diphthamine biosynthesis 3provided by MGI
Primary source
MGI:MGI:1922658
See related
Ensembl:ENSMUSG00000021905 AllianceGenome:MGI:1922658
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
Desr1; KTI11; Zcsl2; DELGIP1; DelgipP1
Summary
Predicted to enable metal ion binding activity. Predicted to be involved in peptidyl-diphthamide biosynthetic process from peptidyl-histidine and tRNA wobble uridine modification. Predicted to be located in cytoplasm and nucleoplasm. Predicted to be active in cytosol and nucleus. Orthologous to several human genes including DPH3 (diphthamide biosynthesis 3). [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in testis adult (RPKM 10.1), cerebellum adult (RPKM 7.7) and 28 other tissues See more
Orthologs
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Genomic context

Location:
14 B; 14 19.4 cM
Exon count:
3
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCm39 (GCF_000001635.27) 14 NC_000080.7 (31802474..31807649, complement)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 14 NC_000080.6 (32080517..32085692, complement)

Chromosome 14 - NC_000080.7Genomic Context describing neighboring genes Neighboring gene predicted gene, 53841 Neighboring gene polypeptide N-acetylgalactosaminyltransferase 15 Neighboring gene STARR-seq mESC enhancer starr_36333 Neighboring gene oxidoreductase NAD-binding domain containing 1 Neighboring gene STARR-seq mESC enhancer starr_36334 Neighboring gene STARR-seq mESC enhancer starr_36335 Neighboring gene predicted gene, 57612 Neighboring gene STARR-seq mESC enhancer starr_36337 Neighboring gene STARR-seq mESC enhancer starr_36339 Neighboring gene predicted gene, 41127 Neighboring gene beta-microseminoprotein

Genomic regions, transcripts, and products

Expression

  • 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

Variation

Alleles

Alleles of this type are documented at Mouse Genome Informatics  (MGI)

Pathways from PubChem

General gene information

Markers

Clone Names

  • 2610018L09Rik, 5730511P15Rik

Gene Ontology Provided by MGI

Function Evidence Code Pubs
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
 
Process Evidence Code Pubs
involved_in protein histidyl modification to diphthamide IMP
Inferred from Mutant Phenotype
more info
PubMed 
Component Evidence Code Pubs
located_in cytoplasm ISO
Inferred from Sequence Orthology
more info
 
located_in cytosol ISO
Inferred from Sequence Orthology
more info
 
located_in nucleoplasm ISO
Inferred from Sequence Orthology
more info
 
located_in nucleus ISO
Inferred from Sequence Orthology
more info
 

General protein information

Preferred Names
diphthamide biosynthesis protein 3
Names
CSL-type zinc finger-containing protein 2
DPH3 homolog (KTI11, S. cerevisiae)
delGEF-interacting protein 1
zinc finger, CSL domain containing 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_001047433.2NP_001040898.1  diphthamide biosynthesis protein 3 isoform 2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) lacks an in-frame exon in the central coding region, compared to variant 1. The encoded isoform (2) is shorter, compared to isoform 1.
    Source sequence(s)
    AC154846, AK048097, DN175457
    Consensus CDS
    CCDS36860.1
    UniProtKB/TrEMBL
    D3YXV3
    Related
    ENSMUSP00000120583.2, ENSMUST00000124303.9
    Conserved Domains (1) summary
    pfam05207
    Location:645
    zf-CSL; CSL zinc finger
  2. NM_001284346.1NP_001271275.1  diphthamide biosynthesis protein 3 isoform 1

    See identical proteins and their annotated locations for NP_001271275.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) differs in the 3' UTR, compared to variant 1. Both variants 1 and 3 encode the same isoform (1).
    Source sequence(s)
    AC154846, AK048097, DN175457
    Consensus CDS
    CCDS36861.1
    UniProtKB/Swiss-Prot
    Q8K0W9
    Related
    ENSMUSP00000022461.5, ENSMUST00000022461.11
    Conserved Domains (1) summary
    pfam05207
    Location:660
    zf-CSL; CSL zinc finger
  3. NM_172254.4NP_758458.1  diphthamide biosynthesis protein 3 isoform 1

    See identical proteins and their annotated locations for NP_758458.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) encodes the longer isoform (1). Both variants 1 and 3 encode the same isoform.
    Source sequence(s)
    AC154846, AK048097, DN175457
    Consensus CDS
    CCDS36861.1
    UniProtKB/Swiss-Prot
    Q8K0W9
    Related
    ENSMUSP00000068491.6, ENSMUST00000067955.12
    Conserved Domains (1) summary
    pfam05207
    Location:660
    zf-CSL; CSL zinc finger

RNA

  1. NR_104303.1 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (4) uses an alternate splice site in the 5'-terminal exon, compared to variant 1. This variant is represented as non-coding because the predicted protein does not meet RefSeq quality criteria.
    Source sequence(s)
    AC154846, AK048097, DN175457
  2. NR_104304.1 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (5) uses an alternate splice site in an internal exon, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AC154846, AK017764, AK048097, DN175457
    Related
    ENSMUST00000112001.9
  3. NR_104305.1 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (6) uses an alternate 5'-terminal exon, compared to variant 1. This variant is represented as non-coding because the predicted protein does not meet RefSeq quality criteria.
    Source sequence(s)
    AC154846, AK048097, BG082470, BY257422

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_000080.7 Reference GRCm39 C57BL/6J

    Range
    31802474..31807649 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)