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CREBRF CREB3 regulatory factor [ Homo sapiens (human) ]

Gene ID: 153222, updated on 3-Apr-2024

Summary

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Official Symbol
CREBRFprovided by HGNC
Official Full Name
CREB3 regulatory factorprovided by HGNC
Primary source
HGNC:HGNC:24050
See related
Ensembl:ENSG00000164463 MIM:617109; AllianceGenome:HGNC:24050
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
Also known as
LRF; C5orf41
Summary
Enables DNA-binding transcription activator activity, RNA polymerase II-specific and RNA polymerase II transcription regulatory region sequence-specific DNA binding activity. Involved in several processes, including negative regulation of endoplasmic reticulum unfolded protein response; positive regulation of transport; and regulation of transcription by RNA polymerase II. Located in cytoplasm and nuclear body. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in thyroid (RPKM 12.2), bone marrow (RPKM 8.3) and 25 other tissues See more
Orthologs
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Genomic context

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See CREBRF in Genome Data Viewer
Location:
5q35.1
Exon count:
12
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (173056352..173139284)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (173596456..173679391)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (172483355..172566287)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene Sharpr-MPRA regulatory region 5956 Neighboring gene inorganic pyrophosphatase 1 pseudogene Neighboring gene ATPase H+ transporting V0 subunit e1 Neighboring gene Sharpr-MPRA regulatory region 12761 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:172444454-172444997 Neighboring gene Sharpr-MPRA regulatory region 4768 Neighboring gene small nucleolar RNA, H/ACA box 74B Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16633 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16634 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16635 Neighboring gene ReSE screen-validated silencer GRCh37_chr5:172508379-172508618 Neighboring gene CDC42 pseudogene 5 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:172555784-172556284 Neighboring gene H3K27ac hESC enhancer GRCh37_chr5:172571727-172572255 Neighboring gene BCL2 interacting protein 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16636 Neighboring gene ReSE screen-validated silencer GRCh37_chr5:172633891-172634070 Neighboring gene ribosomal protein L7a pseudogene 33

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. Multivariate analysis of a missense variant in CREBRF reveals associations with measures of adiposity in people of Polynesian ancestries. Zhang JZ, et al. Genet Epidemiol, 2023 Feb. PMID 36352773, Free PMC Article
  2. The protective effect of rs373863828 on type 2 diabetes does not operate through a body composition pathway in adult Samoans. Hawley NL, et al. Obesity (Silver Spring), 2022 Dec. PMID 36284436, Free PMC Article
  3. The missense variant, rs373863828, in CREBRF plays a role in longitudinal changes in body mass index in Samoans. Fu H, et al. Obes Res Clin Pract, 2022 May-Jun. PMID 35606300, Free PMC Article
  4. The minor allele of the CREBRF rs373863828 p.R457Q coding variant is associated with reduced levels of myostatin in males: Implications for body composition. Lee K, et al. Mol Metab, 2022 May. PMID 35218947, Free PMC Article
  5. CREBRF missense variant rs373863828 has both direct and indirect effects on type 2 diabetes and fasting glucose in Polynesian peoples living in Samoa and Aotearoa New Zealand. Russell EM, et al. BMJ Open Diabetes Res Care, 2022 Feb. PMID 35144939, Free PMC Article

See all (33) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. miR-181d-5p, which is upregulated in fetal growth restriction placentas, inhibits trophoblast fusion via CREBRF.
    Title: miR-181d-5p, which is upregulated in fetal growth restriction placentas, inhibits trophoblast fusion via CREBRF.
  2. Multivariate analysis of a missense variant in CREBRF reveals associations with measures of adiposity in people of Polynesian ancestries.
    Title: Multivariate analysis of a missense variant in CREBRF reveals associations with measures of adiposity in people of Polynesian ancestries.
  3. The protective effect of rs373863828 on type 2 diabetes does not operate through a body composition pathway in adult Samoans.
    Title: The protective effect of rs373863828 on type 2 diabetes does not operate through a body composition pathway in adult Samoans.
  4. The missense variant, rs373863828, in CREBRF plays a role in longitudinal changes in body mass index in Samoans.
    Title: The missense variant, rs373863828, in CREBRF plays a role in longitudinal changes in body mass index in Samoans.
  5. The minor allele of the CREBRF rs373863828 p.R457Q coding variant is associated with reduced levels of myostatin in males: Implications for body composition.
    Title: The minor allele of the CREBRF rs373863828 p.R457Q coding variant is associated with reduced levels of myostatin in males: Implications for body composition.
  6. CREBRF missense variant rs373863828 has both direct and indirect effects on type 2 diabetes and fasting glucose in Polynesian peoples living in Samoa and Aotearoa New Zealand.
    Title: CREBRF missense variant rs373863828 has both direct and indirect effects on type 2 diabetes and fasting glucose in Polynesian peoples living in Samoa and Aotearoa New Zealand.
  7. A missense variant in CREBRF, rs373863828, is associated with fat-free mass, not fat mass in Samoan infants.
    Title: A missense variant in CREBRF, rs373863828, is associated with fat-free mass, not fat mass in Samoan infants.
  8. The Pacific-specific CREBRF rs373863828 allele protects against gestational diabetes mellitus in Maori and Pacific women with obesity.
    Title: The Pacific-specific CREBRF rs373863828 allele protects against gestational diabetes mellitus in Māori and Pacific women with obesity.
  9. Population-specific reference panels are crucial for genetic analyses: an example of the CREBRF locus in Native Hawaiians.
    Title: Population-specific reference panels are crucial for genetic analyses: an example of the CREBRF locus in Native Hawaiians.
  10. A missense variant in CREBRF is associated with taller stature in Samoans.
    Title: A missense variant in CREBRF is associated with taller stature in Samoans.
Submit: New GeneRIF Correction See all GeneRIFs (20)

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

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

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • DKFZp313F2319, DKFZp686G2059

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables DNA-binding transcription activator activity, RNA polymerase II-specific IDA
Inferred from Direct Assay
more info
 PubMed 
enables DNA-binding transcription factor activity, RNA polymerase II-specific IBA
Inferred from Biological aspect of Ancestor
more info
  
enables RNA polymerase II transcription regulatory region sequence-specific DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables RNA polymerase II transcription regulatory region sequence-specific DNA binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in positive regulation of transcription by RNA polymerase II IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in response to unfolded protein IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
  
located_in nucleoplasm TAS
Traceable Author Statement
more info
  
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
  

General protein information

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Preferred Names
CREB3 regulatory factor
Names
UPF0474 protein C5orf41
adult retina protein
luman recruitment factor
luman-recruiting factor
luman/CREB3 recruitment factor

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_001168393.2 → NP_001161865.1  CREB3 regulatory factor isoform 2

    See identical proteins and their annotated locations for NP_001161865.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR, 3' UTR and coding region, compared to variant 1. The resulting protein (isoform 2) has a distinct C-terminus and is shorter than isoform 1. Both variant 2 and variant 3 encode the same isoform (2).
    Source sequence(s)
    BX647768
    Consensus CDS
    CCDS54948.1
    UniProtKB/Swiss-Prot
    Q8IUR6
    Related
    ENSP00000431107.1, ENST00000522692.5

  2. NM_001168394.2 → NP_001161866.1  CREB3 regulatory factor isoform 2

    See identical proteins and their annotated locations for NP_001161866.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) differs in the 3' UTR and coding region, compared to variant 1. The resulting protein (isoform 2) has a distinct C-terminus and is shorter than isoform 1. Both variant 2 and variant 3 encode the same isoform (2).
    Source sequence(s)
    AY174896, BX647768
    Consensus CDS
    CCDS54948.1
    UniProtKB/Swiss-Prot
    Q8IUR6
    Related
    ENSP00000428290.1, ENST00000520420.5

  3. NM_153607.3 → NP_705835.2  CREB3 regulatory factor isoform 1

    See identical proteins and their annotated locations for NP_705835.2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longer isoform (1).
    Source sequence(s)
    AC008378, AY139008, BX647768
    Consensus CDS
    CCDS34293.1
    UniProtKB/Swiss-Prot
    B3DFH2, B3KW49, D3DQM2, F5GXN3, Q5HYG4, Q5HYK0, Q86YR3, Q8IUR6, Q8IZG1
    UniProtKB/TrEMBL
    A8K6L2
    Related
    ENSP00000296953.2, ENST00000296953.6
    Conserved Domains (1) summary
    cd14809
    Location:525 → 563
    bZIP_AUREO-like; Basic leucine zipper (bZIP) domain of blue light (BL) receptor aureochrome (AUREO) and similar bZIP domains

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_000005.10 Reference GRCh38.p14 Primary Assembly

    Range
    173056352..173139284
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_005265821.4 → XP_005265878.1  CREB3 regulatory factor isoform X2

    See identical proteins and their annotated locations for XP_005265878.1

    UniProtKB/TrEMBL
    A8K6L2
    Conserved Domains (1) summary
    cd14809
    Location:517 → 555
    bZIP_AUREO-like; Basic leucine zipper (bZIP) domain of blue light (BL) receptor aureochrome (AUREO) and similar bZIP domains

  2. XM_011534442.2 → XP_011532744.1  CREB3 regulatory factor isoform X2

    See identical proteins and their annotated locations for XP_011532744.1

    UniProtKB/TrEMBL
    A8K6L2
    Conserved Domains (1) summary
    cd14809
    Location:517 → 555
    bZIP_AUREO-like; Basic leucine zipper (bZIP) domain of blue light (BL) receptor aureochrome (AUREO) and similar bZIP domains

  3. XM_047416801.1 → XP_047272757.1  CREB3 regulatory factor isoform X1

    UniProtKB/Swiss-Prot
    B3DFH2, B3KW49, D3DQM2, F5GXN3, Q5HYG4, Q5HYK0, Q86YR3, Q8IUR6, Q8IZG1

  4. XM_047416802.1 → XP_047272758.1  CREB3 regulatory factor isoform X1

    UniProtKB/Swiss-Prot
    B3DFH2, B3KW49, D3DQM2, F5GXN3, Q5HYG4, Q5HYK0, Q86YR3, Q8IUR6, Q8IZG1

  5. XM_006714822.5 → XP_006714885.1  CREB3 regulatory factor isoform X1

    See identical proteins and their annotated locations for XP_006714885.1

    UniProtKB/Swiss-Prot
    B3DFH2, B3KW49, D3DQM2, F5GXN3, Q5HYG4, Q5HYK0, Q86YR3, Q8IUR6, Q8IZG1
    UniProtKB/TrEMBL
    A8K6L2
    Conserved Domains (1) summary
    cd14809
    Location:525 → 563
    bZIP_AUREO-like; Basic leucine zipper (bZIP) domain of blue light (BL) receptor aureochrome (AUREO) and similar bZIP domains

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060929.1 Alternate T2T-CHM13v2.0

    Range
    173596456..173679391
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054351768.1 → XP_054207743.1  CREB3 regulatory factor isoform X2

  2. XM_054351767.1 → XP_054207742.1  CREB3 regulatory factor isoform X2

  3. XM_054351764.1 → XP_054207739.1  CREB3 regulatory factor isoform X1

    UniProtKB/Swiss-Prot
    B3DFH2, B3KW49, D3DQM2, F5GXN3, Q5HYG4, Q5HYK0, Q86YR3, Q8IUR6, Q8IZG1

  4. XM_054351766.1 → XP_054207741.1  CREB3 regulatory factor isoform X1

    UniProtKB/Swiss-Prot
    B3DFH2, B3KW49, D3DQM2, F5GXN3, Q5HYG4, Q5HYK0, Q86YR3, Q8IUR6, Q8IZG1

  5. XM_054351765.1 → XP_054207740.1  CREB3 regulatory factor isoform X1

    UniProtKB/Swiss-Prot
    B3DFH2, B3KW49, D3DQM2, F5GXN3, Q5HYG4, Q5HYK0, Q86YR3, Q8IUR6, Q8IZG1
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q8IUR6.2 GenPept UniProtKB/Swiss-Prot:Q8IUR6

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