Afp alpha-fetoprotein [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Afpprovided by RGD
Official Full Name: alpha-fetoproteinprovided by RGD
Primary source: RGD:2065
See related: Ensembl:ENSRNOG00000002889 AllianceGenome:RGD:2065
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Summary: Predicted to enable fatty acid binding activity and zinc ion binding activity. Involved in several processes, including cellular response to retinoic acid; liver regeneration; and response to dexamethasone. Located in cytosol and extracellular space. Biomarker of hepatitis. Human ortholog(s) of this gene implicated in hepatitis C. Orthologous to human AFP (alpha fetoprotein). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Restricted expression toward (RPKM 7579.0) See more
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Genomic context

Location:: 14p22

Exon count:: 16

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	14	NC_086032.1 (17857584..17875645, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	14	NC_051349.1 (17573412..17591476, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	14	NC_005113.4 (19141755..19159919, complement)

Chromosome 14 - NC_086032.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
BioProject: PRJNA238328
Publication: PMID 24510058
Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

maternal serum level associated with adverse pregnancy outcome in placental inflammation
Title: A rat model of placental inflammation explains the unexplained elevated maternal serum alpha-fetoprotein associated with adverse pregnancy outcomes.
In this work show that alpha-fetoprotein (AFP) is present in the brain during embryonic development, its concentrations peaking at E15.5 and at E19.5. AFP concentrations plummeted concurrently with a sharp increase in serum albumin concentrations.
Title: Alpha-fetoprotein (AFP) modulates the effect of serum albumin on brain development by restraining the neurotrophic effect of oleic acid.
Data suggest that glucocorticoids promote the development of rat colon, and that AFP appears to be involved, in part, in mediating the effects of GCs in the developmental colon.
Title: α-fetoprotein involvement during glucocorticoid-induced precocious maturation in rat colon.
This study has for the first time demonstrated that AFP is localized in the mesenchyme of rat colon from the embryo to the weaning stage by immunofluorescence.
Title: Expression and location of alpha-fetoprotein during rat colon development.
alpha-fetoprotein-gene-expression, and the function of the secretory apparatus during rat liver development.
Title: Kinetics of albumin- and alpha-fetoprotein-production during rat liver development.
The dynamic expression of AFP in pancreas from different stages indicates that AFP might be involved in some aspects of pancreatic development.
Title: Alpha-fetoprotein is dynamically expressed in rat pancreas during development.
role in bile acid inhibition of sterol 12alpha-hydroxylase gene
Title: On the mechanism of bile acid inhibition of rat sterol 12alpha-hydroxylase gene (CYP8B1) transcription: roles of alpha-fetoprotein transcription factor and hepatocyte nuclear factor 4alpha.
Thus expression of the afp gene requires functional interactions between HNF-6 molecules and between HNF-6 and RORalpha.
Title: Hepatocyte nuclear factor-6 stimulates transcription of the alpha-fetoprotein gene and synergizes with the retinoic-acid-receptor-related orphan receptor alpha-4.
In adult cells, the silenced gene was actively repressed at the promoter and two proximal enhancers, characterized by the absence of coactivators and acetylated histone 4, and the presence of corepressors and K9-methylated histone 3.
Title: Characterization of distant enhancers and promoters in the albumin-alpha-fetoprotein locus during active and silenced expression.
Nkx2.8 bound to the active AFP promoter, and antisense inhibition of Nkx2.8 mRNA translation selectively reduced expression of both the endogenous human AFP gene and transfected reporters containing the rat AFP promoter.
Title: Regulation of alpha-fetoprotein expression by Nkx2.8.

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General gene information

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Markers

PMC275467P5 (e-PCR)
- UniSTS:272386

Afp (e-PCR), detects polymorphism
- UniSTS:532534

D14Wox8 (e-PCR)
- UniSTS:119423

d14mit2 (e-PCR)
- UniSTS:120964

UniSTS:275850 (e-PCR)
- UniSTS:275850

Afp (e-PCR), detects polymorphism
- UniSTS:275850

BI285802 (e-PCR)
- UniSTS:244897

D14Wox9 (e-PCR)
- UniSTS:119253

RH94533 (e-PCR)
- UniSTS:119781

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables metal ion binding	IEA Inferred from Electronic Annotation more info
enables small molecule binding	IBA Inferred from Biological aspect of Ancestor more info

Process	Evidence Code	Pubs
involved_in animal organ regeneration	IEP Inferred from Expression Pattern more info	PubMed
involved_in cellular response to retinoic acid	IEP Inferred from Expression Pattern more info	PubMed
involved_in liver development	IEP Inferred from Expression Pattern more info	PubMed
involved_in liver regeneration	IEP Inferred from Expression Pattern more info	PubMed
involved_in ovulation from ovarian follicle	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within ovulation from ovarian follicle	ISO Inferred from Sequence Orthology more info
involved_in pancreas development	IEP Inferred from Expression Pattern more info	PubMed
involved_in progesterone metabolic process	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within progesterone metabolic process	ISO Inferred from Sequence Orthology more info
involved_in response to dexamethasone	IEP Inferred from Expression Pattern more info	PubMed
involved_in response to organic substance	IEP Inferred from Expression Pattern more info	PubMed
acts_upstream_of_or_within sexual reproduction	ISO Inferred from Sequence Orthology more info
involved_in transport	IBA Inferred from Biological aspect of Ancestor more info

Component	Evidence Code	Pubs
is_active_in cytoplasm	IBA Inferred from Biological aspect of Ancestor more info
located_in cytoplasm	IEA Inferred from Electronic Annotation more info
located_in cytoplasm	ISO Inferred from Sequence Orthology more info
located_in extracellular space	IDA Inferred from Direct Assay more info	PubMed
located_in extracellular space	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: alpha-fetoprotein

Names: alpha-1-fetoprotein; alpha-fetoglobulin; chloride intracellular channel 6

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)

NM_012493.2 → NP_036625.2 alpha-fetoprotein precursor

See identical proteins and their annotated locations for NP_036625.2

Status: VALIDATED

Source sequence(s)

AW141770, DY309525, DY310963, DY317147

UniProtKB/TrEMBL

A6KKF8, G3V6D0, Q4QR90

Related

ENSRNOP00000003879.2, ENSRNOT00000003879.4

Conserved Domains (1) summary

smart00103
Location:406 → 596

ALBUMIN; serum albumin

RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

Reference GRCr8

Genomic

NC_086032.1 Reference GRCr8

Range

17857584..17875645 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_039091614.2 → XP_038947542.1 alpha-fetoprotein isoform X1

UniProtKB/TrEMBL

A6KKF9

Conserved Domains (2) summary

smart00103
Location:120 → 310

ALBUMIN; serum albumin

cl00031
Location:1 → 112

ALBUMIN; Albumin domain, contains five or six internal disulphide bonds; albuminoid superfamily includes alpha-fetoprotein which binds various cations, fatty acids and bilirubin; vitamin D-binding protein which binds to vitamin D, its metabolites, and fatty acids; ...