Afm (afamin) - Rat Genome Database

Send us a Message
Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Search RGD Grant Resources Citing RGD About Us Contact Us
Genes Variants Community Projects QTLs Strains Markers Genome Information Ontologies Cell Lines References Download Submit Data
OntoMate (Literature Search) JBrowse (Genome Browser) Synteny Browser (VCMap) Variant Visualizer Multi-Ontology Enrichment (MOET) Gene-Ortholog Location Finder (GOLF) InterViewer (Protein-Protein Interactions) PhenoMiner (Quatitative Phenotypes) Gene Annotator OLGA (Gene List Generator) AllianceMine GViewer (Genome Viewer)
Aging & Age-Related Disease Cancer & Neoplastic Disease Cardiovascular Disease Coronavirus Disease Developmental Disease Diabetes Hematologic Disease Immune & Inflammatory Disease Infectious Disease Liver Disease Neurological Disease Obesity & Metabolic Syndrome Renal Disease Respiratory Disease Sensory Organ Disease
Find Models   new Genetic Models Autism Models Rat PhenoMiner (Quantitative Phenotypes) Chinchilla PhenoMiner Expected Ranges (Quantitative Phenotype) PhenoMiner Term Comparison Hybrid Rat Diversity Panel Phenotypes Phenotypes in Other Animal Models Animal Husbandry Strain Medical Records Phylogenetics Strain Availability Calendar Rats 101 Submissions Photo Archive
Pathways
Rat Community Forum Directory of Rat Laboratories Video Tutorials News RGD Publications RGD Presentations Archive Nomenclature Guidelines Resource Links Laboratory Resources Employment Resources
Gene: Afm (afamin) Mus musculus
Analyze
Symbol: Afm
Name: afamin
RGD ID: 735381
MGI Page MGI
Description: Predicted to enable vitamin E binding activity. Predicted to be involved in protein stabilization; protein transport within extracellular region; and vitamin transport. Predicted to act upstream of or within protein transport. Predicted to be located in extracellular space. Predicted to be active in cytoplasm. Is expressed in several structures, including gut; liver; and metanephros. Orthologous to human AFM (afamin).
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: A; Alf; alpha albumin; alpha-Alb; alpha-albumin; MGC118711
RGD Orthologs
Human
Rat
Bonobo
Dog
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: GRCm39 - Mouse Genome Assembly GRCm39
Position:
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39590,666,808 - 90,701,403 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl590,666,791 - 90,701,402 (+)EnsemblGRCm39 Ensembl
GRCm38590,518,949 - 90,553,544 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl590,518,932 - 90,553,543 (+)EnsemblGRCm38mm10GRCm38
MGSCv37590,947,975 - 90,982,570 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36591,594,163 - 91,641,425 (+)NCBIMGSCv36mm8
Celera588,680,306 - 88,704,975 (+)NCBICelera
Cytogenetic Map5E1NCBI
cM Map544.78NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Function

Phenotype Annotations     Click to see Annotation Detail View

Mammalian Phenotype
References

References - curated
# Reference Title Reference Citation
1. Alpha-fetoprotein, the major fetal serum protein, is not essential for embryonic development but is required for female fertility. Gabant P, etal., Proc Natl Acad Sci U S A 2002 Oct 1;99(20):12865-70. Epub 2002 Sep 24.
2. Electronic Transfer of Homolog Data MGD and Homologene mouse data transfer
3. MGDs mouse GO annotations MGD data from the GO Consortium
4. Mouse MP Annotation Import Pipeline RGD automated import pipeline
5. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
6. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:10349636   PMID:11042159   PMID:11076861   PMID:11217851   PMID:12466851   PMID:12477932   PMID:15489334   PMID:16141072   PMID:16141073   PMID:16944957   PMID:17330941   PMID:19733224  
PMID:20979532   PMID:21267068   PMID:21677750   PMID:21873635   PMID:22749887  


Genomics

Comparative Map Data
Afm
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39590,666,808 - 90,701,403 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl590,666,791 - 90,701,402 (+)EnsemblGRCm39 Ensembl
GRCm38590,518,949 - 90,553,544 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl590,518,932 - 90,553,543 (+)EnsemblGRCm38mm10GRCm38
MGSCv37590,947,975 - 90,982,570 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36591,594,163 - 91,641,425 (+)NCBIMGSCv36mm8
Celera588,680,306 - 88,704,975 (+)NCBICelera
Cytogenetic Map5E1NCBI
cM Map544.78NCBI
AFM
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38473,481,745 - 73,504,001 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl473,481,745 - 73,504,001 (+)EnsemblGRCh38hg38GRCh38
GRCh37474,347,462 - 74,369,718 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36474,566,326 - 74,588,582 (+)NCBINCBI36Build 36hg18NCBI36
Build 34474,712,496 - 74,734,753NCBI
Celera471,707,194 - 71,729,436 (+)NCBICelera
Cytogenetic Map4q13.3NCBI
HuRef470,158,855 - 70,181,099 (+)NCBIHuRef
CHM1_1474,383,462 - 74,405,708 (+)NCBICHM1_1
T2T-CHM13v2.0476,825,372 - 76,847,610 (+)NCBIT2T-CHM13v2.0
Afm
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81417,815,194 - 17,848,042 (-)NCBIGRCr8
mRatBN7.21417,531,022 - 17,563,868 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1417,531,024 - 17,563,870 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1417,525,337 - 17,550,140 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01418,844,268 - 18,869,067 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01417,536,413 - 17,568,193 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01419,078,678 - 19,132,212 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1419,078,680 - 19,132,208 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01419,035,336 - 19,039,510 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Rnor_5.01418,988,809 - 19,008,149 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41419,049,664 - 19,082,977 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11419,049,663 - 19,082,977 (-)NCBI
Celera1416,899,392 - 16,930,240 (-)NCBICelera
Cytogenetic Map14p22NCBI
AFM
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2356,559,516 - 56,583,201 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1456,748,574 - 56,771,840 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0450,691,556 - 50,714,140 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1456,523,712 - 56,545,919 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl456,519,389 - 56,545,974 (-)Ensemblpanpan1.1panPan2
AFM
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11362,212,230 - 62,235,136 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1362,053,814 - 62,294,709 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1361,881,887 - 61,904,769 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.01363,021,767 - 63,044,655 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl1363,021,855 - 63,044,642 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.11362,633,366 - 62,656,263 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01362,126,432 - 62,149,372 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01363,262,556 - 63,285,453 (+)NCBIUU_Cfam_GSD_1.0
AFM
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl869,706,896 - 69,728,255 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1869,706,823 - 69,728,269 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2873,806,942 - 73,828,360 (+)NCBISscrofa10.2Sscrofa10.2susScr3
AFM
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1721,950,222 - 21,972,612 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl721,950,705 - 21,972,739 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_023666084824,453 - 846,386 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Afm
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462473533,945,107 - 34,015,900 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Afm
25 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:403
Count of miRNA genes:334
Interacting mature miRNAs:360
Transcripts:ENSMUST00000113179, ENSMUST00000128740
Prediction methods:Miranda, Rnahybrid
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


QTLs in Region (GRCm39)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
11341716Rvfs3_mRift Valley fever susceptibility 3 (mouse)526441234138455402Mouse
4140990Lgq6_mlate growth QTL 6 (mouse)Not determined32133234100777931Mouse
4141219W10q16_mweight 10 weeks QTL 16 (mouse)Not determined32133234100777931Mouse
1301524Lmb2_mlupus in MRL and B6 F2 cross (mouse)Not determined537581488112465722Mouse
11041665Lmr24_mleishmaniasis resistance 24 (mouse)552694462107321041Mouse
11041899Lmr24a_mleishmaniasis resistance 24a (mouse)552694462107321041Mouse
4142064Tmc1m4_mTmc1 modifier 4 (mouse)Not determined554500177127001072Mouse
1301243Bmd2_mbone mineral density 2 (mouse)Not determined555388334100455525Mouse
4142317Rgcs1_mretinal ganglion cell susceptible 1 (mouse)Not determined55388334108762627Mouse
10044005Ahl7_mage related hearing loss 7 (mouse)Not determined55833050292330641Mouse
11040591Lmr3c_mleishmaniasis resistance 3c (mouse)55960280193602980Mouse
11040592Lmr3d_mleishmaniasis resistance 3d (mouse)55960280193602980Mouse
11040589Lmr3a_mleishmaniasis resistance 3a (mouse)55960280193602980Mouse
11040590Lmr3b_mleishmaniasis resistance 3b (mouse)55960280193602980Mouse
1301843Listr1_mlisteriosis resistance 1 (mouse)Not determined56024608194246203Mouse
13464247Ahl14_mage related hearing loss, early onset 14 (mouse)56040306294403160Mouse
11252124Modvl6_mmodifier of vacuolated lens 6 (mouse)56265056896650688Mouse
4142428Modvl1_mmodifier of vacuolated lens 1 (mouse)Not determined6265056896650688Mouse
1301010ahl2_mage related hearing loss 2 (mouse)Not determined56265056896650688Mouse
13464250Ahl15_mage related hearing loss, early onset 15 (mouse)56265056896650688Mouse
10045972Tir5_mtrypanosome infection response 5 (mouse)Not determined563705442104387065Mouse
11049560Lmr24d_mleishmaniasis resistance 24d (mouse)56437487798374996Mouse
12904739M2fscn2_mmodifier 2 of FSCN2 (mouse)566529661100529661Mouse
12904740M1fscn2_mmodifier 1 of Fscn2 (mouse)566529661100529661Mouse
26884395Humsd2_mhumerus midshaft diameter 2, 10 week (mouse)570057343132528839Mouse
10043993Hbnr10_mHeligmosomoides bakeri nematode resistance 10 (mouse)Not determined572418876106419011Mouse
27226719Tibw6_mtibia width 6, proximal, 16 week (mouse)572857343139985755Mouse
25314315Mlh1fc4_mMLH1 foci count 4 (mouse)574460661132528839Mouse
13506928Recrq8_mrecombination rate in male meiosis QTL 8 (mouse)574460661132528839Mouse
4141124Dshv2_mdorsal hippocampal volume 2 (mouse)Not determined57531534898019803Mouse
1357431Cia27_mcollagen induced arthritis 27 (mouse)Not determined575315348120018629Mouse
4141438Skmw13_mskeletal muscle weight 13 (mouse)Not determined576190263110190479Mouse
4141505Chlq14_mcirculating hormone level QTL 14 (mouse)Not determined576280786110280917Mouse
1300986Hdlq2_mHDL QTL 2 (mouse)Not determined576280786110280917Mouse
1301691Cdcs10_mcytokine deficiency colitis susceptibility 10 (mouse)Not determined576280786110280917Mouse
1301829Thyls2_mthymic lymphoma susceptibility 2 (mouse)Not determined576445064110445225Mouse
1301713Dbsty2_mdiabesity 2 (mouse)Not determined576445064110445225Mouse
13464249Ahl16_mage related hearing loss, early onset 16 (mouse)576445064110445225Mouse
1300931Cocrb6_mcocaine related behavior 6 (mouse)Not determined576445064110445225Mouse
12910784Pwgrq15_mpost-weaning growth rate QTL 15 (mouse)57717582397658215Mouse
12910816Ogrq2_moverall growth rate QTL 2 (mouse)57717582397658215Mouse
10401246Bglu13_mblood glucose level 13 (mouse)Not determined579539640113539786Mouse
10755524Mono1_mmonocyte differential 1 (mouse)580849259114849259Mouse
1301419Cypr3_mcytokine production 3 (mouse)Not determined581019649115019803Mouse
10401245Bglu18_mblood glucose level 18 (mouse)Not determined582838468116838597Mouse
13464242Ahl17_mage related hearing loss, early onset 17 (mouse)582838468116838597Mouse
10043958Chldq12_mcholesterol and HDL QTL 12 (mouse)Not determined587386871121387065Mouse
1301126Bwem1_mbody weight day 30 males 1 (mouse)Not determined587386871121387065Mouse
13464241Ahl18_mage related hearing loss, early onset 18 (mouse)587386871121387065Mouse
1300801Drb2_mdopamine receptor binding 2 (mouse)Not determined587386871121387065Mouse
1301399Cpfd3_mcerebellum pattern fissures (mouse)Not determined587386871121387065Mouse
1357725Eae39_mexperimental allergic encephalomyelitis 39 (mouse)Not determined589418876118864028Mouse
1300968Skts4_mskin tumor susceptibility 4 (mouse)Not determined589418876124238239Mouse
1301362Prnr1_mprion resistance 1 (mouse)Not determined589418876146787935Mouse
11049562Lmr24f_mleishmaniasis resistance 24f (mouse)590320962124321041Mouse
1301457Cfsw2_mcystic fibrosis survival to weaning 2 (mouse)Not determined590561006124561151Mouse
1300993Hycdc_mhypercapnic duty cycle (mouse)Not determined590561006124561151Mouse

Markers in Region
Afm  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm38590,548,828 - 90,550,274UniSTSGRCm38
MGSCv37590,977,854 - 90,979,300UniSTSGRCm37
Celera588,700,256 - 88,701,702UniSTS
Cytogenetic Map5E1UniSTS
cM Map5 UniSTS


Expression


Sequence


Reference Sequences
RefSeq Acc Id: ENSMUST00000113179   ⟹   ENSMUSP00000108804
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl590,666,791 - 90,701,402 (+)Ensembl
GRCm38.p6 Ensembl590,518,932 - 90,553,543 (+)Ensembl
RefSeq Acc Id: ENSMUST00000128740   ⟹   ENSMUSP00000117180
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl590,666,808 - 90,696,916 (+)Ensembl
GRCm38.p6 Ensembl590,518,949 - 90,549,057 (+)Ensembl
RefSeq Acc Id: NM_145146   ⟹   NP_660128
RefSeq Status: VALIDATED
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39590,666,808 - 90,701,403 (+)NCBI
GRCm38590,518,949 - 90,553,544 (+)ENTREZGENE
MGSCv37590,947,975 - 90,982,570 (+)RGD
Celera588,680,306 - 88,704,975 (+)RGD
cM Map5 ENTREZGENE
Sequence:
Reference Protein Sequences
RefSeq Acc Id: NP_660128   ⟸   NM_145146
- Peptide Label: precursor
- UniProtKB: Q497E6 (UniProtKB/Swiss-Prot),   Q3UNV0 (UniProtKB/Swiss-Prot),   Q8R0J9 (UniProtKB/Swiss-Prot),   O89020 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSMUSP00000108804   ⟸   ENSMUST00000113179
RefSeq Acc Id: ENSMUSP00000117180   ⟸   ENSMUST00000128740
Protein Domains
Albumin

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-O89020-F1-model_v2 AlphaFold O89020 1-608 view protein structure

Promoters
RGD ID:6887114
Promoter ID:EPDNEW_M7008
Type:single initiation site
Name:Afm_1
Description:Mus musculus afamin , mRNA.
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm38590,518,949 - 90,519,009EPDNEW
RGD ID:6837007
Promoter ID:MM_KWN:42839
Type:Non-CpG
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:Kidney,   Liver
Transcripts:OTTMUST00000083498,   OTTMUST00000083555
Position:
Mouse AssemblyChrPosition (strand)Source
MGSCv36590,947,706 - 90,948,206 (+)MPROMDB

Additional Information

Database Acc Id Source(s)
AGR Gene MGI:2429409 AgrOrtholog
Ensembl Genes ENSMUSG00000029369 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSMUST00000113179 ENTREZGENE
  ENSMUST00000113179.9 UniProtKB/Swiss-Prot
  ENSMUST00000128740.2 UniProtKB/Swiss-Prot
Gene3D-CATH 1.10.246.10 UniProtKB/Swiss-Prot
InterPro ALB/AFP/VDB UniProtKB/Swiss-Prot
  Serum_albumin-like UniProtKB/Swiss-Prot
  Serum_albumin/AFP/Afamin UniProtKB/Swiss-Prot
  Serum_albumin_CS UniProtKB/Swiss-Prot
  Serum_albumin_N UniProtKB/Swiss-Prot
KEGG Report mmu:280662 UniProtKB/Swiss-Prot
MGD MGI:2429409 ENTREZGENE
NCBI Gene 280662 ENTREZGENE
PANTHER AFAMIN UniProtKB/Swiss-Prot
  PTHR11385 UniProtKB/Swiss-Prot
Pfam Serum_albumin UniProtKB/Swiss-Prot
PhenoGen Afm PhenoGen
PIRSF Serum_albumin_subgroup UniProtKB/Swiss-Prot
PRINTS AFETOPROTEIN UniProtKB/Swiss-Prot
  SERUMALBUMIN UniProtKB/Swiss-Prot
PROSITE ALBUMIN_1 UniProtKB/Swiss-Prot
  ALBUMIN_2 UniProtKB/Swiss-Prot
SMART ALBUMIN UniProtKB/Swiss-Prot
Superfamily-SCOP SSF48552 UniProtKB/Swiss-Prot
UniProt AFAM_MOUSE UniProtKB/Swiss-Prot, ENTREZGENE
  Q3UNV0 ENTREZGENE
  Q497E6 ENTREZGENE
  Q8R0J9 ENTREZGENE
UniProt Secondary Q3UNV0 UniProtKB/Swiss-Prot
  Q497E6 UniProtKB/Swiss-Prot
  Q8R0J9 UniProtKB/Swiss-Prot