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FAM19A3 Gene

protein-coding   GIFtS: 44
GCID: GC01P113263

Family With Sequence Similarity 19 (Chemokine (C-C Motif)-Like),...

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(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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Aliases
Family With Sequence Similarity 19 (Chemokine (C-C Motif)-Like), Member
A31 2
Chemokine-Like Protein TAFA-32 3
TAFA32 3
TAFA-32
Protein FAM19A32

External Ids:    HGNC: 215901   Entrez Gene: 2844672   Ensembl: ENSG000001845997   UniProtKB: Q7Z5A83   

Export aliases for FAM19A3 gene to outside databases

Previous GC identifers: GC01P112976 GC01P113064 GC01P111122


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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Entrez Gene summary for FAM19A3 Gene:
This gene is a member of the TAFA family which is composed of five highly homologous genes that encode small
secreted proteins. These proteins contain conserved cysteine residues at fixed positions, and are distantly
related to MIP-1alpha, a member of the CC-chemokine family. The TAFA proteins are predominantly expressed in
specific regions of the brain, and are postulated to function as brain-specific chemokines or neurokines, that
act as regulators of immune and nervous cells. Alternatively spliced transcript variants encoding multiple
isoforms have been observed for this gene. (provided by RefSeq, Nov 2011)

GeneCards Summary for FAM19A3 Gene:
FAM19A3 (family with sequence similarity 19 (chemokine (C-C motif)-like), member A3) is a protein-coding gene. An important paralog of this gene is FAM19A4.




(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence at NCBI GenBank:
NC_000001.10  NT_032977.10  NC_018912.2  
Regulatory elements:
   Regulatory transcription factor binding sites in the FAM19A3 gene promoter:
         GR   Ik-2   AP-1   p53   GR-beta   GR-alpha   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidFAM19A3 promoter sequence
   Search Chromatin IP Primers for FAM19A3

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat FAM19A3


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 1p13.2   Ensembl cytogenetic band:  1p13.2   HGNC cytogenetic band: 1p13.2

FAM19A3 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
FAM19A3 gene location

GeneLoc information about chromosome 1         GeneLoc Exon Structure

GeneLoc location for GC01P113263:  view genomic region     (about GC identifiers)

Start:
113,263,041 bp from pter      End:
113,269,857 bp from pter
Size:
6,817 bases      Orientation:
plus strand

(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, Cloud-Clone Corp., and/or eBioscience,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., and/or eBioscience, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, Cloud-Clone Corp, and/or others.)
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UniProtKB/Swiss-Prot: F19A3_HUMAN, Q7Z5A8 (See protein sequence)
Recommended Name: Protein FAM19A3 precursor  
Size: 133 amino acids; 14776 Da
Secondary accessions: B7ZLU0 Q2M1P9 Q7Z5A6
Alternative splicing: 2 isoforms:  Q7Z5A8-1   Q7Z5A8-2   

Explore the universe of human proteins at neXtProt for FAM19A3: NX_Q7Z5A8

Explore proteomics data for FAM19A3 at MOPED


See FAM19A3 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

REFSEQ proteins (2 alternative transcripts): 
NP_001004440.1  NP_877436.1  

ENSEMBL proteins: 
 ENSP00000358644   ENSP00000355042  

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(According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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1 InterPro protein domain:
 IPR020350 Chemokine-like_FAM19A2

Graphical View of Domain Structure for InterPro Entry Q7Z5A8

ProtoNet protein and cluster: Q7Z5A8

UniProtKB/Swiss-Prot: F19A3_HUMAN, Q7Z5A8
Similarity: Belongs to the FAM19/TAFA family


Find genes that share domains with FAM19A3           About GenesLikeMe


(According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, genOway,
transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, Vector BioLabs and/or Addgene, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Flow cytometry from eBioscience, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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Animal Models:
   inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for FAM19A3
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hsa-mir-122-5p (MIRT023353)

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hsa-miR-215 hsa-miR-192
SwitchGear 3'UTR luciferase reporter plasmidFAM19A3 3' UTR sequence
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(According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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Subcellular locations from UniProtKB/Swiss-Prot
F19A3_HUMAN, Q7Z5A8: Secreted
Subcellular locations from COMPARTMENTS: 

CompartmentConfidence
extracellular5
nucleus1

Gene Ontology (GO): 1 cellular component term:    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0005576extracellular region IEA--

Find genes that share ontologies with FAM19A3           About GenesLikeMe


(SuperPaths according to PathCards, Pathways according to R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to QIAGEN, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene).
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    Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for FAM19A3
Interactions:

    Search GeneGlobe Interaction Network for FAM19A3

(Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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Browse Small Molecules at EMD Millipore
   Browse drugs & compounds from Enzo Life Sciences
  Browse compounds at ApexBio 

Browse Tocris compounds for FAM19A3 (F19A3)



(Secondary structures according to fRNAdb,
GenBank/EMBL/DDBJ Accessions according to
Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
RefSeq according to Entrez Gene,
DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, and/or Addgene, Primers from OriGene, and/or QIAGEN, Flow cytometry from eBioscience )
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REFSEQ mRNAs for FAM19A3 gene (2 alternative transcripts): 
NM_001004440.1  NM_182759.2  

Unigene Cluster for FAM19A3:

Family with sequence similarity 19 (chemokine (C-C motif)-like), member A3
Hs.439116  [show with all ESTs]
Unigene Representative Sequence: AY325119
2 Ensembl transcripts including schematic representations, and UCSC links where relevant:
ENST00000369630(uc001ecu.3 uc001ecv.3 uc010owk.2 uc010owl.2)
ENST00000361886
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hsa-miR-215 hsa-miR-192
SwitchGear 3'UTR luciferase reporter plasmidFAM19A3 3' UTR sequence
Inhib. RNA
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Additional mRNA sequence: 

AY325116.1 AY325119.1 BC112268.1 BC117479.1 BC143949.1 BC144042.1 BC144043.1 

2 DOTS entries:

DT.101980155  DT.97823929 

12 AceView cDNA sequences:

NM_182759 BE731725 BM694096 BQ638101 NM_001004440 AI873311 AY325119 AY325116 
AI141820 BU732283 BU632147 BM692070 

GeneLoc Exon Structure

2 Alternative Splicing Database (ASD) splice patterns (SP) for FAM19A3    About this scheme

ExUns: 1 ^ 2 ^ 3 ^ 4a · 4b ^ 5
SP1:                                    
SP2:                    -               


ECgene alternative splicing isoforms for FAM19A3

(RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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FAM19A3 expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>2/3
CGAP TAG: TTGCAGGAAA
FAM19A3 Expression
About this image


FAM19A3 expression in embryonic tissues and stem cells    About this table
Data from LifeMap, the Embryonic Development and Stem Cells Database
 selected tissues (see all 3) fully expand
 
 Neurons
         Type1 Off Cone Bipolar Cells Inner Nuclear Layer
 
 Blood (Hematopoietic System)
         Natural Killer Cells Peripheral Blood
 
 Eye (Sensory Organs)
         Type1 Off Cone Bipolar Cells Inner Nuclear Layer
FAM19A3 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

FAM19A3 Protein Expression

SOURCE GeneReport for Unigene cluster: Hs.439116

UniProtKB/Swiss-Prot: F19A3_HUMAN, Q7Z5A8
Tissue specificity: Brain-specific

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In Situ
Assay Products:
 

 
Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for FAM19A3

(Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
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This gene was present in the common ancestor of chordates.

Orthologs for FAM19A3 gene from Selected species (see all 11)    About this table
Organism Taxonomic
classification
Gene Description Human
Similarity
Orthology
Type
Details
mouse
(Mus musculus)
Mammalia Fam19a31 , 5 family with sequence similarity 19, member A31, 5 87.28(n)1
87.02(a)1
  3 (45.84 cM)5
3297311  NM_183224.31  NP_899047.11 
 1047674065 
chicken
(Gallus gallus)
Aves FAM19A31 family with sequence similarity 19 (chemokine (C-C more 76.95(n)
82.24(a)
  419874  XM_004934994.1  XP_004935051.1 
lizard
(Anolis carolinensis)
Reptilia --
Uncharacterized protein
26(a)
many ↔ many
GL343382.1(408434-447528)
tropical clawed frog
(Xenopus tropicalis)
Amphibia fam19a31 family with sequence similarity 19 (chemokine (C-C more 66.98(n)
78.5(a)
  100380203  XM_002932118.1  XP_002932164.1 
zebrafish
(Danio rerio)
Actinopterygii si:ch211-254n4.31 si:ch211-254n4.3 72.98(n)
85.26(a)
  100003386  NM_001130795.1  NP_001124267.1 


ENSEMBL Gene Tree for FAM19A3 (if available)
TreeFam Gene Tree for FAM19A3 (if available)

(Paralogs according to 1HomoloGene,
2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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Paralogs for FAM19A3 gene
FAM19A42  FAM19A12  FAM19A22  FAM19A52  
4 SIMAP similar genes for FAM19A3 using alignment to 1 protein entry:     F19A3_HUMAN:
FAM19A4    FAM19A2    FAM19A1    FAM19A5

Find genes that share paralogs with FAM19A3           About GenesLikeMe



(SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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Selected SNPs for FAM19A3 (see all 216)    About this table                                 

Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance
Chr 1 posSequence#AA
Chg
TypeMore#Allele
freq
PopTotal
sample
More
----------
rs1464734891,2
--113261217(+) AACATG/TCCACT 2 -- us2k10--------
rs1807297331,2
--113261373(+) TTCAGC/GGTTTT 2 -- us2k10--------
rs74155971,2
C,H--113261455(+) TCTCCC/TTTCCT 2 -- us2k1 tfbs3 trp32Minor allele frequency- T:0.00NS NA 226
rs1848614831,2
--113261976(+) AGGGGA/GGTTTG 2 -- us2k10--------
rs1144638151,2
F--113262064(+) CAGCCT/ACACTA 2 -- us2k11Minor allele frequency- A:0.08WA 118
rs1148934571,2
C,F--113262065(+) AGCCTC/AACTAA 2 -- us2k11Minor allele frequency- A:0.08WA 118
rs1896714111,2
--113262141(+) ACACAC/TCCCAG 2 -- us2k10--------
rs1432633881,2
--113262193(+) ATGCCA/CGGGAT 2 -- us2k10--------
rs779932801,2
C,F--113262272(+) CCTAGG/AAGAGA 2 -- us2k11Minor allele frequency- A:0.13WA 118
rs1133543811,2
C,F--113262411(+) GAAAGG/AGGCAC 2 -- us2k11Minor allele frequency- A:0.50CSA 2

HapMap Linkage Disequilibrium report for FAM19A3 (113263041 - 113269857 bp)

Structural Variations
     Database of Genomic Variants (DGV) 4 variations for FAM19A3:    About this table    
Variant IDTypeSubtypePubMed ID
dgv332n71CNV Loss21882294
esv27598CNV Loss19812545
nsv818378CNV Gain17921354
essv21692CNV CNV17122850

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(in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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Find genes that share disorders with FAM19A3           About GenesLikeMe

Genetic Association Database (GAD): FAM19A3

Export disorders for FAM19A3 gene to outside databases

(in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
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PubMed articles for FAM19A3 gene integrated from 10 sources:
(articles sorted by number of sources associating them with FAM19A3)
    Utopia: connect your pdf to the dynamic
world of online information

  1. TAFA: a novel secreted family with conserved cysteine residues and restricted expression in the brain. (PubMed id 15028294)1, 2, 3 Tom Tang Y....Rupp F. (Genomics 2004)
  2. The DNA sequence and biological annotation of human chromosome 1. (PubMed id 16710414)1, 2 Gregory S.G.... Bentley D.R. (Nature 2006)
  3. Genome-wide association scan of quantitative traits for attention deficit hyperactivity disorder identifies novel associations and confirms candidate gene associations. (PubMed id 18821565)4 Lasky-Su J....Faraone S.V. (Am. J. Med. Genet. B Neuropsychiatr. Genet. 2008)
  4. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)2 Gerhard D.S.... Malek J. (Genome Res. 2004)
  5. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PubMed id 12477932)1 Strausberg R.L....Marra M.A. (Proc. Natl. Acad. Sci. U.S.A. 2002)
  6. Expressed sequence tag analysis of human retina for the NEIBank project: retbindin, an abundant, novel retinal cDNA and alternative splicing of other retina-preferred gene transcripts. (PubMed id 12107411)1 Wistow G.... Peterson K. (Mol. Vis. 2002)

(in PubMed, OMIM, and NCBI Bookshelf)
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 ANDOR
Aliases
Free Text  

  Query String
PubMed
OMIM
NCBI Bookshelf
  (Note: In FireFox, select the above section and copy using Ctrl-C)

(According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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Entrez Gene: 284467 HGNC: 21590 AceView: TAFA3 Ensembl:ENSG00000184599 euGenes: HUgn284467
ECgene: FAM19A3 H-InvDB: FAM19A3

(According to HUGE)
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  --

(According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
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NameDescription
PharmGKB entry for FAM19A3 Pharmacogenomics, SNPs, Pathways

(Patent information from GeneIP,
Licensable technologies from WIS Yeda, Salk, Tufts,
IP news from LifeMap Sciences, Inc.)
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Patent Information for FAM19A3 gene:
Search GeneIP for patents involving FAM19A3

GeneCards and IP:
Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



(Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, LSBio, eBioscience, and/or others, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Addgene, Cell lines from GenScript, and ESI BIO, Flow cytometery from eBioscience, PCR Arrays from QIAGEN, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, Enzo Life Sciences, and/or ApexBio, In Situ Hybridization Assays from
Advanced Cell Diagnostics, Animal models from inGenious Targeting Laboratory, genOway)
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 inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for FAM19A3
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 Search Addgene for plasmids for FAM19A3
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GeneCards Homepage - Last full update: 7 May 2014 - Incrementals: 9 May 2014 , 2 Jun 2014 , 26 Jun 2014 , 30 Jun 2014 , 21 Aug 2014 , 8 Sep 2014

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