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Category Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21

GIFtS
-

FAM53A Gene

protein-coding GIFtS: 39
GCID: GC04M001610

family with sequence similarity 53, member A

Search for FAM53A
in

MalaCards

our new
Human Malady Compendium

(According to ¹HGNC, ²Entrez Gene,
³UniProtKB/Swiss-Prot, ⁴UniProtKB/TrEMBL, ⁵OMIM, ⁶GeneLoc, ⁷Ensembl, ⁸DME, ⁹miRBase, and/or ¹⁰fRNAdb)
About This Section

Aliases
Family With Sequence Similarity 53, Member A¹ ²
DNTNP¹ ²
Dorsal Neural-Tube Nuclear Protein² ³
Protein FAM53A²

External Ids:	HGNC: 31860¹	Entrez Gene: 152877²	Ensembl: ENSG00000174137⁷	UniProtKB: Q6NSI3³

Export aliases for FAM53A gene to outside databases

(According to Entrez Gene, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section

UniProtKB/Swiss-Prot: FA53A_HUMAN, Q6NSI3

Function: May play an important role in neural development; the dorsomedial roof of the third ventricle (By similarity)

(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 69), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section

RefSeq DNA sequence:

NC_000004.11 NC_018915.1 NT_006051.18

Regulatory elements:

SABiosciences Regulatory transcription factor binding sites in the FAM53A gene promoter:
STAT5B RP58 LHX3b/Lhx3b Nkx2-2 CUTL1 LCR-F1 GATA-1 SRY FOXO4 LHX3a/Lhx3a
Other transcription factors

SwitchGear Promoter luciferase reporter plasmid: FAM53A promoter sequence

Search SABiosciences Chromatin IP Primers for FAM53A

Epigenetics:

QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat FAM53A

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

Entrez Gene cytogenetic band: 4p16.3 Ensembl cytogenetic band: 4p16.3 HGNC cytogenetic band: 4p16.3

FAM53A Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
FAM53A gene location

GeneLoc information about chromosome 4 GeneLoc Exon Structure

GeneLoc location for GC04M001610: view genomic region (about GC identifiers)

Start:	1,619,642 bp from pter	End:	1,686,029 bp from pter
Size:	66,388 bases	Orientation:	minus strand

(According to ¹UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to ²PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE MOPED and PaxDb, 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, and/or Uscn,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Uscn, Ontologies according to Gene Ontology Consortium 01 Mar 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, and/or Uscn)
About This Section

UniProtKB/Swiss-Prot: FA53A_HUMAN, Q6NSI3 (See protein sequence)

Recommended Name: Protein FAM53A

Size: 398 amino acids; 42585 Da

Subcellular location: Nucleus (By similarity). Note=Subnuclear distribution (By similarity)

Secondary accessions: Q6ZUL5

Explore the universe of human proteins at neXtProt for FAM53A: NX_Q6NSI3

Post-translational modifications:

View modification sites using PhosphoSitePlus²

View neXtProt modification sites for NX_Q6NSI3

FAM53A Protein expression data from MOPED and PaxDb: About this image

REFSEQ proteins (2 alternative transcripts):

NP_001013644.1 NP_001167541.1

ENSEMBL proteins:

ENSP00000423987 ENSP00000419044 ENSP00000418243 ENSP00000426260 ENSP00000417615

ENSP00000310057

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Gene Ontology (GO): 1 cellular component term (GO ID links to tree view): About this table

GO ID	Qualified GO term	Evidence	PubMed IDs
GO:0005634	nucleus	IEA	--

FAM53A for ontologies About GeneDecksing

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(According to InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
About This Section

ProtoNet protein and cluster: Q6NSI3

UniProtKB/Swiss-Prot: FA53A_HUMAN, Q6NSI3

Similarity: Belongs to the FAM53 family

(According to ¹UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or ²DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory,
bound targets from SABiosciences, miRNA Gene Targets from miRTarBase, shRNA from OriGene, Sirion Biotech, RNAi from EMD Millipore, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, Gene Editing from DNA2.0, Sirion Biotech, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, LifeMap BioReagents, Sirion Biotech, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene.)
About This Section

Molecular Function:

UniProtKB/Swiss-Prot Summary: FA53A_HUMAN, Q6NSI3

Function: May play an important role in neural development; the dorsomedial roof of the third ventricle (By similarity)

Animal Models:

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(Pathways according to EMD Millipore, R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to SABiosciences, 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 Mar 2013 via Entrez Gene).
About This Section

Interactions:

Search SABiosciences Gene Network Central^TM Interacting Genes and Proteins Networks for FAM53A

(Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB, with drugs/clinical trials/news search links to CenterWatch)
About This Section

Browse Small Molecules at EMD Millipore

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Search CenterWatch for drugs/clinical trials and news about FAM53A / FA53A

(Secondary structures according to fRNAdb,
GenBank/EMBL/DDBJ Accessions according to
Unigene (Build 235 Homo sapiens; Mar 10 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,
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Tagged/untagged cDNA clones from OriGene, SwitchGear Genomics, GenScript, DNA2.0, Vector BioLabs, Primers from OriGene, SABiosciences, and/or QIAGEN )
About This Section

REFSEQ mRNAs for FAM53A gene (2 alternative transcripts):

NM_001013622.3 NM_001174070.1

Unigene Cluster for FAM53A:

Family with sequence similarity 53, member A

Hs.143314 [show with all ESTs]

Unigene Representative Sequence: BC042071

7 Ensembl transcripts including schematic representations, and UCSC links where relevant:

ENST00000489029 ENST00000489363(uc010ibw.3) ENST00000461064 ENST00000472884

ENST00000467215 ENST00000463238 ENST00000308132(uc021xkk.1 uc021xkl.1)

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Additional cDNA sequence:

AK125566.1 BC042071.1 BC070112.1

5 DOTS entries:

DT.101954888 DT.95291564 DT.97775987 DT.100008454 DT.320784

24/243 AceView cDNA sequences (see all 243):

AU098556 AA744535 CR611828 BM676712 AU102851 BQ230125 AI924261 CR625037

BU195724 CR612255 CB305349 CR617547 BX353544 AW264286 AW768672 AA705380

NM_006527 BU616659 CD368390 CB529003 BE549971 Z71188 CR607040 BM679830

GeneLoc Exon Structure

(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™, plus additional links to Genevestigator, and/or SOURCE, and/or BioGPS, and/or UniProtKB,
PCR Arrays from SABiosciences, Primers from OriGene, SABiosciences, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
About This Section

FAM53A expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS
CGAP TAG: AATCTGCAAA

About this image

FAM53A expression in embryonic tissues and stem cells
Expression by the Database of Embryonic development, Stem cell research, and Regenerative medicine About this table

2 LifeMap In Vivo Development Anatomical Compartments/Cells

Tissue

Anatomical Compartment

Cell

Category (developmental path)

Reproductive System

Mesonephros

Mesonephric cells

Reproductive System

Reproductive System

Mesonephros

Reproductive System

Expression:

Positive

Negative

Selective marker

Experimental details:

Curated

Microarrays

In-situ hybridization

See FAM53A Protein Expression from SPIRE MOPED and PaxDB
Genevestigator expression for FAM53A

SOURCE GeneReport for Unigene cluster: Hs.143314

SABiosciences Custom PCR Arrays for FAM53A

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In Situ
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(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)
About This Section

This gene was present in the common ancestor of chordates.

Orthologs for FAM53A gene from 1/6 species (see all 6) About this table

Organism	Taxonomic classification	Gene	Description	Human Similarity	Orthology Type	Details
chicken (Gallus gallus)	Aves	FAM53A¹	family with sequence similarity 53, member A	60.76(n) 56.96(a)		378905 NM_204388.2 NP_989719.2

ENSEMBL Gene Tree for FAM53A (if available)
TreeFam Gene Tree for FAM53A (if available)

(Paralogs according to ¹HomoloGene,
²Ensembl, and ³SIMAP, Pseudogenes according to ⁴Pseudogene.org Build 68)
About This Section

Paralogs for FAM53A gene

FAM53C² FAM53B²

FAM53A for paralogs About GeneDecksing

(SNPs/Variants according to the ¹NCBI SNP Database, ²Ensembl, ³PupaSUITE, UniProtKB, 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) and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers from QIAGEN, Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
About This Section

SNP ID	Valid	Clinical significance	Chr 4 pos	Sequence	#	AA Chg	Type	More	#	Allele freq	Pop	Total sample	More
Genomic Data					Transcription Related Data				Allele Frequencies
				--	--	--		--	--
rs111501440^1,2	C,F	--	1615323(+)	`GAGCCC/ACCAGC`	1	--	int¹		3		NA WA	6
rs34096982^1,2	C,F	--	1615663(+)	`GCCACG/AGCCCG`	1	--	int¹		3		NA WA	6
rs1562363^1,2	C,H	--	1641256(-)	`CTGTCG/ATTGGC`	2	--	ds500¹		14		MN NA WA CSA EA	560
rs139996770^1,2		--	1641280(+)	`CCCGGA/GCCAGC`	2	--	ds500¹		0	--	--	--	--
rs1562362^1,2	C,H	--	1641313(-)	`CCTCCG/ATTGGG`	2	--	ds500¹		13		NA WA CSA EA	376
rs73795190^1,2	C	--	1641367(+)	`CCCAAA/CCTCCC`	2	--	ds500¹		3		WA EA	240
rs186171988^1,2		--	1641514(+)	`GATCTA/GTGGCC`	2	--	ds500¹		0	--	--	--	--
rs6829285^1,2	C,F,A,H	--	1641578(+)	`TATTGA/GGAAAA`	2	--	ds500¹		23		NS EA NA WA	2352
rs77743978^1,2	C,F	--	1641622(+)	`TCTTTT/CGCTAT`	2	--	ut3¹		1		NA	120
rs2121457^1,2	C	--	1641695(-)	`CCAGAC/AAAGGC`	2	--	ut3¹		4		NA WA EA	360

HapMap Linkage Disequilibrium report for FAM53A (1619642 - 1686029 bp)
Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
Database of Genomic Variants (DGV): 4 variations for FAM53A
4 CNVs: 30192 68617 3476 30191

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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.)
About This Section

(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)
About This Section

PubMed articles for FAM53A gene integrated from 9 sources:
(articles sorted by number of sources associating them with FAM53A)

Utopia: connect your pdf to the dynamic
world of online information

The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)^{1, 2} Gerhard D.S....Malek J. (2004)
Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)^{1, 2} Ota T.... Sugano S. (2004)
Interactions of pathological hallmark proteins: tubul in polymerization promoting protein/p25, beta-amyloid, and alpha-synuclein. (PubMed id 21832049)¹ OlA!h J....OvA!di J. (2011)
Isolation of DNTNP, which encodes a potential nuclear protein that is expressed in the developing, dorsal neural tube. (PubMed id 11984880)¹ Jun L....Bergemann A.D. (2002)
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. (2002)
Normalization and subtraction: two approaches to facilitate gene discovery. (PubMed id 8889548)¹ Bonaldo M.F.... Soares M.B. (1996)

(in PubMed, OMIM, and NCBI Bookshelf)
About This Section

		AND	OR
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)
About This Section

Entrez Gene: 152877	HGNC: 31860	AceView: SLBP	Ensembl:ENSG00000174137	euGenes: HUgn152877
ECgene: FAM53A	H-InvDB: FAM53A

(According to HUGE)
About This Section

(According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
About This Section

Name	Description
PharmGKB entry for FAM53A	Pharmacogenomics, SNPs, Pathways

Intellectual Property for FAM53A gene
(Patent information from GeneIP, Licensable technologies from WIS Yeda, Salk, Tufts, IP news from LifeMap Sciences, Inc.)

About This Section

Patent Information for FAM53A gene:
Search GeneIP for patents involving FAM53A

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, SABiosciences, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Uscn, Thermo Fisher Scientific, Gene Editing from DNA2.0 and Sirion Biotech, Clones from EMD Millipore, OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Cell lines from GenScript, LifeMap BioReagents, and Sirion Biotech, PCR Arrays from SABiosciences, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, and/or Enzo Life Sciences, In Situ Hybridization Assays from
Advanced Cell Diagnostics, Animal models from inGenious Targeting Laboratory)
About This Section


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Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for FAM53A

	SwitchGear 3'UTR luciferase reporter plasmids for FAM53A
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ThermoFisher Antibodies for FAM53A

Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat FAM53A

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GeneCards Homepage - Last full update: 6 May 2013 -

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Category			VWF (GIFTS: 73) von Willebrand factor
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FAM53A Gene

family with sequence similarity 53, member A

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FAM53A Gene

family with sequence similarity 53, member A

Aliasesfor FAM53A gene

Summariesfor FAM53A gene

Genomic Viewsfor FAM53A gene

Proteinsfor FAM53A gene

Protein Domains /Familiesfor FAM53A gene

Functionfor FAM53A gene

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Specialized Databases showing FAM53A gene

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for FAM53A gene

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for FAM53A gene

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for FAM53A gene

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for FAM53A gene

Protein Domains /
Families
for FAM53A gene

Function
for FAM53A gene

Pathways & Interactions
for FAM53A gene

Drugs & Compounds
for FAM53A gene

Transcripts
for FAM53A gene

Expression
for FAM53A gene

Orthologs
for FAM53A gene

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for FAM53A gene

Genomic Variants
for FAM53A gene

Disorders / Diseases
for FAM53A gene

Publications
for FAM53A gene

Intellectual Property
for FAM53A gene

Products
for FAM53A gene