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Category   Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21
GIFtS

FAM161A Gene

protein-coding   GIFtS: 48
GCID: GC02M062051

family with sequence similarity 161, member A

(Previous name: retinitis pigmentosa 28 (autosomal recessive) )
(Previous symbol: RP28)
 Explore 5 diseases affiliated with
FAM161A via our new
 Human Malady Compendium 
Biological research products
for FAM161A
    

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

This gene clusters with an RNA gene
Subcategory (RNA class): lncRNA

Quality score for the ORGUL clustered with this gene is 3

Aliases
Family With Sequence Similarity 161, Member A1 2
RP281 2 5
Retinitis Pigmentosa 28 (Autosomal Recessive)1 2
FLJ133051
Protein FAM161A2

External Ids:    HGNC: 258081   Entrez Gene: 841402   Ensembl: ENSG000001702647   OMIM: 6135965   UniProtKB: Q3B8203   
ORGUL members:         
NONCODE:n410543    

Export aliases for FAM161A gene to outside databases

Previous GC identifers: GC02M061905 GC02M061792


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

Entrez Gene summary for FAM161A:
This gene belongs to the FAM161 family. It is expressed mainly in the retina. Mouse studies suggested that this gene is
involved in development of retinal progenitors during embryogenesis, and that its activity is restricted to mature
photoreceptors after birth. Mutations in this gene cause autosomal recessive retinitis pigmentosa-28. Alternatively
spliced transcript variants have been identified.(provided by RefSeq, Jan 2011)

UniProtKB/Swiss-Prot: F161A_HUMAN, Q3B820
Function: Involved in ciliogenesis




(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_000002.11  NC_018913.1  NT_022184.15  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the FAM161A gene promoter:
         SRF   ER-alpha   C/EBPbeta   AML1a   LUN-1   HNF-1A   SRY   FOXC1   CP2   HNF-1   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidFAM161A promoter sequence
   Search SABiosciences Chromatin IP Primers for FAM161A

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat FAM161A


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

Entrez Gene cytogenetic band: 2p15   Ensembl cytogenetic band:  2p15   HGNC cytogenetic band: 2p15

FAM161A Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
FAM161A gene location

GeneLoc information about chromosome 2         GeneLoc Exon Structure

GeneLoc location for GC02M062051:  view genomic region     (about GC identifiers)

Start:
62,051,983 bp from pter      End:
62,081,278 bp from pter
Size:
29,296 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: F161A_HUMAN, Q3B820 (See protein sequence)
Recommended Name: Protein FAM161A  
Size: 660 amino acids; 76752 Da
Subunit: Interacts (via C-terminus) with microtubules. Interacts with LCA5, CEP290 and SDCCAG8. Interacts with FAM161B
Subcellular location: Cytoplasm, cytoskeleton, cilium basal body. Cell projection, cilium. Note=Localized to the region
between the outer and inner photoreceptor segments, corresponding to the photoreceptor connecting cilium
Sequence caution: Sequence=BAG58969.1; Type=Erroneous initiation; Note=Translation N-terminally extended;
Secondary accessions: B4DJV7 Q9H8R2
Alternative splicing: 3 isoforms:  Q3B820-1   Q3B820-2   Q3B820-3   (No experimental confirmation available)

Explore the universe of human proteins at neXtProt for FAM161A: NX_Q3B820

Post-translational modifications:

  • View modification sites using PhosphoSitePlus2
  • View neXtProt modification sites for NX_Q3B820

  • FAM161A Protein expression data from MOPED and PaxDb:    About this image 
    FAM161A Protein Expression
    REFSEQ proteins (2 alternative transcripts): 
    NP_001188472.1  NP_115556.2  

    ENSEMBL proteins: 
     ENSP00000396105   ENSP00000416861   ENSP00000385158   ENSP00000385893   ENSP00000303170  

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    Uscn Proteins for FAM161A

    Gene Ontology (GO): 4 cellular component terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005737cytoplasm IEA--
    GO:0005813centrosome IDA--
    GO:0032391photoreceptor connecting cilium IDA--
    GO:0036064cilium basal body IDA--

    FAM161A for ontologies           About GeneDecksing



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    Uscn ELISAs and CLIAs for FAM161A


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

    FAM161A for domains           About GeneDecksing

    1 InterPro domain/family:
     IPR019579 UPF0564

    Graphical View of Domain Structure for InterPro Entry Q3B820

    ProtoNet protein and cluster: Q3B820

    UniProtKB/Swiss-Prot: F161A_HUMAN, Q3B820
    Similarity: Belongs to the FAM161 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: F161A_HUMAN, Q3B820
    Function: Involved in ciliogenesis

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005515protein binding IPI--
         
    FAM161A for ontologies           About GeneDecksing


    Animal Models:
       inGenious Targeting Laboratory - Customizable classic, inducible, and humanized mouse model solutions for FAM161A 

    miRNA
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    hsa-miR-548am hsa-miR-148b hsa-miR-548v hsa-miR-152 hsa-miR-183* hsa-miR-542-3p hsa-miR-548x hsa-miR-1183
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    In Situ Assay
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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 CentralTM Interacting Genes and Proteins Networks for FAM161A

    STRING Interaction Network Preview (showing 1 interactants - click image to see more details)

    1 Interacting protein for FAM161A (Q3B8203 ENSP000003858934) via UniProtKB, MINT, STRING, and/or I2D
    InteractantInteraction Details
    GeneCardExternal ID(s)
    PPM1FP495933, ENSP000002632124I2D: score=3 STRING: ENSP00000263212
    About this table

    Gene Ontology (GO): 3 biological process terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0007601visual perception IEA--
    GO:0042384cilium assembly IMP--
    GO:0050896response to stimulus IEA--

    FAM161A for ontologies           About GeneDecksing



    (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
    Browse drugs & compounds from Enzo Life Sciences

    Browse Tocris compounds for FAM161A
    Search CenterWatch for drugs/clinical trials and news about FAM161A / F161A 

    (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,
    RNAi Products from EMD Millipore,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, Sirion Biotech, microRNA from QIAGEN,
    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 FAM161A gene (2 alternative transcripts): 
    NM_001201543.1  NM_032180.2  

    Unigene Cluster for FAM161A:

    Family with sequence similarity 161, member A
    Hs.440466  [show with all ESTs]
    Unigene Representative Sequence: NM_001201543
    7 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000456262 ENST00000418113(uc010fcm.1) ENST00000404929(uc002sbm.4)
    ENST00000405894(uc002sbn.4 uc010ypo.2) ENST00000478494 ENST00000496369
    ENST00000307507(uc010fcn.1)

    miRNA
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    8/11 QIAGEN miScript miRNA Assays for microRNAs that regulate FAM161A (see all 11):
    hsa-miR-548am hsa-miR-148b hsa-miR-548v hsa-miR-152 hsa-miR-183* hsa-miR-542-3p hsa-miR-548x hsa-miR-1183
    Browse SwitchGear 3'UTR luciferase reporter plasmids
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    Additional cDNA sequence: 

    AK023367.1 AK091575.1 AK296255.1 BC036448.1 BX648834.1 BX649029.1 NR_037710.1 

    8 DOTS entries:

    DT.100681070  DT.101981288  DT.99982740  DT.40304266  DT.97787963  DT.100008998  DT.308778  DT.100675177 

    24/37 AceView cDNA sequences (see all 37):

    BF110321 AA580947 AI700529 AW964482 AI914090 CD678265 BX649029 BX509886 
    BX648834 AA928868 BQ640161 BC036448 BU542254 CD359154 BQ215453 AI690681 
    AK023367 BU742300 AA319279 BM706877 BF572354 AU134161 N20913 CD299162 

    GeneLoc Exon Structure

    3 Alternative Splicing Database (ASD) splice patterns (SP) for FAM161A    About this scheme

    ExUns: 1a · 1b · 1c ^ 2 ^ 3 ^ 4a · 4b · 4c ^ 5a · 5b
    SP1:                                                            
    SP2:                    -                                       
    SP3:                    -           -                           


    ECgene alternative splicing isoforms for FAM161A

    (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

    FAM161A expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS
    CGAP TAG: --
    FAM161A Expression
    About this image

    FAM161A expression in embryonic tissues and stem cells
    Expression by the Database of Embryonic development, Stem cell research, and Regenerative medicine    About this table

    1 LifeMap In Vivo Development Anatomical Compartment/Cell 
    Tissue Anatomical Compartment CellCategory (developmental path)
    EyeOuter Nuclear LayerMature Rod CellsPhotoreceptors, Retina
    Expression: Positive    Negative     Selective marker
    Experimental details: Curated     Microarrays     In-situ hybridization

    See FAM161A Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for FAM161A

    SOURCE GeneReport for Unigene cluster: Hs.440466

    UniProtKB/Swiss-Prot: F161A_HUMAN, Q3B820
    Tissue specificity: Isoform 1 and isoform 3 are widely expressed with highest levels in retina and testis, with isoform
    1 being the most abundant in all tissues tested

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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 animals.

    Orthologs for FAM161A gene from 5/17 species (see all 17)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    chicken
    (Gallus gallus)
    Aves FAM161A1 family with sequence similarity 161, member A 57.07(n)
    46.37(a)
      769188  XM_001232413.2  XP_001232414.2 
    lizard
    (Anolis carolinensis)
    Reptilia FAM161A6
    --
    46(a)
    1 ↔ 1
    1(121579937-121590679)
    zebrafish
    (Danio rerio)
    Actinopterygii LOC5583201 protein FAM161A-like 49.2(n)
    38.98(a)
      558320  XM_681520.5  XP_686612.5 
    fruit fly
    (Drosophila melanogaster)
    Insecta CG11136
    --
    10(a)
    1 → many
    3R(1078875-1081125)
    worm
    (Caenorhabditis elegans)
    Secernentea Y38H6C.146
    Protein Y38H6C.14
    12(a)
    1 → many
    V(20529922-20534138)


    ENSEMBL Gene Tree for FAM161A (if available)
    TreeFam Gene Tree for FAM161A (if available) 

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for FAM161A gene
    FAM161B2  

    FAM161A 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

    10/585 NCBI SNPs in FAM161A are shown (see all 585    About this table
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 2 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs2021932011,2
    Cpathogenic62066572(+) TTCTCA/C/GTCCTC 8 R G * nc-transcript-variantmis1 stg10--------
    rs2006910421,2
    Cpathogenic62066830(+) GTATCA/TCTCAG 5 R * stg10--------
    rs19194811,2
    C,F,O,H--62051524(+) ATCATG/ATCTAA 3 -- ds500124Minor allele frequency- A:0.42MN NA NS EA WA 2700
    rs2007415341,2
    C--62051835(+) GGCTGG/TGGAGT 3 -- ds50010--------
    rs1490646941,2
    --62052010(+) CCTTTA/GTTAAG 3 -- nc-transcript-variantut310--------
    rs1818145801,2
    --62052039(+) TACTGG/TTCCAA 3 -- nc-transcript-variantut310--------
    rs75639001,2
    C--62052041(+) CTGTTA/CCAAAT 3 -- nc-transcript-variantut31 ese30--------
    rs1855764141,2
    --62052132(+) TAACAC/TGAACT 3 -- ut31 nc-transcript-variant0--------
    rs1483527431,2
    --62052222(+) CAGTTG/TGGAAA 3 -- ut31 nc-transcript-variant0--------
    rs1902881691,2
    --62052309(+) ATGCTA/GTATTA 3 -- ut31 nc-transcript-variant0--------

    HapMap Linkage Disequilibrium report for FAM161A (62051983 - 62081278 bp)
    Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
    Database of Genomic Variants (DGV): 2 variations for FAM161A
         2 CNVs: 48014 97870
    Human Gene Mutation Database (HGMD): FAM161A

    SABiosciences Cancer Mutation PCR Assays
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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

    FAM161A for disorders           About GeneDecksing

    OMIM gene information: 613596   
    OMIM disorders: 606068  
    UniProtKB/Swiss-Prot: F161A_HUMAN, Q3B820
  • Defects in FAM161A are the cause of retinitis pigmentosa type 28 (RP28) [MIM:606068]. A retinal dystrophy
  • belonging to the group of pigmentary retinopathies. Retinitis pigmentosa is characterized by retinal pigment deposits
    visible on fundus examination and primary loss of rod photoreceptor cells followed by secondary loss of cone
    photoreceptors. Patients typically have night vision blindness and loss of midperipheral visual field. As their
    condition progresses, they lose their far peripheral visual field and eventually central vision as well

    5 diseases for FAM161A:    About MalaCards
    retinitis pigmentosa 28    retinitis pigmentosa    retinitis    pigmentary retinopathy
    blindness

    1 disease from the University of Copenhagen DISEASES database for FAM161A:
    Retinitis pigmentosa

    Export disorders for FAM161A 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)
    About This Section

    PubMed articles for FAM161A gene, integrated from 9 sources (see all 16):
    (articles sorted by number of sources associating them with FAM161A)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Homozygosity mapping reveals null mutations in FAM161 A as a cause of autosomal-recessive retinitis pigmentosa. (PubMed id 20705279)1, 2, 3 Bandah-Rozenfeld D....Sharon D. (2010)
    2. Nonsense mutations in FAM161A cause RP28-associated r ecessive retinitis pigmentosa. (PubMed id 20705278)1, 2, 3 Langmann T....Rivolta C. (2010)
    3. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (2004)
    4. Autosomal recessive retinitis pigmentosa locus RP28 maps between D2S1337 and D2S286 on chromosome 2p11-p15 in an Indian family. (PubMed id 10507729)1, 3 Gu S....Gal A. (1999)
    5. The retinitis pigmentosa 28 protein FAM161A is a novel ciliary protein involved in intermolecular protein interaction and microtubule association. (PubMed id 22791751)2 Zach F.... Stohr H. (2012)
    6. FAM161A, associated with retinitis pigmentosa, is a component of the cilia-basal body complex and interacts with proteins involved in ciliopathies. (PubMed id 22940612)2 Di Gioia S.A.... Rivolta C. (2012)
    7. The full-ORF clone resource of the German cDNA consortium. (PubMed id 17974005)2 Bechtel S.... Schupp I. (2007)
    8. The LIFEdb database in 2006. (PubMed id 16381901)1 Mehrle A....Wiemann S. (2006)
    9. A human protein-protein interaction network: a resource for annotating the proteome. (PubMed id 16169070)1 Stelzl U.... Wanker E.E. (2005)
    10. Generation and annotation of the DNA sequences of human chromosomes 2 and 4. (PubMed id 15815621)2 Hillier L.W....Wilson R.K. (2005)

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    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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    Entrez Gene: 84140 HGNC: 25808 AceView: FLJ13305 Ensembl:ENSG00000170264 euGenes: HUgn84140
    ECgene: FAM161A H-InvDB: FAM161A

    (According to HUGE)
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    NameDescription
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