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

FAM138D Gene

RNA gene   GIFtS: 24
GCID: GC12M000147

Family With Sequence Similarity 138, Member D

  Search for FAM138D
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
About This Section

Subcategory (RNA class): lncRNA

Quality score for this RNA gene is 3

Aliases
Family With Sequence Similarity 138, Member D1 2
F3792

External Ids:    HGNC: 335831   Entrez Gene: 6777842   Ensembl: ENSG000002061147   UniProtKB: Q6VEP23   
ORGUL members:         
NONCODE14:n377663 n378628      

Export aliases for FAM138D gene to outside databases

Previous GC identifers: GC12U900769 GC12M000019


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

GeneCards Summary for FAM138D Gene: 
FAM138D (family with sequence similarity 138, member D) is an RNA gene, and is affiliated with the lncRNA class.


(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 73), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000012.11  NC_018923.2  NT_009759.16  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the FAM138D gene promoter:
         SREBP-1c   Brachyury   NF-kappaB   E4BP4   SREBP-1b   POU2F1   POU2F1b   POU2F1a   POU2F1c   NF-kappaB1   
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids
   Search SABiosciences Chromatin IP Primers for FAM138D

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat FAM138D


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

Entrez Gene cytogenetic band: 12p13.33   Ensembl cytogenetic band:  12p13.33   HGNC cytogenetic band: 12p13.33

FAM138D Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
FAM138D gene location

GeneLoc information about chromosome 12         GeneLoc Exon Structure

GeneLoc location for GC12M000147:  view genomic region     (about GC identifiers)

Start:
147,073 bp from pter      End:
149,412 bp from pter
Size:
2,340 bases      Orientation:
minus strand
ORGUL member locations:
Legend (see complete legend)

ORGUL Member Locations for FAM138D

(According to UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MAXQB 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 Cloud-Clone Corp.,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Cloud-Clone Corp., Ontologies according to Gene Ontology Consortium 01 Oct 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, and/or Cloud-Clone Corp.)
About This Section

UniProtKB/Swiss-Prot: F138D_HUMAN, Q6VEP2 (See protein sequence)
Recommended Name: Protein FAM138D  
Size: 85 amino acids; 9302 Da

Explore the universe of human proteins at neXtProt for FAM138D: NX_Q6VEP2

Explore proteomics data for FAM138D at MOPED 

FAM138D Protein expression data from MOPED1, PaxDb2 and MAXQB3 :    About this image 

FAM138D Protein Expression

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(According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
About This Section
HGNC Gene Families: 
LNCRNA: Long non-coding RNAs

1 InterPro protein domain:
 IPR023245 FAM138

Graphical View of Domain Structure for InterPro Entry Q6VEP2

ProtoNet protein and cluster: Q6VEP2

UniProtKB/Swiss-Prot: F138D_HUMAN, Q6VEP2
Similarity: Belongs to the FAM138 family


FAM138D for domains           About GeneDecksing


(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,
bound targets from SABiosciences, miRNA Gene Targets from miRTarBase, shRNA from OriGene, 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, Vector BioLabs, and Sirion Biotech, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Oct 2013 via Entrez Gene.)
About This Section

Animal Models:
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miRNA
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(Pathways according to EMD Millipore, 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 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 Oct 2013 via Entrez Gene).
About This Section



Interactions:

    Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for FAM138D

(Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, 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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Browse Tocris compounds for FAM138D (F138D)

Search CenterWatch for drugs/clinical trials and news about FAM138D

(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,
Conferences by KenesGroup, 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, microRNA from QIAGEN,
Tagged/untagged cDNA clones from OriGene, SwitchGear Genomics, GenScript, DNA2.0, Vector BioLabs, Sirion Biotech, Primers from OriGene, SABiosciences, and/or QIAGEN )
About This Section

Unigene Cluster for FAM138D:

Family with sequence similarity 138, member D
Hs.722487  [show with all ESTs]
Unigene Representative Sequence: NR_026823
2 Ensembl transcripts including schematic representations, and UCSC links where relevant:
ENST00000440796(lincRNA) ENST00000320165(lincRNA)
miRNA
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Additional mRNA sequence: 

AY341951.1 NR_026823.1 

3 DOTS entries:

DT.97806839  DT.97826448  DT.121039192 

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

Expression evidence for FAM138D:none

FAM138D expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>2/3
CGAP TAG: --
FAM138D Expression
About this image


See FAM138D Protein Expression from SPIRE MOPED and PaxDB
SOURCE GeneReport for Unigene cluster: Hs.722487
    SABiosciences Custom PCR Arrays for FAM138D
Primer
Products:
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In Situ
Assay Products:
 

 
Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for FAM138D

(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
  --

ENSEMBL Gene Tree for FAM138D (if available)
TreeFam Gene Tree for FAM138D (if available)

(Paralogs according to 1HomoloGene,
2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
About This Section
Paralogs for FAM138D gene
18/57 SIMAP similar genes for FAM138D using alignment to 1 protein entry:     F138D_HUMAN(see all similar genes):
FAM138C    FAM138A    FAM138B    FAM138F    LRRC37A3    ETFA
NUDT7    PODXL    UBA1    CGRRF1    DNAPTP3    SIPA1L3
ZCCHC10    GOSR2    ZNF573    C14orf178    POMZP3    AHSA1

FAM138D for paralogs           About GeneDecksing



(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) 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

10/97 SNPs in FAM138D are shown (see all 97)    About this table     
Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance
Chr 12 posSequence#AA
Chg
TypeMore#Allele
freq
PopTotal
sample
More
----------
rs714333991,2
C--147454(+) GCCTGG/AGAACG 1 -- ds50012Minor allele frequency- A:0.25NA 4
rs619071981,2
C,F--147499(+) CATTCG/ACAGGT 1 -- ds50014Minor allele frequency- A:0.50WA NA 8
rs619071991,2
C,F--147523(+) CCCAGG/ATGGGA 1 -- ds50014Minor allele frequency- A:0.43NA CSA 7
rs1926458811,2
--147527(+) GATGGG/TAAGAA 1 -- ds50010--------
rs772920501,2
C,F--147604(+) CCTAAC/GAATCT 1 -- ds50014Minor allele frequency- G:0.40NA CSA 10
rs740558141,2
C,F--147617(+) ACCCAA/GCGACT 1 -- ds50016Minor allele frequency- G:0.43WA NA CSA 14
rs740558161,2
C,F--147684(+) GAGTCT/CTAGGA 1 -- ds50015Minor allele frequency- C:0.42WA NA CSA 12
rs781499081,2
C,F--147753(+) GAGACG/ACCTAA 1 -- ds50013Minor allele frequency- A:0.50NA 8
rs71338211,2
C,F,A,H--147767(+) TTGGTG/TGGGGG 1 -- ds50014Minor allele frequency- T:0.16NA CSA EA 128
rs796460041,2
C,F--147769(+) GGTGGG/AGGGGT 1 -- ds50013Minor allele frequency- A:0.38NA 8

HapMap Linkage Disequilibrium report for FAM138D (147073 - 149412 bp)

Structural Variations
     Database of Genomic Variants (DGV) 6 variations for FAM138D:    About this table     
Variant IDTypeSubtypePubMed ID
nsv821041CNV Duplication20802225
nsv826169CNV Gain20364138
esv24198CNV Gain+Loss19812545
nsv428269CNV Gain+Loss18775914
nsv832301CNV Gain+Loss17160897
nsv8882CNV Gain+Loss18304495

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(in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Conferences by KenesGroup, 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 FAM138D gene integrated from 9 sources:
(articles sorted by number of sources associating them with FAM138D)
    Utopia: connect your pdf to the dynamic
world of online information

  1. Diverse fates of paralogs following segmental duplication of telomeric genes. (PubMed id 15233989)1, 2, 3 Wong A....Ledbetter D.H. (2004)
  2. Identification of a novel retina-specific gene located in a subtelomeric region with polymorphic distribution among multiple human chromosomes. (PubMed id 11779631)1, 3 Mah N.... Weber B.H.F. (2001)

(in PubMed, OMIM, and NCBI Bookshelf)
About This Section
 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)
About This Section
Entrez Gene: 677784 HGNC: 33583 Ensembl:ENSG00000206114 euGenes: HUgn677784 ECgene: FAM138D
H-InvDB: FAM138D

(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
NameDescription
PharmGKB entry for FAM138D Pharmacogenomics, SNPs, Pathways

(Patent information from GeneIP,
Licensable technologies from WIS Yeda, Salk, Tufts,
IP news from LifeMap Sciences, Inc.)
About This Section
Patent Information for FAM138D gene:
Search GeneIP for patents involving FAM138D

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, Cloud-Clone Corp., Thermo Fisher Scientific, LSBio, Gene Editing from DNA2.0 and Sirion Biotech, Clones from EMD Millipore, OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Sirion Biotech, Cell lines from GenScript, and LifeMap BioReagents, PCR Arrays from SABiosciences, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, and/or Enzo Life Sciences, In Situ Hybridization Assays from
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About This Section

 
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