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TLCD1 Gene

protein-coding   GIFtS: 41
GCID: GC17M027140

TLC Domain Containing 1

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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
TLC Domain Containing 11 2
TLC Domain-Containing Protein 12

External Ids:    HGNC: 251771   Entrez Gene: 1162382   Ensembl: ENSG000001606067   UniProtKB: Q96CP73   

Export aliases for TLCD1 gene to outside databases

Previous GC identifers: GC17M024076 GC17M027052 GC17M023260 GC17M027053


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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GeneCards Summary for TLCD1 Gene:
TLCD1 (TLC domain containing 1) is a protein-coding gene. An important paralog of this gene is TLCD2.


(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_000017.10  NT_010783.16  NC_018928.2  
Regulatory elements:
   Regulatory transcription factor binding sites in the TLCD1 gene promoter:
         CHOP-10   AP-1   ATF-2   Nkx2-5   c-Jun   Tal-1beta   C/EBPalpha   E47   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidTLCD1 promoter sequence
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Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat TLCD1


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

Entrez Gene cytogenetic band: 17q11.2   Ensembl cytogenetic band:  17q11.2   HGNC cytogenetic band: 17q11.2

TLCD1 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
TLCD1 gene location

GeneLoc information about chromosome 17         GeneLoc Exon Structure

GeneLoc location for GC17M027140:  view genomic region     (about GC identifiers)

Start:
27,051,366 bp from pter      End:
27,054,953 bp from pter
Size:
3,588 bases      Orientation:
minus 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: TLCD1_HUMAN, Q96CP7 (See protein sequence)
Recommended Name: TLC domain-containing protein 1 precursor  
Size: 247 amino acids; 28548 Da

Explore the universe of human proteins at neXtProt for TLCD1: NX_Q96CP7

Explore proteomics data for TLCD1 at MOPED


See TLCD1 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

REFSEQ proteins (2 alternative transcripts): 
NP_001153879.1  NP_612472.1  

ENSEMBL proteins: 
 ENSP00000292090   ENSP00000468670   ENSP00000378391   ENSP00000466264  

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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:
 IPR006634 TLC-dom

Graphical View of Domain Structure for InterPro Entry Q96CP7

ProtoNet protein and cluster: Q96CP7

1 Blocks protein domain: IPB006634 TRAM

UniProtKB/Swiss-Prot: TLCD1_HUMAN, Q96CP7
Similarity: Contains 1 TLC (TRAM/LAG1/CLN8) domain


Find genes that share domains with TLCD1           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 TLCD1
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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
TLCD1_HUMAN, Q96CP7: Membrane; Multi-pass membrane protein (Potential)
Subcellular locations from COMPARTMENTS: 

CompartmentConfidence
plasma membrane3
cytosol1
extracellular1
mitochondrion1
peroxisome1

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

GO IDQualified GO termEvidencePubMed IDs
GO:0016021integral component of membrane IEA--

Find genes that share ontologies with TLCD1           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 TLCD1
Interactions:

    Search GeneGlobe Interaction Network for TLCD1

(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 TLCD1



(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 TLCD1 gene (2 alternative transcripts): 
NM_001160407.1  NM_138463.3  

Unigene Cluster for TLCD1:

TLC domain containing 1
Hs.499952  [show with all ESTs]
Unigene Representative Sequence: BQ683306
4 Ensembl transcripts including schematic representations, and UCSC links where relevant:
ENST00000292090(uc002hco.3) ENST00000581236 ENST00000394933(uc010waw.2)
ENST00000580518
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Additional mRNA sequence: BC014072.2 

7 DOTS entries:

DT.112441  DT.99985192  DT.92070622  DT.95094793  DT.120945230  DT.97840062  DT.92070621 

Selected AceView cDNA sequences (see all 476):

BQ672354 CR612854 BF001688 BQ962073 AW008736 CF126767 BM728685 AI874277 
BU186966 CF127918 BM982469 BI768064 CB125701 AW769494 BU526908 CN482771 
CR622817 AK027312 CR596043 AI123915 AA470878 CR600820 BQ671309 CA420397 

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™, 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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TLCD1 expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>2/3
CGAP TAG: TCCCCAAGAA
TLCD1 Expression
About this image


TLCD1 expression in embryonic tissues and stem cells    About this table
Data from LifeMap, the Embryonic Development and Stem Cells Database
 
 Bone (Muscoskeletal System)
         Zeugopod Growth Plate
TLCD1 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

TLCD1 Protein Expression

SOURCE GeneReport for Unigene cluster: Hs.499952
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In Situ
Assay Products:
 

 
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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)
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This gene was present in the common ancestor of animals.

Orthologs for TLCD1 gene from Selected species (see all 11)    About this table
Organism Taxonomic
classification
Gene Description Human
Similarity
Orthology
Type
Details
mouse
(Mus musculus)
Mammalia Tlcd11 , 5 TLC domain containing 11, 5 84.76(n)1
87.61(a)1
  11 (46.74 cM)5
683851  NM_026708.11  NP_080984.11 
 781767115 
chicken
(Gallus gallus)
Aves TLCD11 TLC domain containing 1 64.25(n)
58.12(a)
  417575  XM_415821.4  XP_415821.1 
zebrafish
(Danio rerio)
Actinopterygii tlcd11 TLC domain containing 1 51.39(n)
40.74(a)
  450051  NM_001006071.1  NP_001006071.1 
worm
(Caenorhabditis elegans)
Secernentea Y48G8AL.136
Y63D3A.86
(see all 3)
Protein Y63D3A.8 (Y63D3A.8) mRNA, complete cds
(see all 3)
18(a)
18(a)
(see all 3)
many ↔ many
many ↔ many
(see all 3)
I(1223956-1229282) WBGene00021691
I(14114194-14118654) WBGene00013407


ENSEMBL Gene Tree for TLCD1 (if available)
TreeFam Gene Tree for TLCD1 (if available)

(Paralogs according to 1HomoloGene,
2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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Paralogs for TLCD1 gene
TLCD22  
1 SIMAP similar gene for TLCD1 using alignment to 4 protein entries:     TLCD1_HUMAN (see all proteins):
TLCD2

Find genes that share paralogs with TLCD1           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 TLCD1 (see all 68)    About this table                                 

Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance
Chr 17 posSequence#AA
Chg
TypeMore#Allele
freq
PopTotal
sample
More
----------
rs2003532011,2
--27051890(+) GATGCC/TGGAGA 4 S G mis10--------
rs1846113351,2
C--27051951(+) AGATGC/TAGACG 2 -- int10--------
rs1894898741,2
--27051974(+) TTTGGG/TGGGTG 2 -- int10--------
rs1815999951,2
--27052011(+) TCCCAA/CATTTC 2 -- int10--------
rs1388078501,2
C--27052052(+) ATGCT-/TTGTTTTG 2 -- int10--------
rs1418926011,2
--27052108(+) TGTGGC/GTGATG 2 -- int10--------
rs1502175461,2
--27052146(+) GGGTTA/GCTGGC 2 -- int10--------
rs728475481,2
C,F--27052155(+) GCCTCA/GGTGAA 2 -- int13Minor allele frequency- G:0.08NA EA NS 388
rs1113046121,2
F--27052171(+) ACAGAG/CTGCCA 2 -- int12Minor allele frequency- C:0.50CSA 6
rs1387419091,2
C--27052263(+) AAGACA/GGAGCT 2 -- int10--------

HapMap Linkage Disequilibrium report for TLCD1 (27051366 - 27054953 bp)

Structural Variations
     Database of Genomic Variants (DGV) 1 variation for TLCD1:    About this table    
Variant IDTypeSubtypePubMed ID
nsv908028CNV Loss21882294

Site Specific Mutation Identification with PCR Assays
SeqTarget long-range PCR primers for resequencing TLCD1
DNA2.0 Custom Variant and Variant Library Synthesis for TLCD1

(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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  --

(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 TLCD1 gene integrated from 10 sources:
(articles sorted by number of sources associating them with TLCD1)
    Utopia: connect your pdf to the dynamic
world of online information

  1. TRAM, LAG1 and CLN8: members of a novel family of lipid-sensing domains? (PubMed id 12151215)1, 3 Winter E. and Ponting C.P. (Trends Biochem. Sci. 2002)
  2. Mass spectrometric analysis of lysine ubiquitylation reveals promiscuity at site level. (PubMed id 21139048)1 Danielsen J.M....Nielsen M.L. (amp 2011)
  3. 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)
  4. 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)

(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: 116238 HGNC: 25177 AceView: RAB34 Ensembl:ENSG00000160606 euGenes: HUgn116238
ECgene: TLCD1 H-InvDB: TLCD1

(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 TLCD1 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 TLCD1 gene:
Search GeneIP for patents involving TLCD1

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 TLCD1
 inGenious Targeting Laboratory: Contact us about creating complex and humanized mouse models for TLCD1
 LSBio Antibodies in human, mouse, rat for TLCD1
Customized transgenic rodents for:
 Humanization
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 Tissue-specific gene expresssion
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 Browse compounds at ApexBio
 Search Addgene for plasmids for TLCD1
  Search eBioscience for proteins for TLCD1
  Search eBioscience for elisas for TLCD1
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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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