Human Gene TLCD1 (uc010waw.2)
  Description: Homo sapiens TLC domain containing 1 (TLCD1), transcript variant 2, mRNA.
Transcript (Including UTRs)
   Position: hg19 chr17:27,051,366-27,053,949 Size: 2,584 Total Exon Count: 4 Strand: -
Coding Region
   Position: hg19 chr17:27,051,528-27,053,826 Size: 2,299 Coding Exon Count: 4 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesmRNA Descriptions
Other NamesModel InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr17:27,051,366-27,053,949)mRNA (may differ from genome)Protein (200 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
H-INVHGNCLynxMGIPubMedTreefam
UniProtKBBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: A8MYP9_HUMAN
DESCRIPTION: SubName: Full=TLC domain containing 1, isoform CRA_b; SubName: Full=TLC domain-containing protein 1;
SIMILARITY: Contains 1 TLC (TRAM/LAG1/CLN8) domain.

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 5.12 RPKM in Testis
Total median expression: 71.50 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -54.50123-0.443 Picture PostScript Text
3' UTR -45.12162-0.279 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR006634 - TLC-dom

Pfam Domains:
PF03798 - TLC domain

ModBase Predicted Comparative 3D Structure on A8MYP9
FrontTopSide
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
      
      
      

-  Descriptions from all associated GenBank mRNAs
  LF209209 - JP 2014500723-A/16712: Polycomb-Associated Non-Coding RNAs.
BC014072 - Homo sapiens TLC domain containing 1, mRNA (cDNA clone MGC:20499 IMAGE:3957355), complete cds.
JD105196 - Sequence 86220 from Patent EP1572962.
JD179432 - Sequence 160456 from Patent EP1572962.
JD071208 - Sequence 52232 from Patent EP1572962.
LF326823 - JP 2014500723-A/134326: Polycomb-Associated Non-Coding RNAs.
JD189938 - Sequence 170962 from Patent EP1572962.
EU831756 - Synthetic construct Homo sapiens clone HAIB:100066785; DKFZo008A1221 TLC domain containing 1 protein (TLCD1) gene, encodes complete protein.
JF432650 - Synthetic construct Homo sapiens clone IMAGE:100073887 TLC domain containing 1 (TLCD1) gene, encodes complete protein.
EU831834 - Synthetic construct Homo sapiens clone HAIB:100066863; DKFZo004A1222 TLC domain containing 1 protein (TLCD1) gene, encodes complete protein.
KJ895309 - Synthetic construct Homo sapiens clone ccsbBroadEn_04703 TLCD1 gene, encodes complete protein.
LF326822 - JP 2014500723-A/134325: Polycomb-Associated Non-Coding RNAs.
LF326821 - JP 2014500723-A/134324: Polycomb-Associated Non-Coding RNAs.
MA562400 - JP 2018138019-A/134326: Polycomb-Associated Non-Coding RNAs.
MA562399 - JP 2018138019-A/134325: Polycomb-Associated Non-Coding RNAs.
MA562398 - JP 2018138019-A/134324: Polycomb-Associated Non-Coding RNAs.
MA444786 - JP 2018138019-A/16712: Polycomb-Associated Non-Coding RNAs.

-  Other Names for This Gene
  Alternate Gene Symbols: A8MYP9, A8MYP9_HUMAN, hCG_31813, NM_001160407, NP_001153879
UCSC ID: uc010waw.2
RefSeq Accession: NM_001160407
Protein: A8MYP9 CCDS: CCDS54102.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_001160407.1
exon count: 4CDS single in 3' UTR: no RNA size: 904
ORF size: 603CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 1406.00frame shift in genome: no % Coverage: 98.23
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.