Human Gene FAM53A (uc021xkl.1)
  Description: Homo sapiens family with sequence similarity 53, member A (FAM53A), transcript variant 2, mRNA.
Transcript (Including UTRs)
   Position: hg19 chr4:1,641,608-1,685,988 Size: 44,381 Total Exon Count: 5 Strand: -
Coding Region
   Position: hg19 chr4:1,643,020-1,670,468 Size: 27,449 Coding Exon Count: 4 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsOther NamesModel InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr4:1,641,608-1,685,988)mRNA (may differ from genome)Protein (398 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCHPRDLynxMGIneXtProtOMIM
PubMedTreefamUniProtKBBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: FA53A_HUMAN
DESCRIPTION: RecName: Full=Protein FAM53A; AltName: Full=Dorsal neural-tube nuclear protein;
FUNCTION: May play an important role in neural development; the dorsomedial roof of the third ventricle (By similarity).
SUBCELLULAR LOCATION: Nucleus (By similarity). Note=Subnuclear distribution (By similarity).
SIMILARITY: Belongs to the FAM53 family.

-  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

+  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: 13.17 RPKM in Testis
Total median expression: 43.03 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 -80.60193-0.418 Picture PostScript Text
3' UTR -654.241412-0.463 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
  Pfam Domains:
PF15242 - Family of FAM53

ModBase Predicted Comparative 3D Structure on Q6NSI3
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     
      
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Cellular Component:
GO:0005634 nucleus


-  Descriptions from all associated GenBank mRNAs
  LF383959 - JP 2014500723-A/191462: Polycomb-Associated Non-Coding RNAs.
LF385430 - JP 2014500723-A/192933: Polycomb-Associated Non-Coding RNAs.
BC070112 - Homo sapiens family with sequence similarity 53, member A, mRNA (cDNA clone MGC:87650 IMAGE:5268061), complete cds.
AK125566 - Homo sapiens cDNA FLJ43578 fis, clone SKNMC1000124, weakly similar to Homo sapiens nuclear protein (STSG4523) mRNA.
BC042071 - Homo sapiens family with sequence similarity 53, member A, mRNA (cDNA clone IMAGE:5742522), with apparent retained intron.
JD173900 - Sequence 154924 from Patent EP1572962.
JD271310 - Sequence 252334 from Patent EP1572962.
JD424003 - Sequence 405027 from Patent EP1572962.
JD227871 - Sequence 208895 from Patent EP1572962.
JD271310 - Sequence 252334 from Patent EP1572962.
JD039313 - Sequence 20337 from Patent EP1572962.
KJ895674 - Synthetic construct Homo sapiens clone ccsbBroadEn_05068 FAM53A gene, encodes complete protein.
JD104788 - Sequence 85812 from Patent EP1572962.
JD371141 - Sequence 352165 from Patent EP1572962.
JD119482 - Sequence 100506 from Patent EP1572962.
JD416787 - Sequence 397811 from Patent EP1572962.
JD087810 - Sequence 68834 from Patent EP1572962.
JD404470 - Sequence 385494 from Patent EP1572962.
LF358174 - JP 2014500723-A/165677: Polycomb-Associated Non-Coding RNAs.
JD391564 - Sequence 372588 from Patent EP1572962.
JD426238 - Sequence 407262 from Patent EP1572962.
MA619536 - JP 2018138019-A/191462: Polycomb-Associated Non-Coding RNAs.
MA621007 - JP 2018138019-A/192933: Polycomb-Associated Non-Coding RNAs.
MA593751 - JP 2018138019-A/165677: Polycomb-Associated Non-Coding RNAs.

-  Other Names for This Gene
  Alternate Gene Symbols: FA53A_HUMAN, NM_001174070, NP_001167541, Q6NSI3, Q6ZUL5
UCSC ID: uc021xkl.1
RefSeq Accession: NM_001174070
Protein: Q6NSI3 (aka FA53A_HUMAN)
CCDS: CCDS33939.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_001174070.1
exon count: 5CDS single in 3' UTR: no RNA size: 2802
ORF size: 1197CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 2272.00frame shift in genome: no % Coverage: 100.00
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.