Human Gene FAM107A (uc003dkn.3)
  Description: Homo sapiens family with sequence similarity 107, member A (FAM107A), transcript variant 2, mRNA.
Transcript (Including UTRs)
   Position: hg19 chr3:58,549,845-58,563,491 Size: 13,647 Total Exon Count: 4 Strand: -
Coding Region
   Position: hg19 chr3:58,552,315-58,555,587 Size: 3,273 Coding Exon Count: 3 

Page IndexSequence and LinksUniProtKB CommentsPrimersGenetic AssociationsMalaCards
CTDGene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein Structure
Other SpeciesGO AnnotationsmRNA DescriptionsOther NamesModel InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr3:58,549,845-58,563,491)mRNA (may differ from genome)Protein (144 aa)
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H-INVHGNCLynxMalacardsMGIneXtProt
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-  Comments and Description Text from UniProtKB
  ID: F107A_HUMAN
DESCRIPTION: RecName: Full=Protein FAM107A; AltName: Full=Down-regulated in renal cell carcinoma 1; AltName: Full=Protein TU3A;
FUNCTION: When transfected into cell lines in which it is not expressed, suppresses cell growth. May play a role in tumor development.
INTERACTION: P81605:DCD; NbExp=1; IntAct=EBI-743396, EBI-395625; P63151:PPP2R2A; NbExp=1; IntAct=EBI-743396, EBI-1048931;
SUBCELLULAR LOCATION: Nucleus.
TISSUE SPECIFICITY: Widely expressed in normal tissues. Expression is reduced or absent in a number of cancer cell lines.
SIMILARITY: Belongs to the FAM107 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


-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): FAM107A
CDC HuGE Published Literature: FAM107A
Positive Disease Associations: Arthritis, Rheumatoid
Related Studies:
  1. Arthritis, Rheumatoid
    Eli A Stahl et al. Nature genetics 2010, Genome-wide association study meta-analysis identifies seven new rheumatoid arthritis risk loci., Nature genetics. [PubMed 20453842]

-  MalaCards Disease Associations
  MalaCards Gene Search: FAM107A
Diseases sorted by gene-association score: renal cell carcinoma (6)

-  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: 375.11 RPKM in Brain - Anterior cingulate cortex (BA24)
Total median expression: 3743.43 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 -156.00461-0.338 Picture PostScript Text
3' UTR -866.642470-0.351 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
IPR009533 - DUF1151

Pfam Domains:
PF06625 - Protein of unknown function (DUF1151)

ModBase Predicted Comparative 3D Structure on O95990
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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
  Molecular Function:
GO:0003674 molecular_function
GO:0005515 protein binding

Biological Process:
GO:0001558 regulation of cell growth
GO:0040008 regulation of growth

Cellular Component:
GO:0005634 nucleus
GO:0016607 nuclear speck
GO:0043005 neuron projection


-  Descriptions from all associated GenBank mRNAs
  AK054720 - Homo sapiens cDNA FLJ30158 fis, clone BRACE2000525, highly similar to Protein FAM107A.
AF089853 - Homo sapiens DRR1 (DRR1) mRNA, complete cds.
AF089854 - Homo sapiens cell-line OV177 DRR1 (DRR1) mRNA, complete cds.
JD449441 - Sequence 430465 from Patent EP1572962.
JD315139 - Sequence 296163 from Patent EP1572962.
JD467811 - Sequence 448835 from Patent EP1572962.
JD250992 - Sequence 232016 from Patent EP1572962.
EU569833 - Homo sapiens family with sequence similarity 107 member A transcript variant (FAM107A) mRNA, complete cds, alternatively spliced.
JD131308 - Sequence 112332 from Patent EP1572962.
JD251574 - Sequence 232598 from Patent EP1572962.
JD078896 - Sequence 59920 from Patent EP1572962.
JD036862 - Sequence 17886 from Patent EP1572962.
JD263700 - Sequence 244724 from Patent EP1572962.
JD287612 - Sequence 268636 from Patent EP1572962.
JD357545 - Sequence 338569 from Patent EP1572962.
JD201160 - Sequence 182184 from Patent EP1572962.
AB023811 - Homo sapiens mRNA for TU3A, complete cds.
BC010561 - Homo sapiens family with sequence similarity 107, member A, mRNA (cDNA clone MGC:17126 IMAGE:4152118), complete cds.
AL050264 - Homo sapiens mRNA; cDNA DKFZp564N0582 (from clone DKFZp564N0582).
BC093012 - Homo sapiens cDNA clone IMAGE:30528214, containing frame-shift errors.
AF035283 - Homo sapiens clone 23916 mRNA sequence.
AK055443 - Homo sapiens cDNA FLJ30881 fis, clone FEBRA2004818, highly similar to DRR1 PROTEIN.
AK128791 - Homo sapiens cDNA FLJ45473 fis, clone BRSTN2016992, highly similar to Protein FAM107A.
JD343486 - Sequence 324510 from Patent EP1572962.
JD516373 - Sequence 497397 from Patent EP1572962.
JD059498 - Sequence 40522 from Patent EP1572962.
JD310086 - Sequence 291110 from Patent EP1572962.
JD154984 - Sequence 136008 from Patent EP1572962.
JD392399 - Sequence 373423 from Patent EP1572962.
JD177914 - Sequence 158938 from Patent EP1572962.
JD076371 - Sequence 57395 from Patent EP1572962.
JD122128 - Sequence 103152 from Patent EP1572962.
JD252581 - Sequence 233605 from Patent EP1572962.
JD415636 - Sequence 396660 from Patent EP1572962.
AK316450 - Homo sapiens cDNA, FLJ79349 complete cds, highly similar to Protein FAM107A.
JD332160 - Sequence 313184 from Patent EP1572962.
JD353677 - Sequence 334701 from Patent EP1572962.
AK298001 - Homo sapiens cDNA FLJ55230 complete cds, highly similar to Protein FAM107A.
JD222072 - Sequence 203096 from Patent EP1572962.
JD271257 - Sequence 252281 from Patent EP1572962.
JD518558 - Sequence 499582 from Patent EP1572962.
JD559482 - Sequence 540506 from Patent EP1572962.
JD445861 - Sequence 426885 from Patent EP1572962.
JD553945 - Sequence 534969 from Patent EP1572962.
JD286965 - Sequence 267989 from Patent EP1572962.
JD467804 - Sequence 448828 from Patent EP1572962.
JD488037 - Sequence 469061 from Patent EP1572962.
JD330582 - Sequence 311606 from Patent EP1572962.
JD338107 - Sequence 319131 from Patent EP1572962.
JD291290 - Sequence 272314 from Patent EP1572962.
JD202142 - Sequence 183166 from Patent EP1572962.
JD445730 - Sequence 426754 from Patent EP1572962.
JD076745 - Sequence 57769 from Patent EP1572962.
JD281700 - Sequence 262724 from Patent EP1572962.
JD157688 - Sequence 138712 from Patent EP1572962.
JD157125 - Sequence 138149 from Patent EP1572962.
JD075378 - Sequence 56402 from Patent EP1572962.
JD147563 - Sequence 128587 from Patent EP1572962.
JD408591 - Sequence 389615 from Patent EP1572962.
JD459101 - Sequence 440125 from Patent EP1572962.
JD160505 - Sequence 141529 from Patent EP1572962.
JD106281 - Sequence 87305 from Patent EP1572962.
DQ891763 - Synthetic construct clone IMAGE:100004393; FLH179708.01X; RZPDo839B08132D family with sequence similarity 107, member A (FAM107A) gene, encodes complete protein.
DQ894947 - Synthetic construct Homo sapiens clone IMAGE:100009407; FLH179704.01L; RZPDo839B08131D family with sequence similarity 107, member A (FAM107A) gene, encodes complete protein.
JD264249 - Sequence 245273 from Patent EP1572962.
KJ893246 - Synthetic construct Homo sapiens clone ccsbBroadEn_02640 FAM107A gene, encodes complete protein.
AM393765 - Synthetic construct Homo sapiens clone IMAGE:100001735 for hypothetical protein (FAM107A gene).
AB489168 - Synthetic construct DNA, clone: pF1KB8324, Homo sapiens FAM107A gene for family with sequence similarity 107, member A, without stop codon, in Flexi system.
CR457133 - Homo sapiens full open reading frame cDNA clone RZPDo834F127D for gene TU3A, TU3A protein; complete cds, incl. stopcodon.
JD404936 - Sequence 385960 from Patent EP1572962.
JD397484 - Sequence 378508 from Patent EP1572962.
JD131795 - Sequence 112819 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: DRR1, F107A_HUMAN, NM_001076778, NP_009108, O95990, Q96NH4, TU3A
UCSC ID: uc003dkn.3
RefSeq Accession: NM_001076778
Protein: O95990 (aka F107A_HUMAN)
CCDS: CCDS2892.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_001076778.1
exon count: 4CDS single in 3' UTR: no RNA size: 3367
ORF size: 435CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 746.00frame shift in genome: no % Coverage: 99.97
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.