Human Gene FAM86C1 (uc001oqw.4)
  Description: Homo sapiens family with sequence similarity 86, member C1 (FAM86C1), transcript variant 2, mRNA.
Transcript (Including UTRs)
   Position: hg19 chr11:71,498,557-71,512,280 Size: 13,724 Total Exon Count: 4 Strand: +
Coding Region
   Position: hg19 chr11:71,498,583-71,510,693 Size: 12,111 Coding Exon Count: 4 

Page IndexSequence and LinksPrimersCTDGene AllelesRNA-Seq Expression
Microarray ExpressionRNA StructureProtein StructureOther SpeciesmRNA DescriptionsOther Names
Model InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr11:71,498,557-71,512,280)mRNA (may differ from genome)Protein (131 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblExonPrimerGeneCardsGeneNetworkH-INV
HGNCLynxMGIPubMedTreefamUniProtKB

-  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: 2.72 RPKM in Thyroid
Total median expression: 71.12 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 -8.9026-0.342 Picture PostScript Text
3' UTR -522.081587-0.329 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:
PF14904 - Family of unknown function

ModBase Predicted Comparative 3D Structure on Q9NVL1-2
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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     
      
      
      

-  Descriptions from all associated GenBank mRNAs
  AK311675 - Homo sapiens cDNA, FLJ18717.
AK130709 - Homo sapiens cDNA FLJ27199 fis, clone SYN03042.
AK311518 - Homo sapiens cDNA, FLJ18560.
BC032519 - Homo sapiens family with sequence similarity 86, member C, mRNA (cDNA clone MGC:45068 IMAGE:5494088), complete cds.
JF432479 - Synthetic construct Homo sapiens clone IMAGE:100073700 family with sequence similarity 86, member C (FAM86C) gene, encodes complete protein.
KJ894153 - Synthetic construct Homo sapiens clone ccsbBroadEn_03547 FAM86C1 gene, encodes complete protein.
AK315454 - Homo sapiens cDNA, FLJ96512.
AK293221 - Homo sapiens cDNA FLJ57700 complete cds, weakly similar to Protein FAM86A.
AK311428 - Homo sapiens cDNA, FLJ18470.
AK001523 - Homo sapiens cDNA FLJ10661 fis, clone NT2RP2006106.
JD131408 - Sequence 112432 from Patent EP1572962.
JD258092 - Sequence 239116 from Patent EP1572962.
JD489510 - Sequence 470534 from Patent EP1572962.
JD297325 - Sequence 278349 from Patent EP1572962.
JD165750 - Sequence 146774 from Patent EP1572962.
JD336027 - Sequence 317051 from Patent EP1572962.
JD336031 - Sequence 317055 from Patent EP1572962.
JD336027 - Sequence 317051 from Patent EP1572962.
JD336027 - Sequence 317051 from Patent EP1572962.
JD336031 - Sequence 317055 from Patent EP1572962.
JD336027 - Sequence 317051 from Patent EP1572962.
JD336031 - Sequence 317055 from Patent EP1572962.
JD336027 - Sequence 317051 from Patent EP1572962.
JD336031 - Sequence 317055 from Patent EP1572962.
JD069357 - Sequence 50381 from Patent EP1572962.
JD111576 - Sequence 92600 from Patent EP1572962.
JD040546 - Sequence 21570 from Patent EP1572962.
JD044521 - Sequence 25545 from Patent EP1572962.
JD178549 - Sequence 159573 from Patent EP1572962.
JD178548 - Sequence 159572 from Patent EP1572962.
JD544133 - Sequence 525157 from Patent EP1572962.
JD515361 - Sequence 496385 from Patent EP1572962.
JD098436 - Sequence 79460 from Patent EP1572962.
JD374259 - Sequence 355283 from Patent EP1572962.
JD343924 - Sequence 324948 from Patent EP1572962.
JD222707 - Sequence 203731 from Patent EP1572962.
JD163179 - Sequence 144203 from Patent EP1572962.
JD520547 - Sequence 501571 from Patent EP1572962.
JD441049 - Sequence 422073 from Patent EP1572962.
JD214613 - Sequence 195637 from Patent EP1572962.
JD475881 - Sequence 456905 from Patent EP1572962.
JD475882 - Sequence 456906 from Patent EP1572962.
JD493483 - Sequence 474507 from Patent EP1572962.
JD379537 - Sequence 360561 from Patent EP1572962.
JD379538 - Sequence 360562 from Patent EP1572962.
JD563510 - Sequence 544534 from Patent EP1572962.
JD109768 - Sequence 90792 from Patent EP1572962.
JD068108 - Sequence 49132 from Patent EP1572962.
JD400487 - Sequence 381511 from Patent EP1572962.
JD464569 - Sequence 445593 from Patent EP1572962.
DQ587039 - Homo sapiens piRNA piR-54151, complete sequence.
JD136662 - Sequence 117686 from Patent EP1572962.
JD391840 - Sequence 372864 from Patent EP1572962.
JD524642 - Sequence 505666 from Patent EP1572962.
JD350806 - Sequence 331830 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: FAM86C, NM_152563, NP_689776, Q9NVL1-2
UCSC ID: uc001oqw.4
RefSeq Accession: NM_152563
Protein: Q9NVL1-2, splice isoform of Q9NVL1 CCDS: CCDS8202.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_152563.2
exon count: 4CDS single in 3' UTR: no RNA size: 2025
ORF size: 396CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 905.00frame shift in genome: no % Coverage: 99.21
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.