Human Gene LINC01547 (uc011afm.2)
  Description: Homo sapiens chromosome 21 open reading frame 67 (LINC01547), transcript variant 1, non-coding RNA.
Transcript (Including UTRs)
   Position: hg19 chr21:46,353,199-46,359,828 Size: 6,630 Total Exon Count: 4 Strand: -
Coding Region
   Position: hg19 chr21:46,354,129-46,359,582 Size: 5,454 Coding Exon Count: 4 

Page IndexSequence and LinksPrimersGene AllelesRNA-Seq ExpressionMicroarray Expression
RNA StructureProtein StructureOther SpeciesmRNA DescriptionsOther NamesModel Information
Methods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr21:46,353,199-46,359,828)mRNA (may differ from genome)Protein (218 aa)
Gene SorterGenome BrowserOther Species FASTATable SchemaAlphaFoldBioGPS
EnsemblExonPrimerGeneCardsLynxMGIPubMed
UniProtKB

-  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


+  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: 3.71 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 39.52 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 -110.80246-0.450 Picture PostScript Text
3' UTR -366.81930-0.394 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
  ModBase Predicted Comparative 3D Structure on P58512-3
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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
      
      
      
      
      

-  Descriptions from all associated GenBank mRNAs
  AY035381 - Homo sapiens C21orf69 protein mRNA, complete cds.
JD434538 - Sequence 415562 from Patent EP1572962.
JD460463 - Sequence 441487 from Patent EP1572962.
JD289854 - Sequence 270878 from Patent EP1572962.
JD153176 - Sequence 134200 from Patent EP1572962.
JD213993 - Sequence 195017 from Patent EP1572962.
BC101235 - Homo sapiens chromosome 21 open reading frame 67, mRNA (cDNA clone IMAGE:40022796).
BC101236 - Homo sapiens chromosome 21 open reading frame 67, mRNA (cDNA clone IMAGE:40022798).
BC101237 - Homo sapiens chromosome 21 open reading frame 67, mRNA (cDNA clone IMAGE:40022801).
BC101238 - Homo sapiens chromosome 21 open reading frame 67, mRNA (cDNA clone IMAGE:40022803).
JD514570 - Sequence 495594 from Patent EP1572962.
JD090232 - Sequence 71256 from Patent EP1572962.
JD250405 - Sequence 231429 from Patent EP1572962.
JD219706 - Sequence 200730 from Patent EP1572962.
KJ900871 - Synthetic construct Homo sapiens clone ccsbBroadEn_10265 C21orf67 gene, encodes complete protein.
JD338130 - Sequence 319154 from Patent EP1572962.
JD338955 - Sequence 319979 from Patent EP1572962.
JD256150 - Sequence 237174 from Patent EP1572962.
AF380178 - Homo sapiens C21orf67 protein (C21orf67) mRNA, complete cds.
AY040088 - Homo sapiens C21orf67 isoform B protein (C21orf67) mRNA, complete cds, alternatively spliced.
BC128244 - Homo sapiens chromosome 21 open reading frame 67, mRNA (cDNA clone IMAGE:40114753).
BC128245 - Homo sapiens chromosome 21 open reading frame 67, mRNA (cDNA clone IMAGE:40114755).
KJ903434 - Synthetic construct Homo sapiens clone ccsbBroadEn_12828 C21orf67 gene, encodes complete protein.
JD123415 - Sequence 104439 from Patent EP1572962.
JD397593 - Sequence 378617 from Patent EP1572962.
AK127059 - Homo sapiens cDNA FLJ45116 fis, clone BRAWH3035154.
JD522562 - Sequence 503586 from Patent EP1572962.
JD372794 - Sequence 353818 from Patent EP1572962.
JD372793 - Sequence 353817 from Patent EP1572962.
JD522995 - Sequence 504019 from Patent EP1572962.
JD161574 - Sequence 142598 from Patent EP1572962.
JD140991 - Sequence 122015 from Patent EP1572962.
JD462127 - Sequence 443151 from Patent EP1572962.
JD406912 - Sequence 387936 from Patent EP1572962.
JD457404 - Sequence 438428 from Patent EP1572962.
JD457405 - Sequence 438429 from Patent EP1572962.
JD457403 - Sequence 438427 from Patent EP1572962.
JD227611 - Sequence 208635 from Patent EP1572962.
JD151879 - Sequence 132903 from Patent EP1572962.
JD457402 - Sequence 438426 from Patent EP1572962.
JD522994 - Sequence 504018 from Patent EP1572962.
JD227610 - Sequence 208634 from Patent EP1572962.
JD547635 - Sequence 528659 from Patent EP1572962.
JD524102 - Sequence 505126 from Patent EP1572962.
JD265767 - Sequence 246791 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: C21orf67, C21orf69, NR_027128, P58512-3
UCSC ID: uc011afm.2
RefSeq Accession: NR_027128
Protein: P58512-3, splice isoform of P58512

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NR_027128.1
exon count: 4CDS single in 3' UTR: no RNA size: 1850
ORF size: 657CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 1043.00frame shift in genome: no % Coverage: 99.08
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.