Human Gene LINC01555 (uc001dke.2)
  Description: Homo sapiens chromosome 1 open reading frame 180 (LINC01555), non-coding RNA.
Transcript (Including UTRs)
   Position: hg19 chr1:85,093,913-85,100,703 Size: 6,791 Total Exon Count: 3 Strand: -
Coding Region
   Position: hg19 chr1:85,096,297-85,097,390 Size: 1,094 Coding Exon Count: 2 

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 (chr1:85,093,913-85,100,703)mRNA (may differ from genome)Protein (123 aa)
Gene SorterGenome BrowserOther Species FASTATable SchemaAlphaFoldBioGPS
EnsemblExonPrimerGeneCardsH-INVHPRDLynx
MGIneXtProtPubMedUniProtKB

-  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: 0.77 RPKM in Testis
Total median expression: 0.95 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 -36.50128-0.285 Picture PostScript Text
3' UTR -692.052384-0.290 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 Q8NAE3
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
      
      
      
      
      

-  Descriptions from all associated GenBank mRNAs
  AK092806 - Homo sapiens cDNA FLJ35487 fis, clone SMINT2008531.
AX747740 - Sequence 1265 from Patent EP1308459.
JD285090 - Sequence 266114 from Patent EP1572962.
JD046450 - Sequence 27474 from Patent EP1572962.
JD080552 - Sequence 61576 from Patent EP1572962.
JD297005 - Sequence 278029 from Patent EP1572962.
JD451099 - Sequence 432123 from Patent EP1572962.
JD551788 - Sequence 532812 from Patent EP1572962.
JD321396 - Sequence 302420 from Patent EP1572962.
JD524006 - Sequence 505030 from Patent EP1572962.
JD427931 - Sequence 408955 from Patent EP1572962.
BC137361 - Homo sapiens chromosome 1 open reading frame 180, mRNA (cDNA clone IMAGE:9021359).
BC137362 - Homo sapiens chromosome 1 open reading frame 180, mRNA (cDNA clone IMAGE:9021360).
BC144607 - Homo sapiens chromosome 1 open reading frame 180, mRNA (cDNA clone IMAGE:9053138).
BC171792 - Homo sapiens chromosome 1 open reading frame 180, mRNA (cDNA clone IMAGE:9054446).
JD335647 - Sequence 316671 from Patent EP1572962.
JD201998 - Sequence 183022 from Patent EP1572962.
JD427625 - Sequence 408649 from Patent EP1572962.
JD374330 - Sequence 355354 from Patent EP1572962.
JD506271 - Sequence 487295 from Patent EP1572962.
JD447843 - Sequence 428867 from Patent EP1572962.
JD482174 - Sequence 463198 from Patent EP1572962.
JD255741 - Sequence 236765 from Patent EP1572962.
JD228178 - Sequence 209202 from Patent EP1572962.
JD072538 - Sequence 53562 from Patent EP1572962.
JD361640 - Sequence 342664 from Patent EP1572962.
JD412434 - Sequence 393458 from Patent EP1572962.
JD197678 - Sequence 178702 from Patent EP1572962.
JD559173 - Sequence 540197 from Patent EP1572962.
JD064303 - Sequence 45327 from Patent EP1572962.
JD295440 - Sequence 276464 from Patent EP1572962.
JD448019 - Sequence 429043 from Patent EP1572962.
JD374502 - Sequence 355526 from Patent EP1572962.
JD384744 - Sequence 365768 from Patent EP1572962.
JD212938 - Sequence 193962 from Patent EP1572962.
JD542877 - Sequence 523901 from Patent EP1572962.
JD262049 - Sequence 243073 from Patent EP1572962.
JD087047 - Sequence 68071 from Patent EP1572962.
JD412435 - Sequence 393459 from Patent EP1572962.
JD247287 - Sequence 228311 from Patent EP1572962.
JD291165 - Sequence 272189 from Patent EP1572962.
JD358549 - Sequence 339573 from Patent EP1572962.
JD563676 - Sequence 544700 from Patent EP1572962.
JD083333 - Sequence 64357 from Patent EP1572962.
JD046562 - Sequence 27586 from Patent EP1572962.
JD137982 - Sequence 119006 from Patent EP1572962.
JD292913 - Sequence 273937 from Patent EP1572962.
JD353938 - Sequence 334962 from Patent EP1572962.
JD119433 - Sequence 100457 from Patent EP1572962.
KJ901242 - Synthetic construct Homo sapiens clone ccsbBroadEn_10636 C1orf180 gene, encodes complete protein.
JD182835 - Sequence 163859 from Patent EP1572962.
JD280358 - Sequence 261382 from Patent EP1572962.
JD172973 - Sequence 153997 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: C1orf180, CA180_HUMAN, NR_027379, Q8NAE3, uc001dke.1
UCSC ID: uc001dke.2
RefSeq Accession: NR_027379
Protein: Q8NAE3 (aka CA180_HUMAN)

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NR_027379.1
exon count: 3CDS single in 3' UTR: no RNA size: 2884
ORF size: 372CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 840.50frame 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.