Human Gene LINC00638 (uc001ypq.4)
  Description: Homo sapiens long intergenic non-protein coding RNA 638 (LINC00638), non-coding RNA.
Transcript (Including UTRs)
   Position: hg19 chr14:105,287,538-105,290,055 Size: 2,518 Total Exon Count: 1 Strand: +
Coding Region
   Position: hg19 chr14:105,287,591-105,287,911 Size: 321 Coding Exon Count: 1 

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

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr14:105,287,538-105,290,055)mRNA (may differ from genome)Protein (106 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaBioGPS
EnsemblExonPrimerGeneCardsGeneNetworkH-INVHGNC
LynxMGIPubMed

-  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: 0.84 RPKM in Thyroid
Total median expression: 15.88 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 -12.5653-0.237 Picture PostScript Text
3' UTR -894.292144-0.417 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.

-  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
  AK095404 - Homo sapiens cDNA FLJ38085 fis, clone CTONG2016505.
AK292179 - Homo sapiens cDNA FLJ77170 complete cds.
BC015579 - Homo sapiens cDNA clone IMAGE:4636445.
BC041036 - Homo sapiens hypothetical LOC196872, mRNA (cDNA clone IMAGE:4662185).
JD110701 - Sequence 91725 from Patent EP1572962.
JD547973 - Sequence 528997 from Patent EP1572962.
JD525584 - Sequence 506608 from Patent EP1572962.
KJ901178 - Synthetic construct Homo sapiens clone ccsbBroadEn_10572 MGC23270 gene, encodes complete protein.
JD149795 - Sequence 130819 from Patent EP1572962.
JD060556 - Sequence 41580 from Patent EP1572962.
JD251246 - Sequence 232270 from Patent EP1572962.
JD336196 - Sequence 317220 from Patent EP1572962.
JD268958 - Sequence 249982 from Patent EP1572962.
JD525479 - Sequence 506503 from Patent EP1572962.
JD171549 - Sequence 152573 from Patent EP1572962.
JD315983 - Sequence 297007 from Patent EP1572962.
JD457051 - Sequence 438075 from Patent EP1572962.
JD443800 - Sequence 424824 from Patent EP1572962.
JD189360 - Sequence 170384 from Patent EP1572962.
JD115639 - Sequence 96663 from Patent EP1572962.
JD459880 - Sequence 440904 from Patent EP1572962.
JD490459 - Sequence 471483 from Patent EP1572962.
JD468089 - Sequence 449113 from Patent EP1572962.
JD338024 - Sequence 319048 from Patent EP1572962.
JD409976 - Sequence 391000 from Patent EP1572962.
JD194750 - Sequence 175774 from Patent EP1572962.
JD537345 - Sequence 518369 from Patent EP1572962.
JD448495 - Sequence 429519 from Patent EP1572962.
JD144041 - Sequence 125065 from Patent EP1572962.
JD230214 - Sequence 211238 from Patent EP1572962.
JD257699 - Sequence 238723 from Patent EP1572962.
JD352076 - Sequence 333100 from Patent EP1572962.
JD269994 - Sequence 251018 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: NR_024396, uc001ypq.3
UCSC ID: uc001ypq.4
RefSeq Accession: NR_024396

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NR_024396.1
exon count: 1CDS single in 3' UTR: no RNA size: 2518
ORF size: 321CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 636.00frame 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.