Human Gene GARIN5B (ENST00000424985.3_7) from GENCODE V47lift37
  Description: golgi associated RAB2 interactor family member 5B (from RefSeq NM_001145402.2)
Gencode Transcript: ENST00000424985.3_7
Gencode Gene: ENSG00000180043.11_11
Transcript (Including UTRs)
   Position: hg19 chr19:55,866,276-55,874,628 Size: 8,353 Total Exon Count: 11 Strand: -
Coding Region
   Position: hg19 chr19:55,866,668-55,874,434 Size: 7,767 Coding Exon Count: 10 

Page IndexSequence and LinksUniProtKB CommentsPrimersGene AllelesRNA-Seq Expression
RNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA DescriptionsOther Names
Model InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr19:55,866,276-55,874,628)mRNA (may differ from genome)Protein (922 aa)
Gene SorterGenome BrowserOther Species FASTATable SchemaAlphaFoldBioGPS
EnsemblEntrez GeneExonPrimerGeneCardsMGIPubMed
UniProtKBBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: F71E2_HUMAN
DESCRIPTION: RecName: Full=Putative protein FAM71E2;
SIMILARITY: Belongs to the FAM71 family.
CAUTION: Product of a dubious CDS prediction.
SEQUENCE CAUTION: Sequence=AAH31875.1; Type=Frameshift; Positions=198; Sequence=AAH31875.1; Type=Miscellaneous discrepancy; Note=Contaminating sequence. Potential poly-A sequence;

-  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: 33.40 RPKM in Testis
Total median expression: 33.62 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -89.80194-0.463 Picture PostScript Text
3' UTR -88.90228-0.390 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
IPR022168 - DUF3699

Pfam Domains:
PF12480 - Protein of unknown function (DUF3699)

ModBase Predicted Comparative 3D Structure on Q8N5Q1
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
Gene DetailsGene Details    
Gene SorterGene Sorter    
 RGD    
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Cellular Component:
GO:0005634 nucleus


-  Descriptions from all associated GenBank mRNAs
  AK128284 - Homo sapiens cDNA FLJ46422 fis, clone THYMU3013241.
AL834316 - Homo sapiens mRNA; cDNA DKFZp434G1729 (from clone DKFZp434G1729).
AK127979 - Homo sapiens cDNA FLJ46094 fis, clone TESTI2018687.
JD184449 - Sequence 165473 from Patent EP1572962.
JD056092 - Sequence 37116 from Patent EP1572962.
JD348590 - Sequence 329614 from Patent EP1572962.
JD329538 - Sequence 310562 from Patent EP1572962.
BC031875 - Homo sapiens family with sequence similarity 71, member E2, mRNA (cDNA clone IMAGE:5165573), complete cds.
JD412426 - Sequence 393450 from Patent EP1572962.
JD216925 - Sequence 197949 from Patent EP1572962.
JD451869 - Sequence 432893 from Patent EP1572962.
JD415562 - Sequence 396586 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: C19orf16, ENST00000424985.1, ENST00000424985.2, FAM71E2, GAR5B_HUMAN, GARIN5B , NM_001145402, Q8N5Q1, Q8ND99, uc319ufm.1, uc319ufm.2
UCSC ID: ENST00000424985.3_7
RefSeq Accession: NM_001145402.2
Protein: Q8N5Q1 (aka F71E2_HUMAN)

-  Gene Model Information
  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.