Human Gene GFER (uc002cob.1)
  Description: erv1-like growth factor
RefSeq Summary (NM_005262): The hepatotrophic factor designated augmenter of liver regeneration (ALR) is thought to be one of the factors responsible for the extraordinary regenerative capacity of mammalian liver. It has also been called hepatic regenerative stimulation substance (HSS). The gene resides on chromosome 16 in the interval containing the locus for polycystic kidney disease (PKD1). The putative gene product is 42% similar to the scERV1 protein of yeast. The yeast scERV1 gene had been found to be essential for oxidative phosphorylation, the maintenance of mitochondrial genomes, and the cell division cycle. The human gene is both the structural and functional homolog of the yeast scERV1 gene. [provided by RefSeq, Jul 2008].
Transcript (Including UTRs)
   Position: hg18 chr16:1,974,151-1,977,751 Size: 3,601 Total Exon Count: 3 Strand: +
Coding Region
   Position: hg18 chr16:1,974,221-1,976,030 Size: 1,810 Coding Exon Count: 3 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDMicroarray Expression
RNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA DescriptionsOther Names
Model InformationMethods
Data last updated at UCSC: 2009-03-03

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr16:1,974,151-1,977,751)mRNA (may differ from genome)Protein (205 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
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PubMedTreefamUniProtKBBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: ALR_HUMAN
DESCRIPTION: RecName: Full=FAD-linked sulfhydryl oxidase ALR; EC=1.8.3.2; AltName: Full=Augmenter of liver regeneration; Short=hERV1; AltName: Full=Hepatopoietin;
FUNCTION: Isoform 1: FAD-dependent sulfhydryl oxidase. Within the mitochondrial intermembrane space, participates in a chain of disulfide exchange reactions with MIA40, that generate disulfide bonds in a number of resident proteins with twin Cx3C and Cx9C motifs.
FUNCTION: Isoform 2: May act as an autocrine hepatotrophic growth factor promoting liver regeneration.
CATALYTIC ACTIVITY: 2 R'C(R)SH + O(2) = R'C(R)S-S(R)CR' + H(2)O(2).
COFACTOR: FAD.
SUBUNIT: Homodimer; disulfide-linked. May form heterodimers of isoform 1 and isoform 2.
SUBCELLULAR LOCATION: Isoform 1: Mitochondrion intermembrane space.
SUBCELLULAR LOCATION: Isoform 2: Cytoplasm. Secreted.
TISSUE SPECIFICITY: Ubiquitously expressed. Highest expression in the testis and liver and low expression in the muscle.
DISEASE: Defects in GFER are a cause of mitochondrial progressive myopathy with congenital cataract hearing loss and developmental delay (MPMCHD) [MIM:613076]; also called combined mitochondrial complex deficiency.
SIMILARITY: Contains 1 ERV/ALR sulfhydryl oxidase domain.
SEQUENCE CAUTION: Sequence=AAA96390.2; Type=Frameshift; Positions=70; Sequence=AAD36986.1; Type=Erroneous initiation; Sequence=AAD56538.1; Type=Erroneous initiation; Sequence=AAH02429.1; Type=Erroneous initiation; Sequence=AAH28348.2; Type=Erroneous initiation;

-  Primer design for this transcript
 

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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           more ... click here to view the complete list

-  Microarray Expression Data
 
Expression ratio colors:

GNF Expression Atlas 2 Data from U133A and GNF1H Chips

      
      
      
     
    
     
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Affymetrix All Exon Microarrays

           
Ratios

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -29.5070-0.421 Picture PostScript Text
3' UTR -791.451721-0.460 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
IPR017905 - ERV/ALR_sulphydryl_oxidase
IPR006863 - Evr1_Alr

Pfam Domains:
PF04777 - Erv1 / Alr family

SCOP Domains:
69000 - FAD-dependent thiol oxidase

Protein Data Bank (PDB) 3-D Structure
MuPIT help
3MBG - X-ray 3O55 - X-ray 3TK0 - X-ray 3U2L - X-ray 3U2M - X-ray


ModBase Predicted Comparative 3D Structure on P55789
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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
Genome BrowserNo orthologNo orthologGenome BrowserGenome BrowserGenome Browser
Gene DetailsGene Details Gene DetailsGene DetailsGene Details
Gene SorterGene Sorter Gene SorterGene SorterGene Sorter
MGIRGD FlyBaseWormBaseSGD
Protein Sequence  Protein SequenceProtein SequenceProtein Sequence
Alignment  AlignmentAlignmentAlignment

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005515 protein binding
GO:0008083 growth factor activity
GO:0015035 protein disulfide oxidoreductase activity
GO:0016491 oxidoreductase activity
GO:0016971 flavin-linked sulfhydryl oxidase activity
GO:0016972 thiol oxidase activity
GO:0050660 flavin adenine dinucleotide binding

Biological Process:
GO:0001889 liver development
GO:0010469 regulation of receptor activity
GO:0055114 oxidation-reduction process

Cellular Component:
GO:0005576 extracellular region
GO:0005737 cytoplasm
GO:0005739 mitochondrion
GO:0005758 mitochondrial intermembrane space
GO:0005829 cytosol


-  Descriptions from all associated GenBank mRNAs
  KJ901451 - Synthetic construct Homo sapiens clone ccsbBroadEn_10845 GFER gene, encodes complete protein.
KR711146 - Synthetic construct Homo sapiens clone CCSBHm_00020805 GFER (GFER) mRNA, encodes complete protein.
AB528688 - Synthetic construct DNA, clone: pF1KB6917, Homo sapiens GFER gene for growth factor, augmenter of liver regeneration, without stop codon, in Flexi system.
AF306863 - Homo sapiens hepatopoietin protein mRNA, complete cds.
BC002429 - Homo sapiens growth factor, augmenter of liver regeneration, mRNA (cDNA clone MGC:1445 IMAGE:3346679), complete cds.
BC028348 - Homo sapiens growth factor, augmenter of liver regeneration, mRNA (cDNA clone MGC:15249 IMAGE:3636052), complete cds.
AF124604 - Homo sapiens hepatopoietin HPO2 mRNA, complete cds.
U31176 - Homo sapiens ERV1 (ERV1) mRNA, complete cds.
AF208342 - Homo sapiens truncated augmenter of liver regeneration (ALR) mRNA, ALR-95 allele, complete cds.
AY550027 - Homo sapiens augmenter of liver regeneration mRNA, complete cds.
AF124603 - Homo sapiens hepatopoietin HPO1 mRNA, partial cds.
JD449161 - Sequence 430185 from Patent EP1572962.
JD373864 - Sequence 354888 from Patent EP1572962.
JD373865 - Sequence 354889 from Patent EP1572962.
JD399325 - Sequence 380349 from Patent EP1572962.
JD452544 - Sequence 433568 from Patent EP1572962.
JD436094 - Sequence 417118 from Patent EP1572962.
JD411578 - Sequence 392602 from Patent EP1572962.
JD418481 - Sequence 399505 from Patent EP1572962.
JD473560 - Sequence 454584 from Patent EP1572962.
JD555807 - Sequence 536831 from Patent EP1572962.
JD485524 - Sequence 466548 from Patent EP1572962.
JD485525 - Sequence 466549 from Patent EP1572962.
JD481296 - Sequence 462320 from Patent EP1572962.
JD473072 - Sequence 454096 from Patent EP1572962.
JD484501 - Sequence 465525 from Patent EP1572962.
JD265097 - Sequence 246121 from Patent EP1572962.
JD101521 - Sequence 82545 from Patent EP1572962.
JD131930 - Sequence 112954 from Patent EP1572962.
JD059866 - Sequence 40890 from Patent EP1572962.
JD120145 - Sequence 101169 from Patent EP1572962.
JD104215 - Sequence 85239 from Patent EP1572962.
JD098658 - Sequence 79682 from Patent EP1572962.
JD262013 - Sequence 243037 from Patent EP1572962.
JD272353 - Sequence 253377 from Patent EP1572962.
JD117375 - Sequence 98399 from Patent EP1572962.
JD037333 - Sequence 18357 from Patent EP1572962.
JD147591 - Sequence 128615 from Patent EP1572962.
JD280581 - Sequence 261605 from Patent EP1572962.
JD195649 - Sequence 176673 from Patent EP1572962.
JD147463 - Sequence 128487 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: NM_005262, NP_005253, Q53YM6, Q53YM6_HUMAN
UCSC ID: uc002cob.1
RefSeq Accession: NM_005262
Protein: P55789 (aka ALR_HUMAN)
CCDS: CCDS32368.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_005262.2
exon count: 3CDS single in 3' UTR: no RNA size: 2447
ORF size: 618CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 1429.00frame shift in genome: no % Coverage: 98.45
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.