Human Gene HERPUD1 (uc002eke.2) Description and Page Index
  Description: Homo sapiens homocysteine-inducible, endoplasmic reticulum stress-inducible, ubiquitin-like domain member 1 (HERPUD1), transcript variant 1, mRNA.
RefSeq Summary (NM_014685): The accumulation of unfolded proteins in the endoplasmic reticulum (ER) triggers the ER stress response. This response includes the inhibition of translation to prevent further accumulation of unfolded proteins, the increased expression of proteins involved in polypeptide folding, known as the unfolded protein response (UPR), and the destruction of misfolded proteins by the ER-associated protein degradation (ERAD) system. This gene may play a role in both UPR and ERAD. Its expression is induced by UPR and it has an ER stress response element in its promoter region while the encoded protein has an N-terminal ubiquitin-like domain which may interact with the ERAD system. This protein has been shown to interact with presenilin proteins and to increase the level of amyloid-beta protein following its overexpression. Alternative splicing of this gene produces multiple transcript variants encoding different isoforms. The full-length nature of all transcript variants has not been determined. [provided by RefSeq, Jan 2013].
Transcript (Including UTRs)
   Position: hg19 chr16:56,966,002-56,977,793 Size: 11,792 Total Exon Count: 8 Strand: +
Coding Region
   Position: hg19 chr16:56,966,157-56,977,202 Size: 11,046 Coding Exon Count: 8 

Page IndexSequence and LinksUniProtKB CommentsGenetic AssociationsCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr16:56,966,002-56,977,793)mRNA (may differ from genome)Protein (391 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCHPRDLynxMGI
neXtProtOMIMPubMedReactomeStanford SOURCEUniProtKB
Wikipedia

-  Comments and Description Text from UniProtKB
  ID: HERP1_HUMAN
DESCRIPTION: RecName: Full=Homocysteine-responsive endoplasmic reticulum-resident ubiquitin-like domain member 1 protein; AltName: Full=Methyl methanesulfonate (MMF)-inducible fragment protein 1;
FUNCTION: Component of the endoplasmic reticulum quality control (ERQC) system also called ER-associated degradation (ERAD) involved in ubiquitin-dependent degradation of misfolded endoplasmic reticulum proteins. Could enhance presenilin-mediated beta-amyloid protein 40 generation.
SUBUNIT: Interacts with PSEN1 and PSEN2. Interacts with SYVN1 and UBXN6.
SUBCELLULAR LOCATION: Endoplasmic reticulum membrane; Multi-pass membrane protein.
TISSUE SPECIFICITY: Widely expressed; in the brain, expression seems to be restricted to neurons and vascular smooth muscle cells. Present in activated microglia in senile plaques in the brain of patients with Alzheimer disease.
INDUCTION: Up-regulated by endoplasmic reticulum stress and CREB3.
MISCELLANEOUS: Although the precise topology is not known, experimental data suggest that both the N- and C-termini face the cytosol.
SIMILARITY: Contains 1 ubiquitin-like domain.

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): HERPUD1
CDC HuGE Published Literature: HERPUD1
Positive Disease Associations: 1-Alkyl-2-acetylglycerophosphocholine Esterase , Cardiovascular Diseases , Cholesterol , Cholesterol, HDL , Cholesterol, LDL , HDL cholesterol , Lipid Metabolism , Lipids , Lipoproteins, HDL , Macular Degeneration , Metabolic Syndrome X , Triglycerides
Related Studies:
  1. 1-Alkyl-2-acetylglycerophosphocholine Esterase
    Harald Grallert et al. European heart journal 2012, Eight genetic loci associated with variation in lipoprotein-associated phospholipase A2 mass and activity and coronary heart disease: meta-analysis of genome-wide association studies from five community-based studies., European heart journal. [PubMed 22003152]
    Levels of Lp-PLA2 mass and activity were associated with PLA2G7, the gene coding for this protein. Lipoprotein-associated phospholipase A2 activity was also strongly associated with genetic variants related to low-density lipoprotein cholesterol levels.
  2. Cardiovascular Diseases
    Erin N Smith et al. PLoS genetics 2010, Longitudinal genome-wide association of cardiovascular disease risk factors in the Bogalusa heart study., PLoS genetics. [PubMed 20838585]
  3. Cholesterol
    Tanya M Teslovich et al. Nature 2010, Biological, clinical and population relevance of 95 loci for blood lipids., Nature. [PubMed 20686565]
           more ... click here to view the complete list

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  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: 136.13 RPKM in Prostate
Total median expression: 2641.29 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 -75.40155-0.486 Picture PostScript Text
3' UTR -169.86591-0.287 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
IPR000626 - Ubiquitin
IPR019955 - Ubiquitin_supergroup

Pfam Domains:
PF00240 - Ubiquitin family

SCOP Domains:
54236 - Ubiquitin-like

Protein Data Bank (PDB) 3-D Structure
MuPIT help

1WGD
- NMR MuPIT


ModBase Predicted Comparative 3D Structure on Q15011
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 orthologGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 RGD    
 Protein Sequence    
 Alignment    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003674 molecular_function
GO:0005515 protein binding
GO:0044325 ion channel binding

Biological Process:
GO:0006511 ubiquitin-dependent protein catabolic process
GO:0006874 cellular calcium ion homeostasis
GO:0006986 response to unfolded protein
GO:0030968 endoplasmic reticulum unfolded protein response
GO:0030970 retrograde protein transport, ER to cytosol
GO:0031396 regulation of protein ubiquitination
GO:0032092 positive regulation of protein binding
GO:0032469 endoplasmic reticulum calcium ion homeostasis
GO:0034976 response to endoplasmic reticulum stress
GO:0036499 PERK-mediated unfolded protein response
GO:0043154 negative regulation of cysteine-type endopeptidase activity involved in apoptotic process
GO:1902235 regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway
GO:1902236 negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway
GO:1903069 regulation of ER-associated ubiquitin-dependent protein catabolic process
GO:1903071 positive regulation of ER-associated ubiquitin-dependent protein catabolic process
GO:2001243 negative regulation of intrinsic apoptotic signaling pathway

Cellular Component:
GO:0005783 endoplasmic reticulum
GO:0005789 endoplasmic reticulum membrane
GO:0016020 membrane
GO:0016021 integral component of membrane
GO:0034704 calcium channel complex
GO:1990037 Lewy body core


-  Descriptions from all associated GenBank mRNAs
  LF208231 - JP 2014500723-A/15734: Polycomb-Associated Non-Coding RNAs.
AK302167 - Homo sapiens cDNA FLJ54200 complete cds, highly similar to Homocysteine-responsive endoplasmic reticulum-resident ubiquitin-like domain member 1protein.
AK304800 - Homo sapiens cDNA FLJ61088 complete cds, highly similar to Homocysteine-responsive endoplasmic reticulum-resident ubiquitin-like domain member 1 protein.
AK291565 - Homo sapiens cDNA FLJ76864 complete cds, highly similar to Homo sapiens homocysteine-inducible, endoplasmic reticulumstress-inducible, ubiquitin-like domain member 1 (HERPUD1), mRNA.
AK292088 - Homo sapiens cDNA FLJ78602 complete cds, highly similar to Homo sapiens homocysteine-inducible, endoplasmic reticulum stress-inducible, ubiquitin-like domain member 1 (HERPUD1), transcript variant 1, mRNA.
AB034989 - Homo sapiens HERPUD1 mRNA for stress protein Herp, complete cds.
AK223233 - Homo sapiens mRNA for homocysteine-inducible, endoplasmic reticulum stress-inducible, ubiquitin-like domain member 1 variant, clone: STM01396.
BC009739 - Homo sapiens homocysteine-inducible, endoplasmic reticulum stress-inducible, ubiquitin-like domain member 1, mRNA (cDNA clone MGC:14571 IMAGE:4095997), complete cds.
DQ837586 - Homo sapiens homocysteine-inducible endoplasmic reticulum stress-inducible ubiquitin-like domain member 1 protein (HERPUD1) mRNA, complete cds, alternatively spliced.
JD173719 - Sequence 154743 from Patent EP1572962.
AF055001 - Homo sapiens clone 24560 unknown mRNA, complete cds.
D14695 - Homo sapiens KIAA0025 mRNA, complete cds.
BC000086 - Homo sapiens homocysteine-inducible, endoplasmic reticulum stress-inducible, ubiquitin-like domain member 1, mRNA (cDNA clone MGC:2246 IMAGE:3504515), complete cds.
BC008320 - Homo sapiens homocysteine-inducible, endoplasmic reticulum stress-inducible, ubiquitin-like domain member 1, mRNA (cDNA clone MGC:15680 IMAGE:3350209), complete cds.
BC032673 - Homo sapiens homocysteine-inducible, endoplasmic reticulum stress-inducible, ubiquitin-like domain member 1, mRNA (cDNA clone MGC:45131 IMAGE:5575914), complete cds.
JD406078 - Sequence 387102 from Patent EP1572962.
AB383712 - Synthetic construct DNA, clone: pF1KSDA0025, Homo sapiens HERPUD1 gene for homocysteine-responsive endoplasmic reticulum-resident ubiquitin-like domain member 1 protein, complete cds, without stop codon, in Flexi system.
DQ891867 - Synthetic construct clone IMAGE:100004497; FLH180738.01X; RZPDo839F06134D homocysteine-inducible, endoplasmic reticulum stress-inducible, ubiquitin-like domain member 1 (HERPUD1) gene, encodes complete protein.
EU176642 - Synthetic construct Homo sapiens clone IMAGE:100011441; FLH180737.01L; RZPDo839H09254D homocysteine-inducible, endoplasmic reticulum stress-inducible, ubiquitin-like domain member 1 (HERPUD1) gene, encodes complete protein.
KJ892836 - Synthetic construct Homo sapiens clone ccsbBroadEn_02230 HERPUD1 gene, encodes complete protein.
CR457116 - Homo sapiens full open reading frame cDNA clone RZPDo834F1012D for gene HERPUD1, homocysteine-inducible, endoplasmic reticulum stress-inducible, ubiquitin-like domain member 1; complete cds, incl. stopcodon.
KU720377 - Homo sapiens homocysteine-inducible endoplasmic reticulum stress-inducible ubiquitin-like domain member 1 isoform 1 (HERPUD1) mRNA, complete cds.
AF055003 - Homo sapiens clone 24414 unknown mRNA, partial cds.
AF217990 - Homo sapiens clone PP1722 unknown mRNA.
LF373667 - JP 2014500723-A/181170: Polycomb-Associated Non-Coding RNAs.
LF373668 - JP 2014500723-A/181171: Polycomb-Associated Non-Coding RNAs.
LF373672 - JP 2014500723-A/181175: Polycomb-Associated Non-Coding RNAs.
JD020162 - Sequence 1186 from Patent EP1572962.
JD033193 - Sequence 14217 from Patent EP1572962.
JD132758 - Sequence 113782 from Patent EP1572962.
JD067000 - Sequence 48024 from Patent EP1572962.
JD549132 - Sequence 530156 from Patent EP1572962.
JD166255 - Sequence 147279 from Patent EP1572962.
MA443808 - JP 2018138019-A/15734: Polycomb-Associated Non-Coding RNAs.
MA609244 - JP 2018138019-A/181170: Polycomb-Associated Non-Coding RNAs.
MA609245 - JP 2018138019-A/181171: Polycomb-Associated Non-Coding RNAs.
MA609249 - JP 2018138019-A/181175: Polycomb-Associated Non-Coding RNAs.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein Q15011 (Reactome details) participates in the following event(s):

R-HSA-380994 ATF4 activates genes
R-HSA-381042 PERK regulates gene expression
R-HSA-381119 Unfolded Protein Response (UPR)
R-HSA-392499 Metabolism of proteins

-  Other Names for This Gene
  Alternate Gene Symbols: HERP, HERP1_HUMAN, KIAA0025, MIF1, NM_014685, NP_055500, O60644, Q15011, Q6IAN8, Q96D92, uc002eke.1
UCSC ID: uc002eke.2
RefSeq Accession: NM_014685
Protein: Q15011 (aka HERP1_HUMAN)
CCDS: CCDS10771.1, CCDS45492.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_014685.3
exon count: 8CDS single in 3' UTR: no RNA size: 1944
ORF size: 1176CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 2552.00frame shift in genome: no % Coverage: 98.87
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.