Human Gene HOMER1 (ENST00000508576.5) Description and Page Index
  Description: Homo sapiens homer scaffold protein 1 (HOMER1), transcript variant 3, mRNA. (from RefSeq NM_001277078)
RefSeq Summary (NM_001277078): This gene encodes a member of the homer family of dendritic proteins. Members of this family regulate group 1 metabotrophic glutamate receptor function. [provided by RefSeq, Jul 2008].
Gencode Transcript: ENST00000508576.5
Gencode Gene: ENSG00000152413.15
Transcript (Including UTRs)
   Position: hg38 chr5:79,375,930-79,512,794 Size: 136,865 Total Exon Count: 6 Strand: -
Coding Region
   Position: hg38 chr5:79,376,191-79,512,774 Size: 136,584 Coding Exon Count: 6 

Page IndexSequence and LinksUniProtKB CommentsCTDRNA-Seq ExpressionMicroarray Expression
RNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA DescriptionsPathways
Other NamesMethods
Data last updated: 2019-09-04

-  Sequence and Links to Tools and Databases
Genomic Sequence (chr5:79,375,930-79,512,794)mRNA (may differ from genome)Protein (177 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaBioGPS
CGAPEnsemblEntrez GeneExonPrimerGeneCardsHGNC
Stanford SOURCEUniProtKBWikipedia

-  Comments and Description Text from UniProtKB
DESCRIPTION: RecName: Full=Homer protein homolog 1; Short=Homer-1;
FUNCTION: Postsynaptic density scaffolding protein. Binds and cross-links cytoplasmic regions of GRM1, GRM5, ITPR1, DNM3, RYR1, RYR2, SHANK1 and SHANK3. By physically linking GRM1 and GRM5 with ER-associated ITPR1 receptors, it aids the coupling of surface receptors to intracellular calcium release. May also couple GRM1 to PI3 kinase through its interaction with AGAP2. Isoform 1 regulates the trafficking and surface expression of GRM5. Isoform 3 acts as a natural dominant negative, in dynamic competition with constitutively expressed isoform 1 to regulate synaptic metabotropic glutamate function. Isoform 3, may be involved in the structural changes that occur at synapses during long-lasting neuronal plasticity and development.
SUBUNIT: Interacts with IFT57 (By similarity). Interacts with OPHN1 (By similarity). Isoform 1 encodes a coiled-coil structure that mediates homo- and heteromultimerization.
SUBCELLULAR LOCATION: Cytoplasm (By similarity). Cell junction, synapse, postsynaptic cell membrane, postsynaptic density (By similarity). Cell junction, synapse (By similarity). Note=Postsynaptic density of neuronal cells. Isoform 1 inhibits surface expression of GRM5 causing it to be retained in the endoplasmic reticulum (By similarity).
DOMAIN: The WH1 domain interacts with the PPXXF motif in GRM1, GRM5, RYR1, RYR2, ITPR1, SHANK 1 and SHANK3.
SIMILARITY: Belongs to the Homer family.
SIMILARITY: Contains 1 WH1 domain.

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene
  • D003042 Cocaine
  • D001564 Benzo(a)pyrene
  • D000431 Ethanol
  • D010634 Phenobarbital
  • D013749 Tetrachlorodibenzodioxin
  • C079148 (3-aminopropyl)(n-butyl)phosphinic acid
  • C049325 1,2-dithiol-3-thione
  • C111118 2',3,3',4',5-pentachloro-4-hydroxybiphenyl
  • C093973 2-(2-amino-3-methoxyphenyl)-4H-1-benzopyran-4-one
  • D015123 7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxide
          more ... click here to view the complete list

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 8.13 RPKM in Brain - Frontal Cortex (BA9)
Total median expression: 102.47 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 -0.4020-0.020 Picture PostScript Text
3' UTR -48.20261-0.185 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
IPR000697 - EVH1
IPR010356 - Haemolysin_E
IPR011993 - PH_like_dom

Pfam Domains:
PF00568 - WH1 domain

ModBase Predicted Comparative 3D Structure on Q86YM7
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 BrowserGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
Protein SequenceProtein Sequence    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005515 protein binding
GO:0035256 G-protein coupled glutamate receptor binding
GO:0035591 signaling adaptor activity
GO:0044325 ion channel binding

Biological Process:
GO:0003009 skeletal muscle contraction
GO:0007206 phospholipase C-activating G-protein coupled glutamate receptor signaling pathway
GO:0007268 chemical synaptic transmission
GO:0009967 positive regulation of signal transduction
GO:0048148 behavioral response to cocaine
GO:0048741 skeletal muscle fiber development
GO:0048875 chemical homeostasis within a tissue
GO:0051592 response to calcium ion
GO:0051928 positive regulation of calcium ion transport
GO:0090279 regulation of calcium ion import
GO:2001256 regulation of store-operated calcium entry
GO:2001257 regulation of cation channel activity

Cellular Component:
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0005886 plasma membrane
GO:0014069 postsynaptic density
GO:0016020 membrane
GO:0030018 Z disc
GO:0030054 cell junction
GO:0030424 axon
GO:0043005 neuron projection
GO:0043034 costamere
GO:0045177 apical part of cell
GO:0045202 synapse
GO:0045211 postsynaptic membrane
GO:0098794 postsynapse

-  Descriptions from all associated GenBank mRNAs
  BC047438 - Homo sapiens homer homolog 1 (Drosophila), mRNA (cDNA clone MGC:48496 IMAGE:5294849), complete cds.
AK223471 - Homo sapiens mRNA for homer 1 variant, clone: FCC117H09.
AF093262 - Homo sapiens homer-1b mRNA, complete cds.
BC015502 - Homo sapiens homer homolog 1 (Drosophila), mRNA (cDNA clone MGC:9092 IMAGE:3904242), complete cds.
Y17829 - Homo sapiens mRNA for Homer-related protein Syn47.
AY189939 - Homo sapiens HOMER1E (HOMER1) mRNA, complete cds, alternatively spliced.
AY189940 - Homo sapiens HOMER1F (HOMER1) mRNA, complete cds, alternatively spliced.
AY189941 - Homo sapiens HOMER1H (HOMER1) mRNA, complete cds, alternatively spliced.
AK312481 - Homo sapiens cDNA, FLJ92840, Homo sapiens homer homolog 1 (Drosophila) (HOMER1), mRNA.
BT009846 - Homo sapiens homer homolog 1 (Drosophila) mRNA, complete cds.
DQ891278 - Synthetic construct clone IMAGE:100003908; FLH170684.01X; RZPDo839A05100D homer homolog 1 (Drosophila) (HOMER1) gene, encodes complete protein.
KJ892775 - Synthetic construct Homo sapiens clone ccsbBroadEn_02169 HOMER1 gene, encodes complete protein.
DQ894466 - Synthetic construct Homo sapiens clone IMAGE:100008926; FLH170680.01L; RZPDo839A0599D homer homolog 1 (Drosophila) (HOMER1) gene, encodes complete protein.
CU677321 - Synthetic construct Homo sapiens gateway clone IMAGE:100017079 5' read HOMER1 mRNA.
JD275795 - Sequence 256819 from Patent EP1572962.

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

Protein Q86YM7 (Reactome details) participates in the following event(s):

R-HSA-6794347 Homer1,2,3 dimerizes
R-HSA-6794355 Homer1,2,3 binds mGluR1a,5
R-HSA-6794344 HOMER binds SHANK proteins
R-HSA-6794361 Neurexins and neuroligins
R-HSA-6794362 Protein-protein interactions at synapses
R-HSA-112316 Neuronal System

-  Other Names for This Gene
  Alternate Gene Symbols: B2R688, HOME1_HUMAN, NM_001277078, O96003, Q86YM5, Q86YM7, SYN47, uc010jab.1, uc010jab.2, uc010jab.3, uc010jab.4, uc010jab.5
UCSC ID: uc010jab.5
RefSeq Accession: NM_001277078
Protein: Q86YM7 (aka HOME1_HUMAN or HOM1_HUMAN)
CCDS: CCDS64189.1

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.