Hmcn1 hemicentin 1 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Hmcn1provided by RGD
Official Full Name: hemicentin 1provided by RGD
Primary source: RGD:1564772
See related: Ensembl:ENSRNOG00000028627 AllianceGenome:RGD:1564772
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Also known as: RGD1564772
Summary: Predicted to enable calcium ion binding activity. Predicted to be involved in synapse organization. Predicted to act upstream of or within response to bacterium. Predicted to be located in several cellular components, including basement membrane; cell cortex; and extracellular region. Predicted to be active in neuron projection membrane. Human ortholog(s) of this gene implicated in age related macular degeneration 1. Orthologous to human HMCN1 (hemicentin 1). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Biased expression in Lung (RPKM 255.6), Spleen (RPKM 214.8) and 8 other tissues See more
Orthologs: human mouse all
NEW: Try the new Gene table
Try the new Transcript table

Genomic context

Location:: 13q21

Exon count:: 108

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	13	NC_086031.1 (65165532..65634681, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	13	NC_051348.1 (62615461..63084524, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	13	NC_005112.4 (67799791..68360664, complement)

Chromosome 13 - NC_086031.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

Go to the top of the page Help

Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

Go to the top of the page Help

See details

Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
BioProject: PRJNA238328
Publication: PMID 24510058
Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

Go to the top of the page Help

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Identify HMCN1 as a new molecule involved in the dynamic changes of podocyte foot processes in glomerular disease.
Title: Hemicentin 1 influences podocyte dynamic changes in glomerular diseases.

Submit: New GeneRIF Correction

Interactions

Go to the top of the page Help

Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

Go to the top of the page Help

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables axon guidance receptor activity	IBA Inferred from Biological aspect of Ancestor more info
enables calcium ion binding	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
involved_in actin cytoskeleton organization	ISO Inferred from Sequence Orthology more info
involved_in axon guidance	IEA Inferred from Electronic Annotation more info
involved_in basement membrane organization	ISO Inferred from Sequence Orthology more info
involved_in homophilic cell adhesion via plasma membrane adhesion molecules	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within response to bacterium	ISO Inferred from Sequence Orthology more info
involved_in synapse organization	IBA Inferred from Biological aspect of Ancestor more info

Component	Evidence Code	Pubs
is_active_in axon	IBA Inferred from Biological aspect of Ancestor more info
located_in basement membrane	ISO Inferred from Sequence Orthology more info
located_in cell cortex	ISO Inferred from Sequence Orthology more info
located_in cell junction	ISO Inferred from Sequence Orthology more info
located_in cytoplasm	ISO Inferred from Sequence Orthology more info
located_in extracellular region	ISO Inferred from Sequence Orthology more info
located_in muscle tendon junction	ISO Inferred from Sequence Orthology more info
is_active_in neuronal cell body	IBA Inferred from Biological aspect of Ancestor more info
is_active_in plasma membrane	IBA Inferred from Biological aspect of Ancestor more info

General protein information

Go to the top of the page Help

Preferred Names: hemicentin-1

NCBI Reference Sequences (RefSeq)

Go to the top of the page Help

NEW Try the new Transcript table

RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

NM_001271292.2 → NP_001258221.1 hemicentin-1 precursor

Status: VALIDATED

Source sequence(s)

JAXUCZ010000013

UniProtKB/TrEMBL

F1M4Q3

Related

ENSRNOP00000094032.1, ENSRNOT00000093469.2

Conserved Domains (13) summary

cd00096
Location:1188 → 1255

Ig; Immunoglobulin domain

smart00408
Location:2493 → 2557

IGc2; Immunoglobulin C-2 Type

smart00179
Location:5432 → 5471

EGF_CA; Calcium-binding EGF-like domain

smart00209
Location:4589 → 4641

TSP1; Thrombospondin type 1 repeats

smart00409
Location:1834 → 1915

IG; Immunoglobulin

smart00410
Location:799 → 884

IG_like; Immunoglobulin like

smart00682
Location:4868 → 5092

G2F; G2 nidogen domain and fibulin

cd00054
Location:5230 → 5263

EGF_CA; Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the ...

pfam07679
Location:2478 → 2567

I-set; Immunoglobulin I-set domain

pfam00047
Location:524 → 606

ig; Immunoglobulin domain

pfam07645
Location:5272 → 5313

EGF_CA; Calcium-binding EGF domain

pfam13519
Location:42 → 212

VWA_2; von Willebrand factor type A domain

cl11960
Location:3244 → 3338

Ig; Immunoglobulin domain

RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCr8

Genomic

NC_086031.1 Reference GRCr8

Range

65165532..65634681 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_039090457.2 → XP_038946385.2 hemicentin-1 isoform X2

UniProtKB/TrEMBL

F1M4Q3
XM_039090458.2 → XP_038946386.2 hemicentin-1 isoform X3

UniProtKB/TrEMBL

F1M4Q3
XM_039090459.2 → XP_038946387.2 hemicentin-1 isoform X4

UniProtKB/TrEMBL

F1M4Q3
XM_039090456.2 → XP_038946384.2 hemicentin-1 isoform X1

UniProtKB/TrEMBL

F1M4Q3
XM_039090460.2 → XP_038946388.2 hemicentin-1 isoform X5

UniProtKB/TrEMBL

F1M4Q3
XM_039090461.2 → XP_038946389.1 hemicentin-1 isoform X6

Conserved Domains (6) summary

smart00408
Location:1843 → 1905

IGc2; Immunoglobulin C-2 Type

cd00198
Location:42 → 198

vWFA; Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of ...

pfam07679
Location:2478 → 2567

I-set; Immunoglobulin I-set domain

pfam13927
Location:3150 → 3228

Ig_3; Immunoglobulin domain

cd00096
Location:451 → 513

Ig; Immunoglobulin domain

cl11960
Location:1262 → 1355

Ig; Immunoglobulin domain