Egflam EGF-like, fibronectin type III and laminin G domains [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Egflamprovided by MGI
Official Full Name: EGF-like, fibronectin type III and laminin G domainsprovided by MGI
Primary source: MGI:MGI:2146149
See related: Ensembl:ENSMUSG00000042961 AllianceGenome:MGI:2146149
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Mus musculus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as: 5930412K08
Summary: Enables glycosaminoglycan binding activity. Acts upstream of or within extracellular matrix organization; peptide cross-linking via chondroitin 4-sulfate glycosaminoglycan; and positive regulation of cell-substrate adhesion. Located in basement membrane and interstitial matrix. Is expressed in hair follicle and rib. Orthologous to human EGFLAM (EGF like, fibronectin type III and laminin G domains). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Broad expression in lung adult (RPKM 9.0), ovary adult (RPKM 6.9) and 16 other tissues See more
Orthologs: human all
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Genomic context

Location:: 15 A1; 15 3.5 cM

Exon count:: 25

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	15	NC_000081.7 (7235598..7428203, complement)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	15	NC_000081.6 (7206120..7398744, complement)

Chromosome 15 - NC_000081.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: Mouse ENCODE transcriptome data
Description: RNA profiling data sets generated by the Mouse ENCODE project.
BioProject: PRJNA66167
Publication: PMID 25409824
Analysis date: n/a

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Pikachurin Protein Required for Increase of Cone Electroretinogram B-Wave during Light Adaptation
Title: Pikachurin Protein Required for Increase of Cone Electroretinogram B-Wave during Light Adaptation.
data suggest the existence of post-translational cleavage of pikachurin protein as well as the extracellular localization of cleaved protein specifically by retinal cells
Title: Cell specific post-translational processing of pikachurin, a protein involved in retinal synaptogenesis.
These results indicate that pikachurin interactions with alpha-dystroglycan and its localization at the photoreceptor ribbon synapse require normal glycosylation of alpha-dystroglycan.
Title: Pikachurin interaction with dystroglycan is diminished by defective O-mannosyl glycosylation in congenital muscular dystrophy models and rescued by LARGE overexpression.
Post-translational maturation of dystroglycan is necessary for pikachurin binding and ribbon synaptic localization.
Title: Post-translational maturation of dystroglycan is necessary for pikachurin binding and ribbon synaptic localization.

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Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics (MGI)

Targeted (1) 1 citation
Endonuclease-mediated (1)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

NoName (e-PCR)
- UniSTS:237262

AU040377 (e-PCR)
- UniSTS:180733

Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables calcium ion binding	IEA Inferred from Electronic Annotation more info
enables glycosaminoglycan binding	IDA Inferred from Direct Assay more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
acts_upstream_of_or_within extracellular matrix organization	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within positive regulation of cell-substrate adhesion	IDA Inferred from Direct Assay more info	PubMed

Component	Evidence Code	Pubs
located_in basement membrane	IDA Inferred from Direct Assay more info	PubMed
located_in cell projection	IEA Inferred from Electronic Annotation more info
located_in extracellular matrix	IDA Inferred from Direct Assay more info	PubMed
located_in extracellular region	IEA Inferred from Electronic Annotation more info
located_in interstitial matrix	IDA Inferred from Direct Assay more info	PubMed
is_active_in photoreceptor ribbon synapse	IDA Inferred from Direct Assay more info	PubMed
located_in synapse	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: pikachurin

Names: EGF-like, fibronectin type-III and laminin G-like domain-containing protein; nectican

NCBI Reference Sequences (RefSeq)

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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_001289496.2 → NP_001276425.1 pikachurin isoform 1 precursor

See identical proteins and their annotated locations for NP_001276425.1

Status: VALIDATED

Description

Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform.

Source sequence(s)

AC109195, AC158747

Consensus CDS

CCDS79359.1

UniProtKB/Swiss-Prot

B2RWU6, B6JU28, Q4VBE4, Q80WX4, Q8BGP3

Related

ENSMUSP00000094238.5, ENSMUST00000096494.5

Conserved Domains (4) summary

cd00054
Location:790 → 820

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 ...

cd00063
Location:36 → 133

FN3; Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all ...

cd00110
Location:391 → 541

LamG; Laminin G domain; Laminin G-like domains are usually Ca++ mediated receptors that can have binding sites for steroids, beta1 integrins, heparin, sulfatides, fibulin-1, and alpha-dystroglycans. Proteins that contain LamG domains serve a variety of ...

pfam02210
Location:868 → 993

Laminin_G_2; Laminin G domain
NM_001289498.1 → NP_001276427.1 pikachurin isoform 3

Status: VALIDATED

Description

Transcript Variant: This variant (3) uses an alternate splice site in the 5' UTR and has multiple coding region differnces compared to variant 1. These differences result in the use of an alternate AUG compared to variant 1. The encoded isoform (3) is shorter and has a distinct N-terminus compared to isoform 1.

Source sequence(s)

AC158747, AK158909

Conserved Domains (4) summary

cd00054
Location:640 → 670

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 ...

cd00063
Location:30 → 86

FN3; Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all ...

cd00110
Location:241 → 391

LamG; Laminin G domain; Laminin G-like domains are usually Ca++ mediated receptors that can have binding sites for steroids, beta1 integrins, heparin, sulfatides, fibulin-1, and alpha-dystroglycans. Proteins that contain LamG domains serve a variety of ...

pfam02210
Location:718 → 843

Laminin_G_2; Laminin G domain
NM_001416486.1 → NP_001403415.1 pikachurin isoform 4 precursor

Status: VALIDATED

Source sequence(s)

AC109195, AC158747
NM_001416487.1 → NP_001403416.1 pikachurin isoform 2 precursor

Status: VALIDATED

Source sequence(s)

AC109195, AC158747
NM_001416488.1 → NP_001403417.1 pikachurin isoform 3

Status: VALIDATED

Source sequence(s)

AC109195, AC158747
NM_001416489.1 → NP_001403418.1 pikachurin isoform 5

Status: VALIDATED

Source sequence(s)

AC109195, AC158747
NM_001416490.1 → NP_001403419.1 pikachurin isoform 5

Status: VALIDATED

Source sequence(s)

AC105969, AC109195, AC158747
NM_001416491.1 → NP_001403420.1 pikachurin isoform 5

Status: VALIDATED

Source sequence(s)

AC109195, AC158747
NM_001416492.1 → NP_001403421.1 pikachurin isoform 5

Status: VALIDATED

Source sequence(s)

AC109195, AC158747
NM_001416493.1 → NP_001403422.1 pikachurin isoform 5

Status: VALIDATED

Source sequence(s)

AC109195, AC158747
NM_001416494.1 → NP_001403423.1 pikachurin isoform 5

Status: VALIDATED

Source sequence(s)

AC109195, AC158747
NM_001416495.1 → NP_001403424.1 pikachurin isoform 6

Status: VALIDATED

Source sequence(s)

AC109195, AC158747
NM_001416496.1 → NP_001403425.1 pikachurin isoform 7

Status: VALIDATED

Source sequence(s)

AC109195, AC158747
NM_178748.7 → NP_848863.1 pikachurin isoform 2 precursor

See identical proteins and their annotated locations for NP_848863.1

Status: VALIDATED

Description

Transcript Variant: This variant (2) lacks an exon in the 3' coding region comapred to variant 1. The encoded isoform (2) is shorter than isoform 1.

Source sequence(s)

AC109195, AC158747

Consensus CDS

CCDS27370.1

UniProtKB/Swiss-Prot

Q4VBE4

Related

ENSMUSP00000055599.4, ENSMUST00000058593.10

Conserved Domains (4) summary

cd00054
Location:790 → 820

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 ...

cd00063
Location:36 → 133

FN3; Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all ...

cd00110
Location:391 → 541

LamG; Laminin G domain; Laminin G-like domains are usually Ca++ mediated receptors that can have binding sites for steroids, beta1 integrins, heparin, sulfatides, fibulin-1, and alpha-dystroglycans. Proteins that contain LamG domains serve a variety of ...

pfam02210
Location:860 → 985

Laminin_G_2; Laminin G domain

RNA

NR_184054.1 RNA Sequence

Status: VALIDATED

Source sequence(s)

AC109195, AC158747

RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

Reference GRCm39 C57BL/6J

Genomic

NC_000081.7 Reference GRCm39 C57BL/6J

Range

7235598..7428203 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_036159432.1 → XP_036015325.1 pikachurin isoform X3

Conserved Domains (4) summary

cd00054
Location:640 → 670

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 ...

cd00063
Location:30 → 86

FN3; Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all ...

cd00110
Location:241 → 391

LamG; Laminin G domain; Laminin G-like domains are usually Ca++ mediated receptors that can have binding sites for steroids, beta1 integrins, heparin, sulfatides, fibulin-1, and alpha-dystroglycans. Proteins that contain LamG domains serve a variety of ...

pfam02210
Location:710 → 835

Laminin_G_2; Laminin G domain
XM_036159431.1 → XP_036015324.1 pikachurin isoform X2

Conserved Domains (1) summary

pfam02210
Location:3 → 128

Laminin_G_2; Laminin G domain