Tmtc3 transmembrane and tetratricopeptide repeat containing 3 [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Tmtc3provided by MGI
Official Full Name: transmembrane and tetratricopeptide repeat containing 3provided by MGI
Primary source: MGI:MGI:3036255
See related: Ensembl:ENSMUSG00000036676 AllianceGenome:MGI:3036255
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: mSmile; 9130014E20Rik; B130008E12Rik
Summary: Predicted to enable dolichyl-phosphate-mannose-protein mannosyltransferase activity. Acts upstream of or within several processes, including lung development; muscle cell development; and post-embryonic development. Predicted to be located in membrane. Predicted to be active in endoplasmic reticulum. Is expressed in several structures, including central nervous system; embryo mesenchyme; genitourinary system; gut; and respiratory system. Human ortholog(s) of this gene implicated in lissencephaly 8. Orthologous to human TMTC3 (transmembrane O-mannosyltransferase targeting cadherins 3). [provided by Alliance of Genome Resources, Nov 2024]
Expression: Ubiquitous expression in limb E14.5 (RPKM 3.8), bladder adult (RPKM 3.8) and 28 other tissues See more
Orthologs: human all
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Genomic context

Location:: 10 D1; 10 51.47 cM

Exon count:: 17

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	10	NC_000076.7 (100279764..100323230, complement)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	10	NC_000076.6 (100443902..100487365, complement)

Chromosome 10 - NC_000076.7 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 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?

Our data suggest that loss of TMTC3 causes cobblestone lissencephaly with minimal eye or muscle involvement.
Title: Biallelic Mutations in TMTC3, Encoding a Transmembrane and TPR-Containing Protein, Lead to Cobblestone Lissencephaly.

Submit: New GeneRIF Correction

Variation

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Alleles

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

Gene trapped (1)
Targeted (2)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables dolichyl-phosphate-mannose-protein mannosyltransferase activity	ISO Inferred from Sequence Orthology more info
enables dolichyl-phosphate-mannose-protein mannosyltransferase activity	ISS Inferred from Sequence or Structural Similarity more info
enables mannosyltransferase activity	IBA Inferred from Biological aspect of Ancestor more info

Process	Evidence Code	Pubs
acts_upstream_of_or_within bud outgrowth involved in lung branching	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within cell differentiation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within lung alveolus development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within lung development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within muscle cell development	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of proteasomal protein catabolic process	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of proteasomal protein catabolic process	ISS Inferred from Sequence or Structural Similarity more info
acts_upstream_of_or_within post-embryonic development	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in protein O-linked mannosylation	IBA Inferred from Biological aspect of Ancestor more info
involved_in protein O-linked mannosylation	ISO Inferred from Sequence Orthology more info
involved_in protein O-linked mannosylation	ISS Inferred from Sequence or Structural Similarity more info
acts_upstream_of_or_within regulation of gene expression	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in response to endoplasmic reticulum stress	ISO Inferred from Sequence Orthology more info
involved_in response to endoplasmic reticulum stress	ISS Inferred from Sequence or Structural Similarity more info

Component	Evidence Code	Pubs
is_active_in endoplasmic reticulum	IBA Inferred from Biological aspect of Ancestor more info
located_in endoplasmic reticulum	ISO Inferred from Sequence Orthology more info
located_in endoplasmic reticulum	ISS Inferred from Sequence or Structural Similarity more info
located_in membrane	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: protein O-mannosyl-transferase TMTC3

Names: transmembrane O-mannosyltransferase targeting cadherins 3; transmembrane and TPR repeat-containing protein 3

NP_001028504.1

EC 2.4.1.109

NP_001103483.1

EC 2.4.1.109

XP_006513693.1

EC 2.4.1.109

XP_011241751.1

EC 2.4.1.109

XP_011241752.1

EC 2.4.1.109

XP_017169426.1

EC 2.4.1.109

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_001033332.2 → NP_001028504.1 protein O-mannosyl-transferase TMTC3 isoform 2

See identical proteins and their annotated locations for NP_001028504.1

Status: VALIDATED

Description

Transcript Variant: This variant (2) uses an alternate splice site in the 3' coding region, creating a novel segment containing a premature stop codon when compared to variant 1. This results in a shorter protein (isoform 2) with a distinct C-terminus, compared to isoform 1.

Source sequence(s)

AK165838

Consensus CDS

CCDS24150.1

UniProtKB/TrEMBL

A0A0R4J173

Related

ENSMUSP00000096921.4, ENSMUST00000099318.10

Conserved Domains (4) summary

sd00006
Location:535 → 562

TPR; TPR repeat [structural motif]

pfam00515
Location:602 → 635

TPR_1; Tetratricopeptide repeat

pfam08409
Location:263 → 336

DUF1736; Domain of unknown function (DUF1736)

pfam13414
Location:569 → 633

TPR_11; TPR repeat
NM_001110013.1 → NP_001103483.1 protein O-mannosyl-transferase TMTC3 isoform 1

See identical proteins and their annotated locations for NP_001103483.1

Status: VALIDATED

Description

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

Source sequence(s)

AC153501, AK149759, AK165838

Consensus CDS

CCDS48684.1

UniProtKB/Swiss-Prot

Q3TMN6, Q8BRH0

UniProtKB/TrEMBL

G5E8C4

Related

ENSMUSP00000061470.9, ENSMUST00000058154.15

Conserved Domains (3) summary

TIGR02917
Location:448 → 807

PEP_TPR_lipo; putative PEP-CTERM system TPR-repeat lipoprotein

sd00006
Location:535 → 562

TPR; TPR repeat [structural motif]

pfam08409
Location:263 → 336

DUF1736; Domain of unknown function (DUF1736)

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_000076.7 Reference GRCm39 C57BL/6J

Range

100279764..100323230 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_011243450.4 → XP_011241752.1 protein O-mannosyl-transferase TMTC3 isoform X1

See identical proteins and their annotated locations for XP_011241752.1

UniProtKB/Swiss-Prot

Q3TMN6, Q8BRH0

UniProtKB/TrEMBL

G5E8C4

Conserved Domains (3) summary

TIGR02917
Location:448 → 807

PEP_TPR_lipo; putative PEP-CTERM system TPR-repeat lipoprotein

sd00006
Location:535 → 562

TPR; TPR repeat [structural motif]

pfam08409
Location:263 → 336

DUF1736; Domain of unknown function (DUF1736)
XM_006513630.5 → XP_006513693.1 protein O-mannosyl-transferase TMTC3 isoform X1

See identical proteins and their annotated locations for XP_006513693.1

UniProtKB/Swiss-Prot

Q3TMN6, Q8BRH0

UniProtKB/TrEMBL

G5E8C4

Conserved Domains (3) summary

TIGR02917
Location:448 → 807

PEP_TPR_lipo; putative PEP-CTERM system TPR-repeat lipoprotein

sd00006
Location:535 → 562

TPR; TPR repeat [structural motif]

pfam08409
Location:263 → 336

DUF1736; Domain of unknown function (DUF1736)
XM_011243449.4 → XP_011241751.1 protein O-mannosyl-transferase TMTC3 isoform X1

See identical proteins and their annotated locations for XP_011241751.1

UniProtKB/Swiss-Prot

Q3TMN6, Q8BRH0

UniProtKB/TrEMBL

G5E8C4

Conserved Domains (3) summary

TIGR02917
Location:448 → 807

PEP_TPR_lipo; putative PEP-CTERM system TPR-repeat lipoprotein

sd00006
Location:535 → 562

TPR; TPR repeat [structural motif]

pfam08409
Location:263 → 336

DUF1736; Domain of unknown function (DUF1736)
XM_017313937.3 → XP_017169426.1 protein O-mannosyl-transferase TMTC3 isoform X2

Conserved Domains (2) summary

TIGR02917
Location:68 → 353

PEP_TPR_lipo; putative PEP-CTERM system TPR-repeat lipoprotein

sd00006
Location:75 → 102

TPR; TPR repeat [structural motif]