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TMTC4 transmembrane O-mannosyltransferase targeting cadherins 4 [ Homo sapiens (human) ]

Gene ID: 84899, updated on 12-Oct-2019

Summary

Official Symbol
TMTC4provided by HGNC
Official Full Name
transmembrane O-mannosyltransferase targeting cadherins 4provided by HGNC
Primary source
HGNC:HGNC:25904
See related
Ensembl:ENSG00000125247 MIM:618203
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Summary
This gene encodes a transmembrane protein that belongs to family of proteins containing an N-terminal transmembrane domain and a C-terminal tetratricopeptide repeat (TPR) domain. TPR domains mediate protein-protein interactions in various cellular processes, such as synaptic vesicle fusion, protein folding, and protein translocation. A pseudogene of this gene has been defined on chromosome 5. [provided by RefSeq, Apr 2017]
Expression
Ubiquitous expression in brain (RPKM 8.0), testis (RPKM 5.8) and 25 other tissues See more
Orthologs

Genomic context

See TMTC4 in Genome Data Viewer
Location:
13q32.3
Exon count:
24
Annotation release Status Assembly Chr Location
109.20190905 current GRCh38.p13 (GCF_000001405.39) 13 NC_000013.11 (100603625..100675631, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 13 NC_000013.10 (101256090..101327103, complement)

Chromosome 13 - NC_000013.11Genomic Context describing neighboring genes Neighboring gene propionyl-CoA carboxylase subunit alpha Neighboring gene uncharacterized LOC107984574 Neighboring gene PCCA antisense RNA 1 Neighboring gene ribosomal protein S26 pseudogene 47 Neighboring gene gamma-glutamylamine cyclotransferase Neighboring gene cytochrome c oxidase subunit 5B pseudogene 6 Neighboring gene NALCN antisense RNA 1 Neighboring gene ADP ribosylation factor 4 pseudogene 3 Neighboring gene Sharpr-MPRA regulatory region 9290

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • FLJ14624, FLJ22153, FLJ42608

Gene Ontology Provided by GOA

Function Evidence Code Pubs
dolichyl-phosphate-mannose-protein mannosyltransferase activity IEA
Inferred from Electronic Annotation
more info
 
mannosyltransferase activity IMP
Inferred from Mutant Phenotype
more info
PubMed 
Process Evidence Code Pubs
protein O-linked mannosylation IMP
Inferred from Mutant Phenotype
more info
PubMed 
Component Evidence Code Pubs
endoplasmic reticulum IEA
Inferred from Electronic Annotation
more info
 
integral component of membrane IEA
Inferred from Electronic Annotation
more info
 

General protein information

Preferred Names
protein O-mannosyl-transferase TMTC4
Names
transmembrane and TPR repeat-containing protein 4
transmembrane and tetratricopeptide repeat containing 4
NP_001073137.1
NP_001273382.1
NP_001337500.1
NP_001337501.1
NP_001337503.1
NP_001337505.1
NP_001337506.1
NP_116202.2
XP_011519424.1
XP_011519425.1
XP_011519427.1
XP_016876286.1
XP_016876287.1
XP_016876288.1
XP_016876289.1

NCBI Reference Sequences (RefSeq)

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.

Genomic

  1. NG_053145.1 RefSeqGene

    Range
    5299..76469
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001079669.4NP_001073137.1  protein O-mannosyl-transferase TMTC4 isoform 2

    See identical proteins and their annotated locations for NP_001073137.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR, has multiple coding region differences, and initiates translation at a downstream start codon, compared to variant 4. The encoded isoform (2) is shorter than isoform 4. Both variants 2 and 5 encode the same isoform (2).
    Source sequence(s)
    AL359085, AW513848, BX647956
    Consensus CDS
    CCDS41904.1
    UniProtKB/Swiss-Prot
    Q5T4D3
    Related
    ENSP00000365408.3, ENST00000376234.7
    Conserved Domains (3) summary
    COG0457
    Location:481717
    TPR; Tetratricopeptide (TPR) repeat [General function prediction only]
    sd00006
    Location:482510
    TPR; TPR repeat [structural motif]
    pfam08409
    Location:294366
    DUF1736; Domain of unknown function (DUF1736)
  2. NM_001286453.3NP_001273382.1  protein O-mannosyl-transferase TMTC4 isoform 3

    See identical proteins and their annotated locations for NP_001273382.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) differs in the 5' UTR, contains multiple differences in the 5' coding region, and initiates translation at a downstream in-frame start codon, compared to variant 1. The encoded isoform (3) is shorter than isoform 1.
    Source sequence(s)
    AF339792, AK299859, AL359085, AW513848, DC377683
    Consensus CDS
    CCDS66575.1
    UniProtKB/Swiss-Prot
    Q5T4D3
    Related
    ENSP00000365409.2, ENST00000328767.9
    Conserved Domains (7) summary
    smart00028
    Location:473506
    TPR; Tetratricopeptide repeats
    sd00006
    Location:371399
    TPR; TPR repeat [structural motif]
    pfam00515
    Location:439472
    TPR_1; Tetratricopeptide repeat
    pfam07719
    Location:371404
    TPR_2; Tetratricopeptide repeat
    pfam08409
    Location:181255
    DUF1736; Domain of unknown function (DUF1736)
    pfam13414
    Location:370436
    TPR_11; TPR repeat
    pfam13431
    Location:393426
    TPR_17; Tetratricopeptide repeat
  3. NM_001350571.2NP_001337500.1  protein O-mannosyl-transferase TMTC4 isoform 4

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) represents the longest transcript and encodes the longest isoform (4).
    Source sequence(s)
    AL359085
    Conserved Domains (3) summary
    COG0457
    Location:558794
    TPR; Tetratricopeptide (TPR) repeat [General function prediction only]
    sd00006
    Location:559587
    TPR; TPR repeat [structural motif]
    pfam08409
    Location:371443
    DUF1736; Domain of unknown function (DUF1736)
  4. NM_001350572.2NP_001337501.1  protein O-mannosyl-transferase TMTC4 isoform 2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) differs in the 5' UTR, has multiple coding region differences, and initiates translation at a downstream start codon, compared to variant 4. The encoded isoform (2) is shorter than isoform 4. Both variants 2 and 5 encode the same isoform (2).
    Source sequence(s)
    AL359085
    Consensus CDS
    CCDS41904.1
    Conserved Domains (3) summary
    COG0457
    Location:481717
    TPR; Tetratricopeptide (TPR) repeat [General function prediction only]
    sd00006
    Location:482510
    TPR; TPR repeat [structural motif]
    pfam08409
    Location:294366
    DUF1736; Domain of unknown function (DUF1736)
  5. NM_001350574.2NP_001337503.1  protein O-mannosyl-transferase TMTC4 isoform 5

    Status: REVIEWED

    Description
    Transcript Variant: This variant (6) differs in the 5' UTR and 5' coding region, and initiates translation at a downstream start codon, compared to variant 4. The encoded isoform (5) is has a shorter and distinct N-terminus compared to isoform 4.
    Source sequence(s)
    AL359085
    Conserved Domains (3) summary
    COG0457
    Location:539775
    TPR; Tetratricopeptide (TPR) repeat [General function prediction only]
    sd00006
    Location:540568
    TPR; TPR repeat [structural motif]
    pfam08409
    Location:352424
    DUF1736; Domain of unknown function (DUF1736)
  6. NM_001350576.2NP_001337505.1  protein O-mannosyl-transferase TMTC4 isoform 6

    Status: REVIEWED

    Description
    Transcript Variant: This variant (7) lacks an alternate in-frame exon in the 5' coding region, compared to variant 4. The encoded isoform (6) is shorter than isoform 4.
    Source sequence(s)
    AL359085
    Conserved Domains (3) summary
    COG0457
    Location:498734
    TPR; Tetratricopeptide (TPR) repeat [General function prediction only]
    sd00006
    Location:499527
    TPR; TPR repeat [structural motif]
    pfam08409
    Location:313383
    DUF1736; Domain of unknown function (DUF1736)
  7. NM_001350577.2NP_001337506.1  protein O-mannosyl-transferase TMTC4 isoform 7

    Status: REVIEWED

    Description
    Transcript Variant: This variant (8) differs in the 5' UTR, has multiple coding region differences, and initiates translation at a downstream start codon, compared to variant 4. The encoded isoform (7) is shorter than isoform 4.
    Source sequence(s)
    AL359085
    Conserved Domains (3) summary
    COG0457
    Location:479715
    TPR; Tetratricopeptide (TPR) repeat [General function prediction only]
    sd00006
    Location:480508
    TPR; TPR repeat [structural motif]
    pfam08409
    Location:294364
    DUF1736; Domain of unknown function (DUF1736)
  8. NM_032813.5NP_116202.2  protein O-mannosyl-transferase TMTC4 isoform 1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) lacks an alternate in-frame exon in the 5' coding region, compared to variant 4. The encoded isoform (1) is shorter than isoform 4.
    Source sequence(s)
    AK056409, AL359085, AW513848, BG830268, CV029196, DA368450
    Consensus CDS
    CCDS9497.2
    UniProtKB/Swiss-Prot
    Q5T4D3
    Related
    ENSP00000343871.5, ENST00000342624.9
    Conserved Domains (7) summary
    smart00028
    Location:603636
    TPR; Tetratricopeptide repeats
    sd00006
    Location:501529
    TPR; TPR repeat [structural motif]
    pfam00515
    Location:569602
    TPR_1; Tetratricopeptide repeat
    pfam07719
    Location:501534
    TPR_2; Tetratricopeptide repeat
    pfam08409
    Location:311385
    DUF1736; Domain of unknown function (DUF1736)
    pfam13414
    Location:500566
    TPR_11; TPR repeat
    pfam13431
    Location:523556
    TPR_17; Tetratricopeptide repeat

RNA

  1. NR_146794.2 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (9) lacks two alternate exons in the 5' region and contains an alternate exon in the 3' region, compared to variant 4. This variant is represented as non-coding because the use of the 5'-most expected translational start codon renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AL359085

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109.20190905

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000013.11 Reference GRCh38.p13 Primary Assembly

    Range
    100603625..100675631 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011521122.3XP_011519424.1  protein O-mannosyl-transferase TMTC4 isoform X1

    See identical proteins and their annotated locations for XP_011519424.1

    Conserved Domains (3) summary
    COG0457
    Location:558794
    TPR; Tetratricopeptide (TPR) repeat [General function prediction only]
    sd00006
    Location:559587
    TPR; TPR repeat [structural motif]
    pfam08409
    Location:371443
    DUF1736; Domain of unknown function (DUF1736)
  2. XM_017020798.1XP_016876287.1  protein O-mannosyl-transferase TMTC4 isoform X5

    Conserved Domains (6) summary
    sd00006
    Location:265293
    TPR; TPR repeat [structural motif]
    pfam00515
    Location:333366
    TPR_1; Tetratricopeptide repeat
    pfam07719
    Location:265298
    TPR_2; Tetratricopeptide repeat
    pfam08409
    Location:75149
    DUF1736; Domain of unknown function (DUF1736)
    pfam13414
    Location:264330
    TPR_11; TPR repeat
    pfam13431
    Location:287320
    TPR_17; Tetratricopeptide repeat
  3. XM_011521123.2XP_011519425.1  protein O-mannosyl-transferase TMTC4 isoform X2

    See identical proteins and their annotated locations for XP_011519425.1

    Conserved Domains (3) summary
    COG0457
    Location:539775
    TPR; Tetratricopeptide (TPR) repeat [General function prediction only]
    sd00006
    Location:540568
    TPR; TPR repeat [structural motif]
    pfam08409
    Location:352424
    DUF1736; Domain of unknown function (DUF1736)
  4. XM_017020799.2XP_016876288.1  protein O-mannosyl-transferase TMTC4 isoform X5

    Conserved Domains (6) summary
    sd00006
    Location:265293
    TPR; TPR repeat [structural motif]
    pfam00515
    Location:333366
    TPR_1; Tetratricopeptide repeat
    pfam07719
    Location:265298
    TPR_2; Tetratricopeptide repeat
    pfam08409
    Location:75149
    DUF1736; Domain of unknown function (DUF1736)
    pfam13414
    Location:264330
    TPR_11; TPR repeat
    pfam13431
    Location:287320
    TPR_17; Tetratricopeptide repeat
  5. XM_017020797.2XP_016876286.1  protein O-mannosyl-transferase TMTC4 isoform X4

    Conserved Domains (7) summary
    smart00028
    Location:425458
    TPR; Tetratricopeptide repeats
    sd00006
    Location:323351
    TPR; TPR repeat [structural motif]
    pfam00515
    Location:391424
    TPR_1; Tetratricopeptide repeat
    pfam07719
    Location:323356
    TPR_2; Tetratricopeptide repeat
    pfam08409
    Location:133207
    DUF1736; Domain of unknown function (DUF1736)
    pfam13414
    Location:322388
    TPR_11; TPR repeat
    pfam13431
    Location:345378
    TPR_17; Tetratricopeptide repeat
  6. XM_011521125.1XP_011519427.1  protein O-mannosyl-transferase TMTC4 isoform X3

    Conserved Domains (7) summary
    sd00006
    Location:559587
    TPR; TPR repeat [structural motif]
    pfam00515
    Location:627660
    TPR_1; Tetratricopeptide repeat
    pfam07719
    Location:559592
    TPR_2; Tetratricopeptide repeat
    pfam08409
    Location:369443
    DUF1736; Domain of unknown function (DUF1736)
    pfam13414
    Location:558624
    TPR_11; TPR repeat
    pfam13431
    Location:581614
    TPR_17; Tetratricopeptide repeat
    pfam13432
    Location:599661
    TPR_16; Tetratricopeptide repeat
  7. XM_017020800.1XP_016876289.1  protein O-mannosyl-transferase TMTC4 isoform X6

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