TULP4 TUB like protein 4 [Homo sapiens (human)] - Gene

Summary

Official Symbol: TULP4provided by HGNC
Official Full Name: TUB like protein 4provided by HGNC
Primary source: HGNC:HGNC:15530
See related: Ensembl:ENSG00000130338 MIM:619442; AllianceGenome:HGNC:15530
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: TUSP
Summary: Predicted to be involved in protein ubiquitination. Located in cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]
Expression: Ubiquitous expression in brain (RPKM 5.2), testis (RPKM 3.3) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 6q25.3

Exon count:: 23

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	6	NC_000006.12 (158232195..158511828)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	6	NC_060930.1 (159476584..159756806)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	6	NC_000006.11 (158733497..158932860)

Chromosome 6 - NC_000006.12 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: 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

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Effects of Tulp4 deficiency on murine embryonic development and adult phenotype.
Title: Effects of Tulp4 deficiency on murine embryonic development and adult phenotype.
In Philippines families, overtransmission of alleles to persons born with CL+/-P. Results : We found statistical evidence of association between a marker of TULP4 (rs651333) with CL+/-P (P = .00007). Conclusions : Our results further support the linkage results for the chromosome 6q region and reveal a novel candidate gene for CL+/-P.
Title: Fine Mapping of 6q23.1 Identifies TULP4 as Contributing to Clefts.
Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.

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Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
Hundreds of variants clustered in genomic loci and biological pathways affect human height. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

WI-14921 (e-PCR)
- UniSTS:81160

SHGC-145905 (e-PCR)
- UniSTS:174866

NIB330 (e-PCR)
- UniSTS:76345

RH46643 (e-PCR)
- UniSTS:71240

RH122728 (e-PCR)
- UniSTS:133999

RH124055 (e-PCR)
- UniSTS:136050

RH48840 (e-PCR)
- UniSTS:54395

D6S437 (e-PCR), detects polymorphism
- UniSTS:87974

SHGC-82563 (e-PCR)
- UniSTS:95658

AB055326 (e-PCR)
- UniSTS:479920

SHGC-156011 (e-PCR)
- UniSTS:185268

STS-H78234 (e-PCR)
- UniSTS:72904

SHGC-105718 (e-PCR)
- UniSTS:169417

stdJ250C19SP6 (e-PCR)
- UniSTS:181733

RH36345 (e-PCR)
- UniSTS:1265

D6S437 (e-PCR), detects polymorphism
- UniSTS:74998

Gene Ontology Provided by GOA

Process	Evidence Code	Pubs
involved_in protein ubiquitination	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
located_in cytoplasm	IDA Inferred from Direct Assay more info	PubMed
located_in cytosol	TAS Traceable Author Statement more info

General protein information

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Preferred Names: tubby-related protein 4

Names: tubby like protein 4; tubby super-family protein; tubby superfamily protein

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_001007466.3 → NP_001007467.1 tubby-related protein 4 isoform 2

See identical proteins and their annotated locations for NP_001007467.1

Status: VALIDATED

Description

Transcript Variant: This variant (2) lacks an exon in the coding region, which results in a frameshift and an early stop codon, compared to variant 1. The encoded isoform (2) is shorter and has a distinct C-terminus compared to isoform 1.

Source sequence(s)

AB037818, AF219946, AF288480, AL360169

Consensus CDS

CCDS34562.1

UniProtKB/Swiss-Prot

Q9NRJ4

Related

ENSP00000356061.2, ENST00000367094.6

Conserved Domains (5) summary

COG2319
Location:67 → 218

WD40; WD40 repeat [General function prediction only]

pfam01167
Location:588 → 646

Tub; Tub family

sd00039
Location:85 → 123

7WD40; WD40 repeat [structural motif]

cl02533
Location:373 → 408

SOCS; SOCS (suppressors of cytokine signaling) box. The SOCS box is found in the C-terminal region of CIS/SOCS family proteins (in combination with a SH2 domain), ASBs (ankyrin repeat-containing proteins with a SOCS box), SSBs (SPRY domain-containing proteins ...

cl02567
Location:78 → 218

WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...
NM_020245.5 → NP_064630.2 tubby-related protein 4 isoform 1

See identical proteins and their annotated locations for NP_064630.2

Status: VALIDATED

Description

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

Source sequence(s)

AF219946, AL353800, AL360169

Consensus CDS

CCDS34561.1

UniProtKB/Swiss-Prot

Q5T3M2, Q5T3M3, Q9HD22, Q9NRJ4, Q9P2F0

Related

ENSP00000356064.3, ENST00000367097.8

Conserved Domains (5) summary

COG2319
Location:67 → 218

WD40; WD40 repeat [General function prediction only]

pfam01167
Location:1466 → 1536

Tub; Tub family

sd00039
Location:85 → 123

7WD40; WD40 repeat [structural motif]

cl02533
Location:373 → 408

SOCS; SOCS (suppressors of cytokine signaling) box. The SOCS box is found in the C-terminal region of CIS/SOCS family proteins (in combination with a SH2 domain), ASBs (ankyrin repeat-containing proteins with a SOCS box), SSBs (SPRY domain-containing proteins ...

cl02567
Location:78 → 213

WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000006.12 Reference GRCh38.p14 Primary Assembly

Range

158232195..158511828

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_047419082.1 → XP_047275038.1 tubby-related protein 4 isoform X1
XM_047419087.1 → XP_047275043.1 tubby-related protein 4 isoform X2

UniProtKB/Swiss-Prot

Q5T3M2, Q5T3M3, Q9HD22, Q9NRJ4, Q9P2F0
XM_047419084.1 → XP_047275040.1 tubby-related protein 4 isoform X2

UniProtKB/Swiss-Prot

Q5T3M2, Q5T3M3, Q9HD22, Q9NRJ4, Q9P2F0
XM_047419081.1 → XP_047275037.1 tubby-related protein 4 isoform X1
XM_047419086.1 → XP_047275042.1 tubby-related protein 4 isoform X2

UniProtKB/Swiss-Prot

Q5T3M2, Q5T3M3, Q9HD22, Q9NRJ4, Q9P2F0
XM_047419085.1 → XP_047275041.1 tubby-related protein 4 isoform X2

UniProtKB/Swiss-Prot

Q5T3M2, Q5T3M3, Q9HD22, Q9NRJ4, Q9P2F0
XM_047419079.1 → XP_047275035.1 tubby-related protein 4 isoform X1
XM_047419083.1 → XP_047275039.1 tubby-related protein 4 isoform X2

UniProtKB/Swiss-Prot

Q5T3M2, Q5T3M3, Q9HD22, Q9NRJ4, Q9P2F0
XM_047419088.1 → XP_047275044.1 tubby-related protein 4 isoform X3
XM_011535946.2 → XP_011534248.1 tubby-related protein 4 isoform X1

Conserved Domains (5) summary

COG2319
Location:67 → 218

WD40; WD40 repeat [General function prediction only]

pfam01167
Location:1489 → 1559

Tub; Tub family

sd00039
Location:85 → 123

7WD40; WD40 repeat [structural motif]

cl02533
Location:396 → 431

SOCS; SOCS (suppressors of cytokine signaling) box. The SOCS box is found in the C-terminal region of CIS/SOCS family proteins (in combination with a SH2 domain), ASBs (ankyrin repeat-containing proteins with a SOCS box), SSBs (SPRY domain-containing proteins ...

cl02567
Location:78 → 213

WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...
XM_017011070.2 → XP_016866559.1 tubby-related protein 4 isoform X2

UniProtKB/Swiss-Prot

Q5T3M2, Q5T3M3, Q9HD22, Q9NRJ4, Q9P2F0

Conserved Domains (5) summary

COG2319
Location:67 → 218

WD40; WD40 repeat [General function prediction only]

pfam01167
Location:1466 → 1536

Tub; Tub family

sd00039
Location:85 → 123

7WD40; WD40 repeat [structural motif]

cl02533
Location:373 → 408

SOCS; SOCS (suppressors of cytokine signaling) box. The SOCS box is found in the C-terminal region of CIS/SOCS family proteins (in combination with a SH2 domain), ASBs (ankyrin repeat-containing proteins with a SOCS box), SSBs (SPRY domain-containing proteins ...

cl02567
Location:78 → 213

WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...
XM_047419089.1 → XP_047275045.1 tubby-related protein 4 isoform X3