Ttc39b MGI Mouse Gene Detail - MGI:1917113 - tetratricopeptide repeat domain 39B

Symbol

Ttc39b
Name

tetratricopeptide repeat domain 39B
Synonyms

1810054D07Rik, 9130422G05Rik

Feature Type

protein coding gene
IDs

MGI:1917113
NCBI Gene: 69863
Gene Overview

MyGene.info: TTC39B
Alliance

gene page
Transcription Start Sites

7 TSS

Sequence Map

Chr4:83220300-83324255 bp, - strand
From Ensembl annotation of GRCm38

View this region in JBrowse
Genome Browsers

Ensembl | UCSC | NCBI

Genetic Map

Chromosome 4, 39.41 cM, cytoband C3
Mapping Data

3 experiments

SNPs within 2kb

946 from dbSNP Build 142
Strain Annotations

18

For selected strains:

Strain	Gene Model ID	Feature Type	Coordinates
C57BL/6J	MGI_C57BL6J_1917113	protein coding gene	Chr4:83220300-83324274 (-)
129S1/SvImJ	MGP_129S1SvImJ_G0028402	protein coding gene	Chr4:82798221-82913636 (-)
A/J	MGP_AJ_G0028363	protein coding gene	Chr4:79919047-80026594 (-)
AKR/J	MGP_AKRJ_G0028312	protein coding gene	Chr4:82006879-82124986 (-)
BALB/cJ	MGP_BALBcJ_G0028383	protein coding gene	Chr4:80153737-80257318 (-)
C3H/HeJ	MGP_C3HHeJ_G0028098	protein coding gene	Chr4:82586039-82708139 (-)
C57BL/6NJ	MGP_C57BL6NJ_G0028822	protein coding gene	Chr4:86069244-86187879 (-)
CAROLI/EiJ	MGP_CAROLIEiJ_G0026122	protein coding gene	Chr4:75879542-75983754 (-)
CAST/EiJ	MGP_CASTEiJ_G0027539	protein coding gene	Chr4:80502228-80612371 (-)
CBA/J	MGP_CBAJ_G0028067	protein coding gene	Chr4:88750335-88870361 (-)
DBA/2J	MGP_DBA2J_G0028216	protein coding gene	Chr4:79701628-79805272 (-)
FVB/NJ	MGP_FVBNJ_G0028182	protein coding gene	Chr4:78722845-78828796 (-)
LP/J	MGP_LPJ_G0028316	protein coding gene	Chr4:83150616-83270838 (-)
NOD/ShiLtJ	MGP_NODShiLtJ_G0028211	protein coding gene	Chr4:93833917-93951673 (-)
NZO/HlLtJ	MGP_NZOHlLtJ_G0028859	protein coding gene	Chr4:82059013-82170667 (-)
PWK/PhJ	MGP_PWKPhJ_G0027262	protein coding gene	Chr4:78043634-78153884 (-)
SPRET/EiJ	MGP_SPRETEiJ_G0027087	protein coding gene	Chr4:79578981-79689772 (-)
WSB/EiJ	MGP_WSBEiJ_G0027615	protein coding gene	Chr4:82234730-82345973 (-)

Human Ortholog

TTC39B, tetratricopeptide repeat domain 39B

Vertebrate Orthologs

9

Human Ortholog

TTC39B, tetratricopeptide repeat domain 39B
Orthology source: HomoloGene, HGNC
Synonyms

C9orf52
Links

HGNC:23704

NCBI Gene ID: 158219

neXtProt AC: NX_Q5VTQ0

UniProt: Q5VTQ0
Chr Location

9p22.3; chr9:15167204-15307360 (-) GRCh38.p7

HomoloGene

Vertebrate Homology Class 25228
1 human;1 mouse;1 rat;1 chimpanzee;1 cattle;1 dog;1 chicken;1 frog, western clawed;1 macaque, rhesus
HCOP

human homology predictions: TTC39B
Gene Tree

Ttc39b

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Phenotype Summary

3 phenotypes from 1 allele in 1 genetic background
12 phenotype references

Phenotype Overview

Blue squares indicate phenotypes directly attributed to mutations/alleles of this gene.

adipose tissue	behavior/neurological	cardiovascular system	cellular	craniofacial	digestive/alimentary system	embryo	endocrine/exocrine glands	growth/size/body	hearing/vestibular/ear	hematopoietic system	homeostasis/metabolism	immune system	integument	limbs/digits/tail	liver/biliary system	mortality/aging	muscle	neoplasm	nervous system	pigmentation	renal/urinary system	reproductive system	respiratory system	skeleton	taste/olfaction	vision/eye

Click cells to view annotations.

All Mutations and Alleles

207
Chemically induced (other)

2
Gene trapped

202
Radiation induced

1
Targeted

2
Genomic Mutations

3 involving Ttc39b
Incidental Mutations

Mutagenetix , APF
Find Mice (IMSR)

85 strains or lines available
Comparison Matrix

Gene Expression + Phenotype

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All GO Annotations

5
GO References

2

External Resources

FuncBase

Molecular Function

carbohydrate derivative binding	cytoskeletal protein binding	DNA binding	enzyme regulator	hydrolase	ligase	lipid binding	oxidoreductase	RNA binding	signaling receptor activity	signaling receptor binding	transcription	transferase	transporter

Biological Process

carbohydrate derivative metabolism	cell death	cell differentiation	cell population proliferation	cellular component organization	establishment of localization	homeostatic process	immune system process	lipid metabolic process	nucleic acid-templated transcription	protein metabolic process	response to stimulus	signaling	system development

Cellular Component

cell projection	cytoplasmic vesicle	cytoskeleton	cytosol	endoplasmic reticulum	endosome	extracellular region	Golgi apparatus	mitochondrion	non-membrane-bounded organelle	nucleus	organelle envelope	organelle lumen	plasma membrane	synapse	vacuole

Click cells to view annotations.

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Expression Overview

GXD's primary emphasis is on endogenous gene expression during development. Click on grid cells to view annotations.

Blue cells = expressed in wild-type.
Gray triangles = other expression annotations only
(e.g. absence of expression or data from mutants).

early conceptus	embryo ectoderm	embryo endoderm	embryo mesoderm	embryo mesenchyme	extraembryonic component	alimentary system	auditory system	branchial arches	cardiovascular system	connective tissue	endocrine system	exocrine system	hemolymphoid system	integumental system	limbs	liver and biliary system	musculoskeletal system	nervous system	olfactory system	reproductive system	respiratory system	urinary system	visual system

Click cells to view annotations.

Assay Results

37
Tissues

2
cDNA Data

54
Literature Summary

2

Images

Tissue x Stage Matrix

Comparison Matrix

Gene Expression + Phenotype

Other Mouse Links

Allen Institute

GEO

Expression Atlas
Other Vertebrate Links

Xenbase ttc39b

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Ttc39b interacts with 456 markers (Mir7-1, Mir7-2, Mir7b, ...) View All

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All Sequences

68
RefSeq

8
UniProt

6
CCDS

CCDS18297.1
UniGene

5540

Ensembl

ENSMUSG00000038172 (Evidence)
NCBI Gene

69863

			Length	Strain/Species	Flank
genomic	ENSMUSG00000038172	Ensembl Gene Model \| MGI Sequence Detail	103956	C57BL/6J	± kb
transcript	ENSMUST00000102823	Ensembl \| MGI Sequence Detail	8831	Not Applicable
polypeptide	ENSMUSP00000099887	Ensembl \| MGI Sequence Detail	617	Not Applicable

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UniProt

6 Sequences
Protein Ontology

PR:000031512 tetratricopeptide repeat protein 39B

(term hierarchy)
InterPro Domains

IPR019412 Inclusion body clearance protein Iml2/Tetratricopeptide repeat protein 39

IPR011990 Tetratricopeptide-like helical domain superfamily

IPR019734 Tetratricopeptide repeat

IPR034305 Tetratricopeptide repeat protein 39B

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All nucleic 54

cDNA 54

Microarray probesets 10

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MGI:1914069, MGI:2140292, MGI:2140529, MGI:2140564

Summaries

All 40

Developmental Gene Expression 2

Gene Ontology 2

Phenotypes 12
Earliest

J:65060 Kawai J, et al., Functional annotation of a full-length mouse cDNA collection. Nature. 2001 Feb 8;409(6821):685-90
Latest

J:235724 Hsieh J, et al., TTC39B deficiency stabilizes LXR reducing both atherosclerosis and steatohepatitis. Nature. 2016 Jul 14;535(7611):303-7

TSS for Ttc39b:

(View these features in JBrowse)

Transcription Start Site	Location	Distance from Gene 5'-end
Tssr42293	Chr4:83324254-83324269 (-)	-7 bp
Tssr42292	Chr4:83324135-83324205 (-)	85 bp
Tssr42290	Chr4:83285171-83285214 (-)	39,062 bp
Tssr42289	Chr4:83285141-83285169 (-)	39,100 bp
Tssr42288	Chr4:83285125-83285138 (-)	39,123 bp
Tssr42286	Chr4:83266038-83266081 (-)	58,195 bp
Tssr42284	Chr4:83233165-83233177 (-)	91,084 bp

Contributing Projects: Mouse Genome Database (MGD), Gene Expression Database (GXD), Mouse Tumor Biology (MTB), Gene Ontology (GO), MouseCyc
Citing These Resources Funding Information Warranty Disclaimer & Copyright Notice Send questions and comments to User Support.	last database update 01/08/2019 MGI 6.13