Ttc39a MGI Mouse Gene Detail - MGI:2444350 - tetratricopeptide repeat domain 39A

Symbol

Ttc39a
Name

tetratricopeptide repeat domain 39A
Synonyms

4922503N01Rik

Feature Type

protein coding gene
IDs

MGI:2444350
NCBI Gene: 230603
Alliance

gene page
Transcription Start Sites

7 TSS

Sequence Map

Chr4:109263820-109301942 bp, + strand
From Ensembl annotation of GRCm39
View this region in JBrowse
Genome Browsers

Ensembl | UCSC | NCBI

Genetic Map

Chromosome 4, 51.29 cM
Mapping Data

2 experiments

SNPs within 2kb

2176 from dbSNP Build 142
Strain Annotations

18

For selected strains:

Strain	Gene Model ID	Feature Type	Coordinates
C57BL/6J	MGI_C57BL6J_2444350	protein coding gene	Chr4:109251344-109301942 (+)
129S1/SvImJ	MGP_129S1SvImJ_G0028570	protein coding gene	Chr4:110183065-110221113 (+)
A/J	MGP_AJ_G0028533	protein coding gene	Chr4:106213626-106251544 (+)
AKR/J	MGP_AKRJ_G0028480	protein coding gene	Chr4:108858378-108896295 (+)
BALB/cJ	MGP_BALBcJ_G0028552	protein coding gene	Chr4:106428230-106466065 (+)
C3H/HeJ	MGP_C3HHeJ_G0028266	protein coding gene	Chr4:109604489-109643622 (+)
C57BL/6NJ	MGP_C57BL6NJ_G0028992	protein coding gene	Chr4:114142496-114180497 (+)
CAROLI/EiJ	MGP_CAROLIEiJ_G0026283	protein coding gene	Chr4:101509079-101549378 (+)
CAST/EiJ	MGP_CASTEiJ_G0027702	protein coding gene	Chr4:107457228-107495299 (+)
CBA/J	MGP_CBAJ_G0028235	protein coding gene	Chr4:117889462-117927566 (+)
DBA/2J	MGP_DBA2J_G0028383	protein coding gene	Chr4:105835195-105873229 (+)
FVB/NJ	MGP_FVBNJ_G0028351	protein coding gene	Chr4:104711484-104749488 (+)
LP/J	MGP_LPJ_G0028484	protein coding gene	Chr4:110431219-110470041 (+)
NOD/ShiLtJ	MGP_NODShiLtJ_G0028377	protein coding gene	Chr4:123070915-123109916 (+)
NZO/HlLtJ	MGP_NZOHlLtJ_G0029028	protein coding gene	Chr4:109100784-109138788 (+)
PWK/PhJ	MGP_PWKPhJ_G0027428	protein coding gene	Chr4:104124598-104162945 (+)
SPRET/EiJ	MGP_SPRETEiJ_G0027252	protein coding gene	Chr4:106483998-106523584 (+)
WSB/EiJ	MGP_WSBEiJ_G0027783	protein coding gene	Chr4:109281656-109320474 (+)

Human Ortholog

TTC39A, tetratricopeptide repeat domain 39A

Vertebrate Orthologs

4

Vertebrate Orthology Source

Alliance of Genome Resources

Human Ortholog

TTC39A, tetratricopeptide repeat domain 39A
Synonyms

C1orf34, DEME-6
Links

HGNC:18657

NCBI Gene ID: 22996

UniProt: Q5SRH9
Chr Location

1p32.3; chr1:51287258-51345116 (-) GRCh38

MGI Vertebrate Homology

Ttc39a stringent orthology
1 human;1 mouse;1 rat;2 zebrafish
HCOP

vertebrate homology predictions: TTC39A
Gene Tree

Ttc39a

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Phenotype Summary

4 phenotypes from 1 allele in 1 genetic background
11 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	integument	immune system	limbs/digits/tail	liver/biliary system	mortality/aging	muscle	nervous system	pigmentation	renal/urinary system	reproductive system	respiratory system	skeleton	taste/olfaction	neoplasm	vision/eye

Click cells to view annotations.

All Mutations and Alleles

7
Chemically induced (other)

2
Radiation induced

1
Targeted

4
Genomic Mutations

4 involving Ttc39a
Incidental Mutations

Mutagenetix , APF
Find Mice (IMSR)

26 strains or lines available
Comparison Matrix

Gene Expression + Phenotype

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All GO Annotations

2
GO References

2

Molecular Function

No experimental evidence to support Molecular Function annotation, following literature review. See J:73796.

Biological Process

No experimental evidence to support Biological Process annotation, following literature review. See J:73796.

Cellular Component

cell projection	cytoplasmic vesicle	cytoskeleton	cytosol	endoplasmic reticulum	endosome	extracellular region	Golgi apparatus	mitochondrion	membraneless organelle	nucleus	organelle envelope	organelle lumen	plasma membrane	protein-containing complex	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

740
Tissues

6
cDNA Data

11
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 ttc39a

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All Sequences

73
RefSeq

22
UniProt

5
CCDS

CCDS18463.1, CCDS51260.1

Ensembl

ENSMUSG00000028555 (Evidence)
NCBI Gene

230603

			Length	Strain/Species	Flank
genomic	ENSMUSG00000028555	Ensembl Gene Model \| MGI Sequence Detail	38123	C57BL/6J	± kb
transcript	ENSMUST00000106618	Ensembl \| MGI Sequence Detail	1970	Not Applicable
polypeptide	ENSMUSP00000102229	Ensembl \| MGI Sequence Detail	578	Not Applicable

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UniProt

5 Sequences
Protein Ontology

PR:000031228 tetratricopeptide repeat protein 39A

(term hierarchy)
InterPro Domains

IPR019412 Inclusion body clearance protein Iml2/Tetratricopeptide repeat protein 39

IPR011990 Tetratricopeptide-like helical domain superfamily

IPR019734 Tetratricopeptide repeat

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All nucleic 11

cDNA 11

Microarray probesets 2

Summaries

All 30

Developmental Gene Expression 2

Gene Ontology 2

Phenotypes 11
Earliest

J:80000 The FANTOM Consortium and The RIKEN Genome Exploration Research Group Phase I & II Team, Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs. Nature. 2002;420:563-573
Latest

J:345621 Adams DJ, et al., Genetic determinants of micronucleus formation in vivo. Nature. 2024 Mar;627(8002):130-136

TSS for Ttc39a:

(View these features in JBrowse)

Transcription Start Site	Location	Distance from Gene 5'-end
Tssr38345	Chr4:109263944-109263960 (+)	132 bp
Tssr38346	Chr4:109264291-109264316 (+)	484 bp
Tssr38347	Chr4:109264318-109264362 (+)	520 bp
Tssr38348	Chr4:109272828-109272845 (+)	9,017 bp
Tssr38349	Chr4:109272854-109272865 (+)	9,040 bp
Tssr38350	Chr4:109272876-109272886 (+)	9,061 bp
Tssr38351	Chr4:109297454-109297470 (+)	33,642 bp

Contributing Projects: Mouse Genome Database (MGD), Gene Expression Database (GXD), Mouse Models of Human Cancer database (MMHCdb) (formerly Mouse Tumor Biology (MTB)), Gene Ontology (GO)
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