Tdrd3 MGI Mouse Gene Detail - MGI:2444023 - tudor domain containing 3

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Tdrd3 Gene Detail

Symbol

Tdrd3
Name

tudor domain containing 3
Synonyms

4732418C03Rik

Feature Type

protein coding gene
IDs

MGI:2444023
NCBI Gene: 219249
Alliance

gene page
Transcription Start Sites

8 TSS
Candidate for QTL

1 QTL

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Sequence Map

Chr14:87654075-87782940 bp, + strand
From Ensembl annotation of GRCm39
View this region in JBrowse
Genome Browsers

Ensembl | UCSC | NCBI

Genetic Map

Chromosome 14, 44.17 cM
Mapping Data

3 experiments

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SNPs within 2kb

3405 from dbSNP Build 142
Strain Annotations

18

For selected strains:

Strain	Gene Model ID	Feature Type	Coordinates	Select Strains
C57BL/6J	MGI_C57BL6J_2444023	protein coding gene	Chr14:87647598-87782944 (+)
129S1/SvImJ	MGP_129S1SvImJ_G0021608	protein coding gene	Chr14:82903127-83046168 (+)
A/J	MGP_AJ_G0021566	protein coding gene	Chr14:80715125-80844065 (+)
AKR/J	MGP_AKRJ_G0021542	protein coding gene	Chr14:83113729-83249011 (+)
BALB/cJ	MGP_BALBcJ_G0021572	protein coding gene	Chr14:80688153-80815993 (+)
C3H/HeJ	MGP_C3HHeJ_G0021350	protein coding gene	Chr14:82843255-82976900 (+)
C57BL/6NJ	MGP_C57BL6NJ_G0022012	protein coding gene	Chr14:86410686-86555073 (+)
CAROLI/EiJ	MGP_CAROLIEiJ_G0019551	protein coding gene	Chr14:78437678-78563951 (+)
CAST/EiJ	MGP_CASTEiJ_G0020867	protein coding gene	Chr14:79896945-80035736 (+)
CBA/J	MGP_CBAJ_G0021318	protein coding gene	Chr14:89353118-89488515 (+)
DBA/2J	MGP_DBA2J_G0021442	protein coding gene	Chr14:80069891-80201862 (+)
FVB/NJ	MGP_FVBNJ_G0021418	protein coding gene	Chr14:79378943-79505338 (+)
LP/J	MGP_LPJ_G0021510	protein coding gene	Chr14:83923911-84082898 (+)
NOD/ShiLtJ	MGP_NODShiLtJ_G0021446	protein coding gene	Chr14:89177854-89318346 (+)
NZO/HlLtJ	MGP_NZOHlLtJ_G0022035	protein coding gene	Chr14:82419348-82552259 (+)
PWK/PhJ	MGP_PWKPhJ_G0020610	protein coding gene	Chr14:76922819-77053835 (+)
SPRET/EiJ	MGP_SPRETEiJ_G0020448	protein coding gene	Chr14:78365148-78507970 (+)
WSB/EiJ	MGP_WSBEiJ_G0020920	protein coding gene	Chr14:82922919-83056461 (+)

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Human Ortholog

TDRD3, tudor domain containing 3

Vertebrate Orthologs

3

Vertebrate Orthology Source

Alliance of Genome Resources

Human Ortholog

TDRD3, tudor domain containing 3
Links

HGNC:20612

NCBI Gene ID: 81550

neXtProt AC: NX_Q9H7E2

UniProt: Q9H7E2
Chr Location

13q21.2; chr13:60395533-60573879 (+) GRCh38

MGI Vertebrate Homology

Tdrd3 stringent orthology
1 human;1 mouse;1 rat;1 zebrafish
HCOP

vertebrate homology predictions: TDRD3
Gene Tree

Tdrd3

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Phenotype Summary

5 phenotypes from 2 alleles in 2 genetic backgrounds
18 phenotype references

Phenotype Overview

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

42
Chemically induced (other)

1
Endonuclease-mediated

4
Gene trapped

34
Targeted

3
Genomic Mutations

1 involving Tdrd3
Incidental Mutations

Mutagenetix , APF
Find Mice (IMSR)

81 strains or lines available

Homozygous mice for a hypomorphic allele show increased genomic instability, and increased c-Myc/Igh translocation and R loop formation in B cells.

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All GO Annotations

23
GO References

8

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 differentiation	cell population proliferation	cellular component organization	DNA-templated transcription	establishment of localization	homeostatic process	immune system process	lipid metabolic process	programmed cell death	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	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

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

706
cDNA Data

69

Tissue x Stage Matrix

Other Mouse Links

Allen Institute

GEO

Expression Atlas
Other Vertebrate Links

Xenbase tdrd3

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All Sequences

74
RefSeq

23
UniProt

2
CCDS

CCDS27305.2, CCDS56972.1

Ensembl

ENSMUSG00000022019 (Evidence)
NCBI Gene

219249

Representative Sequences				Length	Strain/Species	Flank
	genomic	ENSMUSG00000022019	Ensembl Gene Model \| MGI Sequence Detail	128866	C57BL/6J	± kb
	transcript	ENSMUST00000168275	Ensembl \| MGI Sequence Detail	2657	Not Applicable
	polypeptide	ENSMUSP00000129019	Ensembl \| MGI Sequence Detail	743	Not Applicable

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UniProt

2 Sequences
Protein Ontology

PR:000016217 tudor domain-containing protein 3

(term hierarchy)
PDB

2D9T
InterPro Domains

IPR013894 RecQ mediated genome instability protein 1, OB-fold domain

IPR042470 RecQ mediated genome instability protein, N-terminal OB-fold domain superfamily

IPR002999 Tudor domain

IPR047379 Tudor domain-containing protein 3, Tudor domain

IPR041915 Tudor domain-containing protein 3, UBA domain

IPR009060 UBA-like superfamily

IPR015940 Ubiquitin-associated domain

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All nucleic 69

cDNA 69

Microarray probesets 6

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Summaries

All 44

Gene Ontology 8

Phenotypes 18
Earliest

J:93290 Araki K, et al., Exchangeable gene trap using the Cre/mutated lox system. Cell Mol Biol (Noisy-Le-Grand). 1999 Jul;45(5):737-50
Latest

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

TSS for Tdrd3:

(View these features in JBrowse)

Transcription Start Site	Location	Distance from Gene 5'-end
Tssr126849	Chr14:87653443-87653458 (+)	-624 bp
Tssr126850	Chr14:87653560-87653578 (+)	-506 bp
Tssr4498	Chr14:87653814-87653845 (+)	-245 bp
Tssr126851	Chr14:87654046-87654091 (+)	-6 bp
Tssr126852	Chr14:87654130-87654159 (+)	70 bp
Tssr126853	Chr14:87654162-87654181 (+)	97 bp
Tssr126854	Chr14:87654198-87654214 (+)	131 bp
Tssr126855	Chr14:87654467-87654502 (+)	410 bp

Tdrd3 is Candidate Gene for:

QTL	Genetic Location*	Genome Location (GRCm39)	Reference	QTL Note
Ccmsa2	Chr14, syntenic		J:276654	To evaluate candidate genes, the authors used the QTLMiner module of GeneNetwork (Alberts and Schughart, 2010), which evaluates all genes in an interval against neocortical gene expression databases within GeneNetwork. The authors used QTLMiner to rank potential candidates among the 48 genes in the Ccmsa2 interval based on the presence of non-synonymous SNPs, of expression levels in mRNA databases (in this case, three neocortical mRNA expression databases: P3, P14, and P60), and cis-eQTL. Using sequence data and QTLMiner, the authors were able to narrow down eight positional and plausible biological candidate genes within the Ccmsa2 interval: The authors first isolated those genes with non-synonymous SNPs or indels, reasoning that only genes with allelic differences between the two parent strains could account for the QTL. Of the 48 genes in the interval, 14 had SNPs between B6 and D2 (4921530L21Rik [Spertl; MGI:1913982], AU017455 [Zfp957; MGI:2145729], Dgkh [MGI:2444188], Diap3 [Diaph3; MGI:1927222], EG629734 [Gm6999; MGI:3647443], Kiaa0564 [Vwa8; MGI:1919008], Klhl1 [MGI:2136335], Mtrf1 [MGI:2384815], Naa16 [MGI:1914147], Pcdh8 [MGI:1306800], Pcdh9 [MGI:1306801], Pcdh20 [MGI:2443376], Tdrd3 [MGI:2444023], Tnfsf11 [MGI:1100089]). The authors next identified those genes that had moderate to high expression in forebrain at some stage of development - values above the average of 8 in at least one neocortical expression database (Dgkh [MGI:2444188], Diap3 [Diaph3; MGI:1927222], Kiaa0564 [Vwa8; MGI:1919008], Mtrf1 [MGI:2384815], Naa16 [MGI:1914147], Pcdh20 [MGI:2443376], Pcd8, Pcdh9 [MGI:1306801], Tdrd3 [MGI:2444023]). Of these, seven were identified as having cis-eQTL in at least one of the expression databases: Dgkh (MGI:2444188), Kiaa0564 (Vwa8; MGI:1919008), Naa16 (MGI:1914147), Mtrf1 (MGI:2384815), Diap3 (Diaph3; MGI:1927222), Tdrd3 (MGI:2444023), and Pcdh9 (MGI:1306801). Finally, the authors examined the interval for genes without non-synonymous SNPs but with significant cis-eQTL, and identified Rgc32 (Rgcc; 1190002H23Rik; MGI:1913464) as another potential candidate (Table 1; Figure 3A). Gene expression of these candidates is highly intercorrelated and their expression correlates with MSACC (Figure 3B). Curator Note: Pcd8 is not in MGD. The authors may have been referring to Pcdh8 (MGI:1306800).

*cM position of peak correlated region/marker

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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