Khdc3 (KH domain containing 3, subcortical maternal complex member) - Rat Genome Database

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Gene: Khdc3 (KH domain containing 3, subcortical maternal complex member) Mus musculus
Analyze
Symbol: Khdc3
Name: KH domain containing 3, subcortical maternal complex member
RGD ID: 1323168
MGI Page MGI
Description: Predicted to enable RNA binding activity. Involved in several processes, including positive regulation of dendrite development; positive regulation of double-strand break repair via homologous recombination; and positive regulation of embryonic development. Acts upstream of or within mitotic spindle assembly and mitotic spindle assembly checkpoint signaling. Located in several cellular components, including cell cortex; centrosome; and mitochondrion. Part of subcortical maternal complex. Is expressed in several structures, including cranial ganglion; early conceptus; gonad; hemolymphoid system gland; and skin. Human ortholog(s) of this gene implicated in gestational trophoblastic neoplasm. Orthologous to human KHDC3L (KH domain containing 3 like, subcortical maternal complex member).
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: 2410004A20Rik; AI467128; ecat; F; FILIA; hypothetical protein LOC66991; KH domain-containing protein 3; OEEP48
RGD Orthologs
Human
Rat
Bonobo
Dog
Pig
Green Monkey
Alliance Genes
More Info more info ...
Latest Assembly: GRCm39 - Mouse Genome Assembly GRCm39
Position:
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39973,008,660 - 73,013,915 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl973,009,118 - 73,011,720 (+)EnsemblGRCm39 Ensembl
GRCm38973,101,381 - 73,106,631 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl973,101,836 - 73,104,438 (+)EnsemblGRCm38mm10GRCm38
MGSCv37972,950,205 - 72,952,250 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36972,899,593 - 72,901,545 (+)NCBIMGSCv36mm8
Celera970,288,684 - 70,290,729 (+)NCBICelera
Cytogenetic Map9DNCBI
cM Map940.08NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
Phenotype Annotations     Click to see Annotation Detail View

Mammalian Phenotype
References

References - curated
# Reference Title Reference Citation
1. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
2. Mouse MP Annotation Import Pipeline RGD automated import pipeline
3. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
4. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:10349636   PMID:11042159   PMID:11076861   PMID:11217851   PMID:12466851   PMID:12477932   PMID:12787504   PMID:14610273   PMID:16141072   PMID:16141073   PMID:17913455   PMID:18057100  
PMID:18804437   PMID:19376971   PMID:20823540   PMID:21267068   PMID:21731673   PMID:21873635   PMID:22206759   PMID:22276159   PMID:25208553   PMID:25936915   PMID:28992324   PMID:29125140  
PMID:31330130   PMID:31575650   PMID:32413845   PMID:33115731   PMID:35623357   PMID:36266342   PMID:37493331  


Genomics

Comparative Map Data
Khdc3
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39973,008,660 - 73,013,915 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl973,009,118 - 73,011,720 (+)EnsemblGRCm39 Ensembl
GRCm38973,101,381 - 73,106,631 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl973,101,836 - 73,104,438 (+)EnsemblGRCm38mm10GRCm38
MGSCv37972,950,205 - 72,952,250 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36972,899,593 - 72,901,545 (+)NCBIMGSCv36mm8
Celera970,288,684 - 70,290,729 (+)NCBICelera
Cytogenetic Map9DNCBI
cM Map940.08NCBI
KHDC3L
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38673,362,658 - 73,364,171 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl673,362,658 - 73,364,171 (+)EnsemblGRCh38hg38GRCh38
GRCh37674,072,381 - 74,073,894 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36674,129,121 - 74,130,615 (+)NCBINCBI36Build 36hg18NCBI36
Celera674,466,955 - 74,468,453 (+)NCBICelera
Cytogenetic Map6q13NCBI
HuRef671,270,839 - 71,272,337 (+)NCBIHuRef
CHM1_1674,239,196 - 74,240,694 (+)NCBICHM1_1
T2T-CHM13v2.0674,539,355 - 74,540,868 (+)NCBIT2T-CHM13v2.0
Khdc3
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8882,722,980 - 82,724,884 (+)NCBIGRCr8
mRatBN7.2873,842,344 - 73,844,248 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl873,842,344 - 73,844,248 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx879,365,352 - 79,367,256 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0877,638,001 - 77,639,905 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0875,475,342 - 75,477,246 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0879,781,941 - 79,783,845 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl879,781,983 - 79,783,592 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0873,303,948 - 73,306,026 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4877,866,809 - 77,868,713 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1877,885,904 - 77,887,514 (+)NCBI
Celera867,911,791 - 67,913,695 (-)NCBICelera
Cytogenetic Map8q24NCBI
KHDC3L
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2593,242,733 - 93,343,618 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1691,168,480 - 91,271,347 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0671,089,817 - 71,190,700 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1674,478,303 - 74,479,826 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl674,478,303 - 74,479,826 (+)Ensemblpanpan1.1panPan2
KHDC3L
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11235,434,123 - 35,435,679 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1235,434,123 - 35,468,943 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1235,302,631 - 35,303,584 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.01235,984,872 - 35,986,564 (+)NCBIROS_Cfam_1.0
UMICH_Zoey_3.11235,525,693 - 35,526,646 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01235,547,520 - 35,548,473 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01235,672,969 - 35,674,735 (+)NCBIUU_Cfam_GSD_1.0
KHDC3L
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1152,996,706 - 52,999,074 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2159,332,357 - 59,333,914 (+)NCBISscrofa10.2Sscrofa10.2susScr3
KHDC3L
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1171,781,156 - 1,783,344 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl171,781,026 - 1,783,111 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_0236660587,697,113 - 7,699,291 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0

Variants

.
Variants in Khdc3
106 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:465
Count of miRNA genes:305
Interacting mature miRNAs:338
Transcripts:ENSMUST00000034737, ENSMUST00000167514, ENSMUST00000172578, ENSMUST00000173734
Prediction methods:Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


QTLs in Region (GRCm39)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1558872Ibdq1_minflammatory bowel disease QTL 1 (mouse)Not determined93397884073439255Mouse
4142042Alpq3_malcohol preference QTL 3 (mouse)Not determined93730619798701707Mouse
12738449Spcq2_msperm count QTL 2 (mouse)93939988573399885Mouse
4141071Ath29_matherosclerosis 29 (mouse)Not determined94041959474607925Mouse
1301702Brm1_mbrachyury modifier 1 (mouse)Not determined94080504774805204Mouse
1301558Stheal8_msoft tissue heal 8 (mouse)Not determined94348071477480860Mouse
10045639Heal28_mwound healing/regeneration 28 (mouse)Not determined94348071477480860Mouse
1301435Trigq1_mtriglyceride QTL 1 (mouse)Not determined94442817478428262Mouse
1300563Pgia5_mproteoglycan induced arthritis 5 (mouse)Not determined94883105682831177Mouse
1300716Cd4ts4_mCD4 T cell subset 4 (mouse)Not determined94883105682831177Mouse
4141224Dxmod_mdoxorubicin nephropathy modifier (mouse)Not determined49452421101406120Mouse
14746993Manh66_mmandible shape 66 (mouse)94981404883814048Mouse
1301184Bdln4_mbody length 4 (mouse)Not determined95015132084151448Mouse
1301241Renf1_mrenal failure 1 (mouse)Not determined95203447899792481Mouse
12790990Tgl7_mtriglyceride 7 (mouse)95455996088559960Mouse
10043877Adip21_madiposity 21 (mouse)Not determined95643910890439255Mouse
4141676Neogq1_mneonatal growth QTL 1 (mouse)Not determined95780504786121973Mouse
1301803Stheal9_msoft tissue heal 9 (mouse)Not determined95902438793024534Mouse
1301172Fembrs6_mfemur breaking strength 6 (mouse)Not determined95902438793024534Mouse
1301456Adip5_madiposity 5 (mouse)Not determined95936994693370128Mouse
1300848Skull13_mskull morphology 13 (mouse)Not determined95936994693370128Mouse
5491195Mobq8_mmultigenic obesity QTL 8 (mouse)Not determined95936994693370128Mouse
13207569Tcq13_mtotal cholesterol QTL 13 (mouse)959897283109089068Mouse
1301611Lrnx3_mlearning contextual 3 (mouse)Not determined96214976796149881Mouse
4141833W10q13_mweight 10 weeks QTL 13 (mouse)Not determined63239711120191934Mouse
4141545Tailaq2_mtail length adjusted QTL 2 (mouse)Not determined63239711120191934Mouse
1357635Splq4_mspleen weight QTL 4 (mouse)Not determined963239711120191934Mouse
11081165Psl6_mpromotion susceptibility QTL 6 (mouse)96504119195522808Mouse
1301290Smgd1_msubmucosal gland distribution 1 (mouse)Not determined96583105686577967Mouse
1301636Lith5_mlithogenic gene 5 (mouse)Not determined966089077100089175Mouse
10045638Heal29_mwound healing/regeneration 29 (mouse)Not determined967006220101006220Mouse
1357610Vtbt8_mvertebral trabecular bone trait 8 (mouse)Not determined968779563102779705Mouse
1301924Bmd10_mbone mineral density 10 (mouse)Not determined968779563102779705Mouse
1301302Pas4_mpulmonary adenoma susceptibility 4 (mouse)Not determined969121898103121973Mouse
10412174Habiir4_mhyperoxic acute lung injury imprinted region 4 (mouse)Not determined96926774798701707Mouse
1301621Hpic1_mhaloperidol-induced catalepsy 1 (mouse)Not determined969428566103428698Mouse
1301573Etohcta8_methanol conditioned taste aversion 8 (mouse)Not determined972859058106859205Mouse
10054068El8_mepilepsy 8 (mouse)Not determined972859058106859205Mouse

Markers in Region
AI467128  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm38973,104,241 - 73,104,347UniSTSGRCm38
MGSCv37972,952,048 - 72,952,154UniSTSGRCm37
Celera970,290,527 - 70,290,633UniSTS
Cytogenetic Map9DUniSTS
Whitehead/MRC_RH9701.68UniSTS


Expression


Sequence


RefSeq Acc Id: ENSMUST00000034737   ⟹   ENSMUSP00000034737
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl973,009,680 - 73,011,720 (+)Ensembl
GRCm38.p6 Ensembl973,102,398 - 73,104,438 (+)Ensembl
RefSeq Acc Id: ENSMUST00000167514   ⟹   ENSMUSP00000132527
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl973,009,792 - 73,011,474 (+)Ensembl
GRCm38.p6 Ensembl973,102,510 - 73,104,192 (+)Ensembl
RefSeq Acc Id: ENSMUST00000172578   ⟹   ENSMUSP00000133850
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl973,009,118 - 73,010,169 (+)Ensembl
GRCm38.p6 Ensembl973,101,836 - 73,102,887 (+)Ensembl
RefSeq Acc Id: ENSMUST00000173734   ⟹   ENSMUSP00000133915
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl973,009,680 - 73,011,720 (+)Ensembl
GRCm38.p6 Ensembl973,102,398 - 73,104,438 (+)Ensembl
RefSeq Acc Id: NM_001311106   ⟹   NP_001298035
RefSeq Status: VALIDATED
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39973,009,680 - 73,011,725 (+)NCBI
GRCm38973,102,398 - 73,104,443 (+)NCBI
Sequence:
RefSeq Acc Id: NM_025890   ⟹   NP_080166
RefSeq Status: VALIDATED
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39973,009,680 - 73,011,725 (+)NCBI
GRCm38973,102,398 - 73,104,443 (+)NCBI
MGSCv37972,950,205 - 72,952,250 (+)RGD
Celera970,288,684 - 70,290,729 (+)RGD
cM Map9 ENTREZGENE
Sequence:
RefSeq Acc Id: XM_006511372   ⟹   XP_006511435
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39973,009,090 - 73,011,617 (+)NCBI
GRCm38973,101,810 - 73,104,335 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006511374   ⟹   XP_006511437
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39973,008,660 - 73,013,915 (+)NCBI
GRCm38973,101,381 - 73,106,631 (+)NCBI
Sequence:
RefSeq Acc Id: NP_080166   ⟸   NM_025890
- Peptide Label: isoform 1
- UniProtKB: A7YIL2 (UniProtKB/Swiss-Prot),   Q9CRD6 (UniProtKB/Swiss-Prot),   Q9CWU5 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006511435   ⟸   XM_006511372
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_006511437   ⟸   XM_006511374
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: NP_001298035   ⟸   NM_001311106
- Peptide Label: isoform 2
- UniProtKB: Q9CWU5 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSMUSP00000133850   ⟸   ENSMUST00000172578
RefSeq Acc Id: ENSMUSP00000034737   ⟸   ENSMUST00000034737
RefSeq Acc Id: ENSMUSP00000133915   ⟸   ENSMUST00000173734
RefSeq Acc Id: ENSMUSP00000132527   ⟸   ENSMUST00000167514
Protein Domains
KH   KH-like RNA-binding

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q9CWU5-F1-model_v2 AlphaFold Q9CWU5 1-440 view protein structure

Promoters
RGD ID:8670166
Promoter ID:EPDNEW_M13113
Type:multiple initiation site
Name:Khdc3_1
Description:Mus musculus KH domain containing 3, subcortical maternal complexmember , transcript variant 1, mRNA.
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm38973,102,462 - 73,102,522EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene MGI:1914241 AgrOrtholog
Ensembl Genes ENSMUSG00000092622 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Transcript ENSMUST00000034737 ENTREZGENE
  ENSMUST00000034737.13 UniProtKB/Swiss-Prot
  ENSMUST00000167514.2 UniProtKB/Swiss-Prot
  ENSMUST00000172578.2 UniProtKB/TrEMBL
  ENSMUST00000173734 ENTREZGENE
  ENSMUST00000173734.9 UniProtKB/Swiss-Prot
Gene3D-CATH 3.30.1370.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro KH_dom_type_1_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  MOEP19_KH-like UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report mmu:66991 UniProtKB/Swiss-Prot
MGD MGI:1914241 ENTREZGENE
NCBI Gene 66991 ENTREZGENE
PANTHER KH DOMAIN-CONTAINING PROTEIN 3 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  OOCYTE-EXPRESSED PROTEIN HOMOLOG-RELATED UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam MOEP19 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Khdc3 PhenoGen
UniProt A7YIL2 ENTREZGENE
  G3UXW5_MOUSE UniProtKB/TrEMBL
  KHDC3_MOUSE UniProtKB/Swiss-Prot
  Q9CRD6 ENTREZGENE
  Q9CWU5 ENTREZGENE
UniProt Secondary A7YIL2 UniProtKB/Swiss-Prot
  Q9CRD6 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2012-06-26 Khdc3  KH domain containing 3, subcortical maternal complex member  2410004A20Rik  RIKEN cDNA 2410004A20 gene  Symbol and/or name change 5135510 APPROVED