Klhl40 (kelch-like family member 40) - Rat Genome Database

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Gene: Klhl40 (kelch-like family member 40) Rattus norvegicus
Analyze
Symbol: Klhl40
Name: kelch-like family member 40
RGD ID: 1305368
Description: Predicted to be involved in regulation of protein metabolic process and skeletal muscle fiber development. Predicted to act upstream of or within skeletal muscle fiber differentiation. Predicted to be located in cytoplasm. Predicted to be part of Cul3-RING ubiquitin ligase complex. Predicted to be active in A band and I band. Human ortholog(s) of this gene implicated in nemaline myopathy 8. Orthologous to human KLHL40 (kelch like family member 40); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 3,7-dihydropurine-6-thione; atrazine.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: Kbtbd5; kelch repeat and BTB (POZ) domain containing 5; kelch repeat and BTB domain-containing protein 5; kelch-like 40; kelch-like 40 (Drosophila); kelch-like protein 40; LOC316088; similar to kelch repeat and BTB (POZ) domain containing 5
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr88130,318,793 - 130,324,309 (+)NCBIGRCr8
mRatBN7.28121,441,285 - 121,446,801 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl8121,441,287 - 121,446,800 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx8127,040,450 - 127,045,966 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.08125,239,517 - 125,245,033 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.08123,068,719 - 123,074,236 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.08130,416,265 - 130,421,871 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl8130,416,355 - 130,421,871 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.08129,596,172 - 129,601,706 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.48127,153,472 - 127,159,307 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.18127,173,602 - 127,178,958 (-)NCBI
Celera8120,575,465 - 120,580,981 (+)NCBICelera
Cytogenetic Map8q32NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
2. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
3. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
4. GOA pipeline RGD automated data pipeline
5. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
6. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:24361185   PMID:24960163   PMID:25940086  


Genomics

Comparative Map Data
Klhl40
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr88130,318,793 - 130,324,309 (+)NCBIGRCr8
mRatBN7.28121,441,285 - 121,446,801 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl8121,441,287 - 121,446,800 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx8127,040,450 - 127,045,966 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.08125,239,517 - 125,245,033 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.08123,068,719 - 123,074,236 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.08130,416,265 - 130,421,871 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl8130,416,355 - 130,421,871 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.08129,596,172 - 129,601,706 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.48127,153,472 - 127,159,307 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.18127,173,602 - 127,178,958 (-)NCBI
Celera8120,575,465 - 120,580,981 (+)NCBICelera
Cytogenetic Map8q32NCBI
KLHL40
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38342,685,537 - 42,692,544 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl342,685,537 - 42,692,544 (+)EnsemblGRCh38hg38GRCh38
GRCh37342,727,029 - 42,734,036 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36342,702,015 - 42,708,942 (+)NCBINCBI36Build 36hg18NCBI36
Build 34342,702,014 - 42,708,942NCBI
Celera342,667,406 - 42,674,333 (+)NCBICelera
Cytogenetic Map3p22.1NCBI
HuRef342,772,653 - 42,779,580 (+)NCBIHuRef
CHM1_1342,678,186 - 42,685,113 (+)NCBICHM1_1
T2T-CHM13v2.0342,703,548 - 42,710,555 (+)NCBIT2T-CHM13v2.0
Klhl40
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm399121,606,673 - 121,612,885 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl9121,606,673 - 121,612,884 (+)EnsemblGRCm39 Ensembl
GRCm389121,777,499 - 121,791,200 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl9121,777,607 - 121,783,818 (+)EnsemblGRCm38mm10GRCm38
MGSCv379121,686,725 - 121,692,937 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv369121,623,722 - 121,632,518 (+)NCBIMGSCv36mm8
Celera9122,250,832 - 122,257,196 (+)NCBICelera
Cytogenetic Map9F4NCBI
cM Map972.61NCBI
Klhl40
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495542028,117,898 - 28,122,270 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495542028,117,553 - 28,122,391 (-)NCBIChiLan1.0ChiLan1.0
KLHL40
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2242,648,634 - 42,657,268 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1342,653,395 - 42,662,029 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0342,592,977 - 42,600,100 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1343,657,128 - 43,664,055 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl343,657,128 - 43,664,055 (+)Ensemblpanpan1.1panPan2
KLHL40
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12311,812,268 - 11,820,426 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2311,813,550 - 11,820,420 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2311,788,054 - 11,794,913 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.02312,103,227 - 12,110,087 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2312,103,414 - 12,110,084 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12311,905,185 - 11,912,008 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02312,047,337 - 12,054,167 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02312,051,398 - 12,058,303 (+)NCBIUU_Cfam_GSD_1.0
Klhl40
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405118200,063,283 - 200,072,287 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049366952,414,573 - 2,424,702 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049366952,417,938 - 2,424,622 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
KLHL40
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1326,202,677 - 26,211,522 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11326,202,607 - 26,211,528 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21328,863,095 - 28,876,907 (+)NCBISscrofa10.2Sscrofa10.2susScr3
KLHL40
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1224,141,759 - 4,149,158 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl224,142,192 - 4,148,710 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_023666041163,051,860 - 163,059,265 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Klhl40
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462473077,007,063 - 77,011,413 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462473077,004,787 - 77,012,643 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Klhl40
9 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:161
Count of miRNA genes:117
Interacting mature miRNAs:128
Transcripts:ENSRNOT00000026234
Prediction methods:Microtar, Miranda, Rnahybrid
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 (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1554321Bmd3Bone mineral density QTL 37.90.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)840952565123900184Rat
2300181Bmd55Bone mineral density QTL 555.70.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)876468691121468691Rat
61437Cia6Collagen induced arthritis QTL 6joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)882460758122812818Rat
738011Anxrr9Anxiety related response QTL 96.1exploratory behavior trait (VT:0010471)number of entries into a discrete space in an experimental apparatus (CMO:0000960)893535351123900184Rat
1358893Bp263Blood pressure QTL 2635.01arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)893965141123900184Rat
1358903Bp252Blood pressure QTL 25270.0001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)893965141123900184Rat
738014Anxrr15Anxiety related response QTL 153.60.005locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)895718998123900184Rat
2300182Bmd56Bone mineral density QTL 565.4femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)895718998123900184Rat

Markers in Region
RH138376  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.28121,446,501 - 121,446,635 (+)MAPPERmRatBN7.2
Rnor_6.08130,421,572 - 130,421,705NCBIRnor6.0
Rnor_5.08129,601,407 - 129,601,540UniSTSRnor5.0
RGSC_v3.48127,153,638 - 127,153,771UniSTSRGSC3.4
Celera8120,580,682 - 120,580,815UniSTS
RH 3.4 Map81256.49UniSTS
Cytogenetic Map8q32UniSTS


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 3 8 11 1 8
Low 43 7 2 2 13 18 7
Below cutoff 2 18 11 10 11 47 8 17 2

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000026234   ⟹   ENSRNOP00000026234
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl8121,441,287 - 121,446,800 (+)Ensembl
Rnor_6.0 Ensembl8130,416,355 - 130,421,871 (+)Ensembl
RefSeq Acc Id: NM_001108195   ⟹   NP_001101665
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr88130,318,793 - 130,324,309 (+)NCBI
mRatBN7.28121,441,285 - 121,446,801 (+)NCBI
Rnor_6.08130,416,355 - 130,421,871 (+)NCBI
Rnor_5.08129,596,172 - 129,601,706 (+)NCBI
RGSC_v3.48127,153,472 - 127,159,307 (-)RGD
Celera8120,575,465 - 120,580,981 (+)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_001101665 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL76818 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000026234
  ENSRNOP00000026234.6
Reference Protein Sequences
RefSeq Acc Id: NP_001101665   ⟸   NM_001108195
- UniProtKB: D4AA43 (UniProtKB/TrEMBL),   A6I459 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000026234   ⟸   ENSRNOT00000026234
Protein Domains
BTB

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D4AA43-F1-model_v2 AlphaFold D4AA43 1-560 view protein structure

Transcriptome

eQTL   View at Phenogen
WGCNA   View at Phenogen
Tissue/Strain Expression   View at Phenogen

Promoters
RGD ID:13696391
Promoter ID:EPDNEW_R6915
Type:single initiation site
Name:Klhl40_1
Description:kelch-like family member 40
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.08130,416,356 - 130,416,416EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1305368 AgrOrtholog
BioCyc Gene G2FUF-28680 BioCyc
Ensembl Genes ENSRNOG00000019390 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000026234 ENTREZGENE
  ENSRNOT00000026234.6 UniProtKB/TrEMBL
Gene3D-CATH 1.25.40.420 UniProtKB/TrEMBL
  2.120.10.80 UniProtKB/TrEMBL
InterPro BACK UniProtKB/TrEMBL
  BTB/POZ-like UniProtKB/TrEMBL
  BTB/POZ_fold UniProtKB/TrEMBL
  Kelch-like_gigaxonin UniProtKB/TrEMBL
  Kelch-typ_b-propeller UniProtKB/TrEMBL
  Kelch_1 UniProtKB/TrEMBL
KEGG Report rno:316088 UniProtKB/TrEMBL
NCBI Gene 316088 ENTREZGENE
PANTHER KELCH PROTEIN UniProtKB/TrEMBL
  PTHR24412:SF22 UniProtKB/TrEMBL
Pfam BACK UniProtKB/TrEMBL
  BTB UniProtKB/TrEMBL
  Kelch_1 UniProtKB/TrEMBL
PhenoGen Klhl40 PhenoGen
PIRSF Kelch-like_protein_gigaxonin UniProtKB/TrEMBL
PROSITE BTB UniProtKB/TrEMBL
RatGTEx ENSRNOG00000019390 RatGTEx
SMART BACK UniProtKB/TrEMBL
  BTB UniProtKB/TrEMBL
  Kelch UniProtKB/TrEMBL
Superfamily-SCOP BTB/POZ_fold UniProtKB/TrEMBL
  SSF117281 UniProtKB/TrEMBL
UniProt A6I459 ENTREZGENE, UniProtKB/TrEMBL
  D4AA43 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2013-05-24 Klhl40  kelch-like family member 40  LOC686128  similar to kelch repeat and BTB (POZ) domain containing 5  Data merged from RGD:1585471 1643240 APPROVED
2013-02-27 Klhl40  kelch-like family member 40  Klhl40  kelch-like 40 (Drosophila)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2013-01-17 Klhl40  kelch-like 40 (Drosophila)  Kbtbd5  kelch repeat and BTB (POZ) domain containing 5  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 Kbtbd5  kelch repeat and BTB (POZ) domain containing 5   Kbtbd5_predicted  kelch repeat and BTB (POZ) domain containing 5 (predicted)  'predicted' is removed 2292626 APPROVED
2006-11-19 LOC686128  similar to kelch repeat and BTB (POZ) domain containing 5      Symbol and Name status set to provisional 70820 PROVISIONAL
2005-01-12 Kbtbd5_predicted  kelch repeat and BTB (POZ) domain containing 5 (predicted)      Symbol and Name status set to approved 70820 APPROVED