Clxn (calaxin) - Rat Genome Database

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Gene: Clxn (calaxin) Rattus norvegicus
Analyze
Symbol: Clxn
Name: calaxin
RGD ID: 1594548
Description: Predicted to enable calcium ion binding activity. Predicted to be involved in regulation of flagellated sperm motility. Predicted to be located in cilium. Human ortholog(s) of this gene implicated in primary ciliary dyskinesia. Orthologous to human CLXN (calaxin); INTERACTS WITH 17beta-estradiol; 17beta-estradiol 3-benzoate; 2,3,7,8-Tetrachlorodibenzofuran.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: EF hand calcium binding domain 1; EF-hand calcium-binding domain-containing protein 1; Efcab1; LOC301957; similar to EF hand calcium binding domain 1
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81199,410,925 - 99,500,713 (-)NCBIGRCr8
mRatBN7.21185,977,231 - 85,996,561 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1185,983,304 - 85,996,538 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1194,725,999 - 94,739,235 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01187,385,950 - 87,399,180 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01186,440,762 - 86,454,000 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01190,214,563 - 90,234,319 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1190,221,056 - 90,234,286 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01193,267,696 - 93,287,964 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Celera1184,713,805 - 84,727,035 (-)NCBICelera
Cytogenetic Map11q23NCBI
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

Biological Process

Cellular Component
cilium  (ISO)

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. GOA pipeline RGD automated data 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

Genomics

Comparative Map Data
Clxn
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81199,410,925 - 99,500,713 (-)NCBIGRCr8
mRatBN7.21185,977,231 - 85,996,561 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1185,983,304 - 85,996,538 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1194,725,999 - 94,739,235 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01187,385,950 - 87,399,180 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01186,440,762 - 86,454,000 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01190,214,563 - 90,234,319 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1190,221,056 - 90,234,286 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01193,267,696 - 93,287,964 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Celera1184,713,805 - 84,727,035 (-)NCBICelera
Cytogenetic Map11q23NCBI
CLXN
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38848,710,789 - 48,735,311 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl848,710,789 - 48,735,311 (-)EnsemblGRCh38hg38GRCh38
GRCh37849,623,348 - 49,647,870 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36849,798,520 - 49,810,344 (-)NCBINCBI36Build 36hg18NCBI36
Celera845,614,709 - 45,635,104 (-)NCBICelera
Cytogenetic Map8q11.21NCBI
HuRef845,091,764 - 45,112,108 (-)NCBIHuRef
CHM1_1849,679,835 - 49,700,230 (-)NCBICHM1_1
T2T-CHM13v2.0849,088,639 - 49,113,160 (-)NCBIT2T-CHM13v2.0
Clxn
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391614,724,315 - 14,786,925 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1614,724,470 - 14,799,235 (+)EnsemblGRCm39 Ensembl
GRCm381614,906,224 - 14,969,061 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1614,906,606 - 14,981,371 (+)EnsemblGRCm38mm10GRCm38
MGSCv371614,906,739 - 14,924,615 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361614,820,224 - 14,838,100 (+)NCBIMGSCv36mm8
Celera1615,485,609 - 15,503,486 (+)NCBICelera
Cytogenetic Map16A1NCBI
cM Map1610.09NCBI
Clxn
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554548,578,068 - 8,591,992 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554548,570,014 - 8,591,904 (-)NCBIChiLan1.0ChiLan1.0
CLXN
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2764,352,177 - 64,373,215 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1840,045,620 - 40,066,631 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0845,144,794 - 45,165,530 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1842,529,560 - 42,550,005 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl842,529,560 - 42,550,005 (-)Ensemblpanpan1.1panPan2
CLXN
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.129941,821 - 964,424 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl29955,631 - 964,507 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha291,368,435 - 1,391,005 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.029998,111 - 1,020,746 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl291,005,818 - 1,020,854 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.129939,944 - 962,492 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0291,166,038 - 1,188,555 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0291,203,459 - 1,226,090 (-)NCBIUU_Cfam_GSD_1.0
Clxn
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440530378,797,027 - 78,808,661 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365903,986,779 - 3,998,530 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049365903,986,827 - 3,998,489 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CLXN
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl479,378,796 - 79,389,520 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1479,375,487 - 79,387,110 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2486,861,769 - 86,870,580 (+)NCBISscrofa10.2Sscrofa10.2susScr3
CLXN
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1844,841,780 - 44,867,521 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl844,855,482 - 44,866,845 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366603997,173,554 - 97,184,711 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Clxn
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247356,781,011 - 6,790,039 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046247356,780,869 - 6,813,671 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Clxn
65 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:263
Count of miRNA genes:175
Interacting mature miRNAs:196
Transcripts:ENSRNOT00000071986
Prediction methods:Microtar, 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 (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
724554Iddm17Insulin dependent diabetes mellitus QTL 170.001blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)111897620886241447Rat
724561Plsm4Polydactyly-luxate syndrome (PLS) morphotypes QTL 40.0003forelimb integrity trait (VT:0010562)front foot phalanges count (CMO:0001947)115445753486241447Rat
7411658Foco27Food consumption QTL 2716.20.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)115635142486241447Rat
10058954Gmadr7Adrenal mass QTL 72.490.0049adrenal gland mass (VT:0010420)both adrenal glands wet weight to body weight ratio (CMO:0002411)116034659086241447Rat
634339Niddm50Non-insulin dependent diabetes mellitus QTL 503.32blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)116642214886241447Rat
1354593Stl12Serum triglyceride level QTL 123.36blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)116642214886241447Rat


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 29 11 11
Low 3 41 22 7 14 7 7 8 45 31 30 7
Below cutoff 2 34 33 5 33 1 2 3 1

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000071986   ⟹   ENSRNOP00000067253
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1185,983,304 - 85,996,538 (-)Ensembl
Rnor_6.0 Ensembl1190,221,056 - 90,234,286 (-)Ensembl
RefSeq Acc Id: NM_001106930   ⟹   NP_001100400
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81199,487,448 - 99,500,682 (-)NCBI
mRatBN7.21185,983,304 - 85,996,538 (-)NCBI
Rnor_6.01190,221,056 - 90,234,286 (-)NCBI
Rnor_5.01193,267,696 - 93,287,964 (-)NCBI
Celera1184,713,805 - 84,727,035 (-)RGD
Sequence:
RefSeq Acc Id: XM_039088258   ⟹   XP_038944186
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81199,486,097 - 99,500,705 (-)NCBI
mRatBN7.21185,981,952 - 85,996,561 (-)NCBI
RefSeq Acc Id: XM_063270453   ⟹   XP_063126523
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81199,491,497 - 99,500,701 (-)NCBI
RefSeq Acc Id: XR_005491018
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81199,480,738 - 99,500,713 (-)NCBI
mRatBN7.21185,977,231 - 85,996,557 (-)NCBI
RefSeq Acc Id: XR_010055947
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81199,480,738 - 99,500,700 (-)NCBI
RefSeq Acc Id: XR_010055948
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81199,410,925 - 99,500,700 (-)NCBI
Protein Sequences
Protein RefSeqs NP_001100400 (Get FASTA)   NCBI Sequence Viewer  
  XP_038944186 (Get FASTA)   NCBI Sequence Viewer  
  XP_063126523 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL77833 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000067253
  ENSRNOP00000067253.1
Reference Protein Sequences
RefSeq Acc Id: NP_001100400   ⟸   NM_001106930
- UniProtKB: M0RCD9 (UniProtKB/TrEMBL),   A6JSS4 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000067253   ⟸   ENSRNOT00000071986
RefSeq Acc Id: XP_038944186   ⟸   XM_039088258
- Peptide Label: isoform X1
RefSeq Acc Id: XP_063126523   ⟸   XM_063270453
- Peptide Label: isoform X2
Protein Domains
EF-hand

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-M0RCD9-F1-model_v2 AlphaFold M0RCD9 1-212 view protein structure

Transcriptome

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

Promoters
RGD ID:13698354
Promoter ID:EPDNEW_R8879
Type:multiple initiation site
Name:Efcab1_1
Description:EF hand calcium binding domain 1
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_6.01190,234,254 - 90,234,314EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1594548 AgrOrtholog
BioCyc Gene G2FUF-20530 BioCyc
Ensembl Genes ENSRNOG00000050091 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000071986 ENTREZGENE
  ENSRNOT00000071986.2 UniProtKB/TrEMBL
Gene3D-CATH EF-hand UniProtKB/TrEMBL
InterPro EF-hand-like_dom UniProtKB/TrEMBL
  EF_Hand_1_Ca_BS UniProtKB/TrEMBL
  EF_hand_dom UniProtKB/TrEMBL
  Recoverin UniProtKB/TrEMBL
KEGG Report rno:301957 UniProtKB/TrEMBL
NCBI Gene 301957 ENTREZGENE
PANTHER EF-HAND CALCIUM-BINDING DOMAIN-CONTAINING PROTEIN 1 UniProtKB/TrEMBL
  PTHR23055 UniProtKB/TrEMBL
Pfam EF-hand_6 UniProtKB/TrEMBL
  EF_hand_5 UniProtKB/TrEMBL
PhenoGen Clxn PhenoGen
PRINTS RECOVERIN UniProtKB/TrEMBL
PROSITE EF_HAND_1 UniProtKB/TrEMBL
  EF_HAND_2 UniProtKB/TrEMBL
RatGTEx ENSRNOG00000050091 RatGTEx
SMART EFh UniProtKB/TrEMBL
Superfamily-SCOP SSF47473 UniProtKB/TrEMBL
UniProt A6JSS4 ENTREZGENE, UniProtKB/TrEMBL
  M0RCD9 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2021-12-09 Clxn  calaxin  Efcab1  EF hand calcium binding domain 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-03-04 Efcab1  EF hand calcium binding domain 1  LOC301957  similar to EF hand calcium binding domain 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-11-20 LOC301957  similar to EF hand calcium binding domain 1      Symbol and Name status set to provisional 70820 PROVISIONAL