Clnk (cytokine-dependent hematopoietic cell linker) - Rat Genome Database

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Gene: Clnk (cytokine-dependent hematopoietic cell linker) Rattus norvegicus
Analyze
Symbol: Clnk
Name: cytokine-dependent hematopoietic cell linker
RGD ID: 1562417
Description: Predicted to be involved in several processes, including mast cell degranulation; negative regulation of natural killer cell activation; and positive regulation of natural killer cell cytokine production. Predicted to be located in mast cell granule. Predicted to be part of protein-containing complex. Orthologous to human CLNK (cytokine dependent hematopoietic cell linker); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; copper atom; copper(0).
Type: protein-coding
RefSeq Status: MODEL
Previously known as: LOC295518; mast cell immunoreceptor signal transducer; Mist; RGD1562417; similar to MIST
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
GRCr81476,136,446 - 76,315,364 (+)NCBIGRCr8
mRatBN7.21471,923,894 - 72,101,180 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1471,873,105 - 72,101,208 (+)EnsemblmRatBN7.2 Ensembl
Rnor_6.01476,657,165 - 76,834,050 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1476,657,311 - 76,833,161 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01476,642,654 - 76,818,423 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41477,226,212 - 77,331,417 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera1470,962,479 - 71,053,885 (+)NCBICelera
Cytogenetic Map14q21NCBI
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
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. 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
Additional References at PubMed
PMID:10562326   PMID:10744659   PMID:12681493   PMID:15199160   PMID:16439675   PMID:26009488  


Genomics

Comparative Map Data
Clnk
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81476,136,446 - 76,315,364 (+)NCBIGRCr8
mRatBN7.21471,923,894 - 72,101,180 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1471,873,105 - 72,101,208 (+)EnsemblmRatBN7.2 Ensembl
Rnor_6.01476,657,165 - 76,834,050 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1476,657,311 - 76,833,161 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01476,642,654 - 76,818,423 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41477,226,212 - 77,331,417 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera1470,962,479 - 71,053,885 (+)NCBICelera
Cytogenetic Map14q21NCBI
CLNK
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38410,486,395 - 10,734,846 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl410,486,395 - 10,684,768 (-)EnsemblGRCh38hg38GRCh38
GRCh37410,488,019 - 10,686,392 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36410,100,934 - 10,295,587 (-)NCBINCBI36Build 36hg18NCBI36
Celera410,956,589 - 11,151,166 (-)NCBICelera
Cytogenetic Map4p16.1NCBI
HuRef49,825,306 - 10,019,669 (-)NCBIHuRef
CHM1_1410,489,788 - 10,684,579 (-)NCBICHM1_1
T2T-CHM13v2.0410,462,366 - 10,710,706 (-)NCBIT2T-CHM13v2.0
Clnk
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39538,858,951 - 39,034,201 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl538,863,805 - 39,034,155 (-)EnsemblGRCm39 Ensembl
GRCm38538,705,588 - 38,876,858 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl538,706,462 - 38,876,812 (-)EnsemblGRCm38mm10GRCm38
MGSCv37539,097,696 - 39,267,932 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36538,994,711 - 39,165,061 (-)NCBIMGSCv36mm8
Celera536,172,576 - 36,340,924 (-)NCBICelera
Cytogenetic Map5B3NCBI
cM Map520.81NCBI
Clnk
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0NW_0049555492,166,891 - 2,375,902 (+)NCBIChiLan1.0ChiLan1.0
CLNK
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2310,738,885 - 10,826,044 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1410,947,036 - 11,034,132 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v044,902,117 - 5,107,145 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1410,209,773 - 10,417,418 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl410,209,803 - 10,469,596 (-)Ensemblpanpan1.1panPan2
CLNK
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1368,929,239 - 69,083,777 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl368,881,358 - 69,080,263 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha371,427,775 - 71,636,882 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0369,636,088 - 69,839,267 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl369,636,081 - 69,835,734 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1368,912,696 - 69,114,388 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0369,075,523 - 69,277,350 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0369,453,965 - 69,655,821 (+)NCBIUU_Cfam_GSD_1.0
Clnk
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440528562,643,205 - 62,726,207 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_00493647716,280,978 - 16,427,110 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_00493647716,364,465 - 16,427,125 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CLNK
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl86,608,853 - 6,769,572 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.186,604,975 - 6,769,769 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
CLNK
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12739,333,435 - 39,574,050 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl2739,481,226 - 39,573,795 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366604786,107,610 - 86,357,594 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Clnk
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462475520,667,325 - 20,817,497 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Clnk
1031 total Variants

QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
631839Niddm37Non-insulin dependent diabetes mellitus QTL 373.37blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)141103062295876975Rat
70187Pancm5Pancreatic morphology QTL 516.7pancreas mass (VT:0010144)pancreas weight to body weight ratio (CMO:0000630)143032009280829842Rat
2313048Bss84Bone structure and strength QTL 843.10.0001tibia strength trait (VT:1000284)tibia total energy absorbed before break (CMO:0001736)143766971982669719Rat
2313084Bss83Bone structure and strength QTL 832.90.0001tibia size trait (VT:0100001)tibia midshaft endosteal cross-sectional area (CMO:0001716)143766971982669719Rat
2313089Bss81Bone structure and strength QTL 813.40.0001body length (VT:0001256)body length, nose to rump (CMO:0000079)143766971982669719Rat
2313100Bss82Bone structure and strength QTL 8230.0001tibia size trait (VT:0100001)tibia midshaft cross-sectional area (CMO:0001717)143766971982669719Rat
738037Hcas6Hepatocarcinoma susceptibility QTL 62.93liver integrity trait (VT:0010547)liver nonremodeling tumorous lesion volume to total liver volume ratio (CMO:0001464)143905723783368335Rat
70214Niddm28Non-insulin dependent diabetes mellitus QTL 284.06blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)143999825175582726Rat
631523Pia13Pristane induced arthritis QTL 133.3joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)144079346098037301Rat
1300136Rf22Renal function QTL 223.9renal blood flow trait (VT:2000006)absolute change in renal vascular resistance (CMO:0001900)144226252995023211Rat
1549834Scl45Serum cholesterol level QTL 455.8blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)145002321195023211Rat
2300197Scl59Serum cholesterol level QTL 59blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)1455147478100147478Rat
9590294Uminl4Urine mineral level QTL 45.660.001urine mineral amount (VT:0015086)urine electrolyte level (CMO:0000593)1455624247100624247Rat
9589034Epfw11Epididymal fat weight QTL 1160.001epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)1455624247100624247Rat
2317879Alcrsp27Alcohol response QTL 273.30.63response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)1456631369101631369Rat
634328Hc5Hypercalciuria QTL 52.3urine calcium amount (VT:0002985)urine calcium excretion rate (CMO:0000763)1458184885103184885Rat
70153Bp59Blood pressure QTL 593.2arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)146875779683368335Rat
1582259Gluco23Glucose level QTL 233.10.0008blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)1470053989104886043Rat
1641900Alcrsp11Alcohol response QTL 11alcohol metabolism trait (VT:0015089)blood ethanol level (CMO:0000535)1470053989104886043Rat

Markers in Region
BF402166  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21472,082,073 - 72,082,225 (+)MAPPERmRatBN7.2
Rnor_6.01476,814,930 - 76,815,081NCBIRnor6.0
Rnor_5.01476,799,322 - 76,799,473UniSTSRnor5.0
RGSC_v3.41477,313,331 - 77,313,482UniSTSRGSC3.4
Celera1471,034,789 - 71,034,940UniSTS
Cytogenetic Map14q21UniSTS


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 1 2
Low 3 11 27 16 18 16 1 1 11 18 15 9 1
Below cutoff 24 18 13 13 7 9 40 17 26 7

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000076730   ⟹   ENSRNOP00000068476
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1471,873,151 - 72,101,208 (+)Ensembl
Rnor_6.0 Ensembl1476,657,311 - 76,833,161 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000088197   ⟹   ENSRNOP00000075554
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1471,873,105 - 72,101,208 (+)Ensembl
Rnor_6.0 Ensembl1476,732,650 - 76,833,013 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000107673   ⟹   ENSRNOP00000078642
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1471,873,151 - 72,101,208 (+)Ensembl
RefSeq Acc Id: XM_006251108   ⟹   XP_006251170
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81476,136,446 - 76,312,824 (+)NCBI
mRatBN7.21471,923,894 - 72,100,164 (+)NCBI
Rnor_6.01476,657,165 - 76,834,050 (+)NCBI
Rnor_5.01476,642,654 - 76,818,423 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017599489   ⟹   XP_017454978
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81476,136,446 - 76,315,364 (+)NCBI
mRatBN7.21471,923,895 - 72,101,180 (+)NCBI
Rnor_6.01476,657,165 - 76,834,050 (+)NCBI
Sequence:
Reference Protein Sequences
RefSeq Acc Id: XP_006251170   ⟸   XM_006251108
- Peptide Label: isoform X2
- UniProtKB: A0A0G2KAW6 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_017454978   ⟸   XM_017599489
- Peptide Label: isoform X1
- UniProtKB: A0A0G2KAW6 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000075554   ⟸   ENSRNOT00000088197
RefSeq Acc Id: ENSRNOP00000068476   ⟸   ENSRNOT00000076730
RefSeq Acc Id: ENSRNOP00000078642   ⟸   ENSRNOT00000107673
Protein Domains
SH2

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-A0A096MKD7-F1-model_v2 AlphaFold A0A096MKD7 1-436 view protein structure

Transcriptome

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


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1562417 AgrOrtholog
BioCyc Gene G2FUF-15412 BioCyc
Ensembl Genes ENSRNOG00000051169 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000076730.3 UniProtKB/TrEMBL
  ENSRNOT00000088197.2 UniProtKB/TrEMBL
  ENSRNOT00000107673.1 UniProtKB/TrEMBL
Gene3D-CATH 3.30.505.10 UniProtKB/TrEMBL
InterPro SH2 UniProtKB/TrEMBL
  SH2_dom_sf UniProtKB/TrEMBL
NCBI Gene 295518 ENTREZGENE
PANTHER CYTOKINE-DEPENDENT HEMATOPOIETIC CELL LINKER UniProtKB/TrEMBL
  SH2 DOMAIN CONTAINING PROTEIN UniProtKB/TrEMBL
Pfam SH2 UniProtKB/TrEMBL
PhenoGen Clnk PhenoGen
PRINTS SH2DOMAIN UniProtKB/TrEMBL
PROSITE SH2 UniProtKB/TrEMBL
RatGTEx ENSRNOG00000051169 RatGTEx
SMART SH2 UniProtKB/TrEMBL
Superfamily-SCOP SSF55550 UniProtKB/TrEMBL
UniProt A0A096MKD7_RAT UniProtKB/TrEMBL
  A0A0G2KAW6 ENTREZGENE, UniProtKB/TrEMBL
  A0A8I5ZLA7_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2010-04-23 Clnk  cytokine-dependent hematopoietic cell linker  Mist  mast cell immunoreceptor signal transducer  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-09-24 Mist  mast cell immunoreceptor signal transducer  Clnk  cytokine-dependent hematopoietic cell linker  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-02-29 Clnk  cytokine-dependent hematopoietic cell linker  RGD1562417_predicted  similar to MIST (predicted)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-01-09 RGD1562417_predicted  similar to MIST (predicted)  LOC682529  similar to cytokine-dependent hematopoietic cell linker  Data merged from RGD:1597945 1643240 APPROVED
2006-11-20 LOC682529  similar to cytokine-dependent hematopoietic cell linker      Symbol and Name status set to provisional 70820 PROVISIONAL
2006-03-07 RGD1562417_predicted  similar to MIST (predicted)  LOC295518  similar to MIST  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC295518  similar to MIST      Symbol and Name status set to provisional 70820 PROVISIONAL