CNTF (ciliary neurotrophic factor) - Rat Genome Database

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Gene: CNTF (ciliary neurotrophic factor) Homo sapiens
Analyze
Symbol: CNTF
Name: ciliary neurotrophic factor
RGD ID: 734034
HGNC Page HGNC
Description: Exhibits growth factor activity and interleukin-6 receptor binding activity. Involved in ciliary neurotrophic factor-mediated signaling pathway; negative regulation of neuron apoptotic process; and positive regulation of macromolecule metabolic process. Predicted to localize to axon and extracellular space. Implicated in Huntington's disease; disease of mental health; glaucoma; multiple sclerosis; and obesity. Biomarker of keratoconus.
Type: protein-coding
RefSeq Status: REVIEWED
Also known as: Ciliary Neuronotrophic Factor; HCNTF
RGD Orthologs
Mouse
Rat
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1158,622,665 - 58,625,733 (+)EnsemblGRCh38hg38GRCh38
GRCh381158,622,665 - 58,625,733 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh371158,390,138 - 58,393,206 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361158,146,721 - 58,149,778 (+)NCBINCBI36hg18NCBI36
Build 341158,146,720 - 58,149,778NCBI
Celera1155,749,246 - 55,752,306 (+)NCBI
Cytogenetic Map11q12.1NCBI
HuRef1154,738,219 - 54,741,279 (+)NCBIHuRef
CHM1_11158,255,656 - 58,258,716 (+)NCBICHM1_1
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
Phenotype Annotations     Click to see Annotation Detail View

Human Phenotype
References

Additional References at PubMed
PMID:1281789   PMID:1714745   PMID:1840538   PMID:1861138   PMID:1883844   PMID:1915374   PMID:2294592   PMID:7597043   PMID:7753485   PMID:7796798   PMID:7810882   PMID:7852996  
PMID:8075647   PMID:8449041   PMID:8627290   PMID:9236223   PMID:10391209   PMID:10812968   PMID:10966616   PMID:11464862   PMID:11849142   PMID:11857064   PMID:12470191   PMID:12477932  
PMID:12643274   PMID:12890930   PMID:14715713   PMID:15047605   PMID:15180291   PMID:15474906   PMID:15489334   PMID:15843428   PMID:16051226   PMID:16181490   PMID:16210701   PMID:16344560  
PMID:16696750   PMID:16797081   PMID:16969278   PMID:17192435   PMID:17272411   PMID:17353931   PMID:17563726   PMID:17651970   PMID:18029348   PMID:18203754   PMID:18282590   PMID:18293418  
PMID:18303965   PMID:18524890   PMID:18583979   PMID:18603262   PMID:18669911   PMID:18728012   PMID:18775332   PMID:19008309   PMID:19082510   PMID:19086053   PMID:19453261   PMID:19525893  
PMID:19573019   PMID:19628720   PMID:19751193   PMID:19833146   PMID:19913121   PMID:20219210   PMID:20378664   PMID:20428961   PMID:20584990   PMID:20628086   PMID:20952820   PMID:21873635  
PMID:21912637   PMID:22337942   PMID:23128233   PMID:23194670   PMID:23653362   PMID:23654315   PMID:23676962   PMID:23944834   PMID:23948898   PMID:24129709   PMID:24191003   PMID:24802752  
PMID:25118897   PMID:25416956   PMID:25833344   PMID:26187860   PMID:26817395   PMID:28065597   PMID:28323167   PMID:28514442   PMID:28765641   PMID:29564604   PMID:29869578   PMID:30209240  
PMID:31925656   PMID:32037156   PMID:32296183   PMID:32814053  


Genomics

Comparative Map Data
CNTF
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1158,622,665 - 58,625,733 (+)EnsemblGRCh38hg38GRCh38
GRCh381158,622,665 - 58,625,733 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh371158,390,138 - 58,393,206 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361158,146,721 - 58,149,778 (+)NCBINCBI36hg18NCBI36
Build 341158,146,720 - 58,149,778NCBI
Celera1155,749,246 - 55,752,306 (+)NCBI
Cytogenetic Map11q12.1NCBI
HuRef1154,738,219 - 54,741,279 (+)NCBIHuRef
CHM1_11158,255,656 - 58,258,716 (+)NCBICHM1_1
Cntf
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391912,740,892 - 12,742,996 (-)NCBIGRCm39mm39
GRCm39 Ensembl1912,741,024 - 12,742,996 (-)Ensembl
GRCm381912,763,528 - 12,765,632 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1912,763,660 - 12,765,632 (-)EnsemblGRCm38mm10GRCm38
MGSCv371912,838,018 - 12,840,122 (-)NCBIGRCm37mm9NCBIm37
MGSCv361912,830,679 - 12,845,972 (-)NCBImm8
Celera1913,428,744 - 13,430,848 (-)NCBICelera
Cytogenetic Map19ANCBI
cM Map198.73NCBI
Cntf
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21209,887,854 - 209,889,877 (-)NCBI
Rnor_6.0 Ensembl1229,599,009 - 229,601,032 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01229,599,009 - 229,601,032 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01236,752,366 - 236,754,389 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41215,842,668 - 215,844,691 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11216,001,097 - 216,003,121 (-)NCBI
Celera1207,298,120 - 207,300,143 (-)NCBICelera
RH 3.4 Map11492.6RGD
Cytogenetic Map1q43NCBI
Cntf
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555113,527,552 - 3,534,348 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049555113,527,552 - 3,531,275 (+)NCBIChiLan1.0ChiLan1.0
CNTF
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11157,336,792 - 57,341,127 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1157,336,792 - 57,341,121 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01153,876,081 - 53,882,870 (+)NCBIMhudiblu_PPA_v0panPan3
CNTF
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11837,758,148 - 37,765,698 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1837,294,972 - 37,302,526 (-)NCBI
ROS_Cfam_1.01838,411,043 - 38,418,605 (-)NCBI
UMICH_Zoey_3.11838,010,392 - 38,017,942 (-)NCBI
UNSW_CanFamBas_1.01837,581,125 - 37,588,678 (-)NCBI
UU_Cfam_GSD_1.01838,203,356 - 38,210,926 (-)NCBI
Cntf
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494713,596,340 - 13,602,966 (-)NCBI
SpeTri2.0NW_0049365813,710,171 - 3,715,753 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CNTF
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1212,492,777 - 12,495,401 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2212,129,497 - 12,133,389 (-)NCBISscrofa10.2Sscrofa10.2susScr3
CNTF
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1114,724,562 - 14,730,698 (-)NCBI
ChlSab1.1 Ensembl114,728,383 - 14,730,150 (-)Ensembl
Cntf
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248641,785,215 - 1,788,608 (-)NCBI

Position Markers
WI-12111  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh371158,388,304 - 58,388,403UniSTSGRCh37
Build 361158,144,880 - 58,144,979RGDNCBI36
Celera1155,747,404 - 55,747,503RGD
Cytogenetic Map11q12.2UniSTS
Cytogenetic Map11q12UniSTS
HuRef1154,736,377 - 54,736,476UniSTS
GeneMap99-GB4 RH Map11218.49UniSTS
Whitehead-RH Map11284.0UniSTS
GDB:194646  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh371158,391,507 - 58,391,992UniSTSGRCh37
Build 361158,148,083 - 58,148,568RGDNCBI36
Celera1155,750,607 - 55,751,092RGD
Cytogenetic Map11q12.2UniSTS
HuRef1154,739,580 - 54,740,065UniSTS
GDB:360980  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh371158,391,403 - 58,391,627UniSTSGRCh37
Build 361158,147,979 - 58,148,203RGDNCBI36
Celera1155,750,503 - 55,750,727RGD
Cytogenetic Map11q12.2UniSTS
HuRef1154,739,476 - 54,739,700UniSTS
D11S4596  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh371158,391,670 - 58,391,952UniSTSGRCh37
Build 361158,148,246 - 58,148,528RGDNCBI36
Celera1155,750,770 - 55,751,052RGD
Cytogenetic Map11q12.2UniSTS
HuRef1154,739,743 - 54,740,025UniSTS
Stanford-G3 RH Map112477.0UniSTS
NCBI RH Map11502.5UniSTS
GeneMap99-G3 RH Map112477.0UniSTS
CNTF_1913  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh371158,392,496 - 58,393,261UniSTSGRCh37
Build 361158,149,072 - 58,149,837RGDNCBI36
Celera1155,751,596 - 55,752,361RGD
HuRef1154,740,569 - 54,741,334UniSTS
ZFP91__4947  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh371158,391,530 - 58,392,322UniSTSGRCh37
Build 361158,148,106 - 58,148,898RGDNCBI36
Celera1155,750,630 - 55,751,422RGD
HuRef1154,739,603 - 54,740,395UniSTS
CNTF  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh371158,393,788 - 58,393,888UniSTSGRCh37
GRCh371158,391,730 - 58,391,886UniSTSGRCh37
Build 361158,148,306 - 58,148,462RGDNCBI36
Celera1155,752,888 - 55,752,988UniSTS
Celera1155,750,830 - 55,750,986RGD
HuRef1154,739,803 - 54,739,959UniSTS
HuRef1154,741,861 - 54,741,963UniSTS
GeneMap99-GB4 RH Map11217.96UniSTS
D1S3694  
Human AssemblyChrPosition (strand)SourceJBrowse
Cytogenetic Map1p36UniSTS
Cytogenetic Map7q34UniSTS
Cytogenetic Map12qUniSTS
Cytogenetic Map6p21.1UniSTS
Cytogenetic Map11q12.2UniSTS
Cytogenetic Map1q31UniSTS
Cytogenetic Map13q34UniSTS
Cytogenetic Map17p13.1UniSTS
Cytogenetic Map11q13.1-q13.3UniSTS
Cytogenetic Map7q36.1UniSTS

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:403
Count of miRNA genes:348
Interacting mature miRNAs:371
Transcripts:ENST00000361987
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.


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 sensory system visual system adipose tissue appendage entire extraembryonic component pharyngeal arch
High 6 6 6
Medium 4 11 1 4 1 645 13 707 1 7 1 4 22 621
Low 2074 1585 1370 410 1223 284 3320 1761 2434 240 1028 1421 141 984 1967 4
Below cutoff 353 1357 340 198 686 170 383 416 577 169 402 187 29 1 198 194 1

Sequence

Nucleotide Sequences
RefSeq Transcripts NG_008776 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_000614 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AK314118 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AP001350 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AP003557 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC068030 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC069167 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC074963 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC074964 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH471076 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  DB241497 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  DB341875 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  S72921 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  X55889 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  X55890 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  X60477 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  X60478 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  X60542 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENST00000361987   ⟹   ENSP00000355370
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl1158,622,665 - 58,625,733 (+)Ensembl
RefSeq Acc Id: NM_000614   ⟹   NP_000605
RefSeq Status: REVIEWED
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh381158,622,665 - 58,625,733 (+)NCBI
GRCh371158,390,146 - 58,393,206 (+)ENTREZGENE
Build 361158,146,721 - 58,149,778 (+)NCBI Archive
HuRef1154,738,219 - 54,741,279 (+)ENTREZGENE
CHM1_11158,255,656 - 58,258,716 (+)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_000605   ⟸   NM_000614
- UniProtKB: P26441 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSP00000355370   ⟸   ENST00000361987

Promoters
RGD ID:6788634
Promoter ID:HG_KWN:12967
Type:Non-CpG
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:Lymphoblastoid
Transcripts:UC001NNA.2
Position:
Human AssemblyChrPosition (strand)Source
Build 361158,146,451 - 58,146,951 (+)MPROMDB
RGD ID:6850152
Promoter ID:EP33035
Type:single initiation site
Name:HS_CNTF
Description:Ciliary neurotrophic factor, CNTF gene.
SO ACC ID:SO:0000170
Source:EPD (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Tissues & Cell Lines:nervous system
Experiment Methods:Primer extension with homologous sequence ladder
Position:
Human AssemblyChrPosition (strand)Source
Build 361158,146,797 - 58,146,857EPD
RGD ID:7220413
Promoter ID:EPDNEW_H15952
Type:initiation region
Name:CNTF_1
Description:ciliary neurotrophic factor
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_H15953  
Experiment Methods:Single-end sequencing.; Paired-end sequencing.
Position:
Human AssemblyChrPosition (strand)Source
GRCh381158,622,672 - 58,622,732EPDNEW
RGD ID:7220415
Promoter ID:EPDNEW_H15953
Type:initiation region
Name:CNTF_2
Description:ciliary neurotrophic factor
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_H15952  
Experiment Methods:Single-end sequencing.; Paired-end sequencing.
Position:
Human AssemblyChrPosition (strand)Source
GRCh381158,624,370 - 58,624,430EPDNEW

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
NM_000614.4(CNTF):c.115-6G>A single nucleotide variant CILIARY NEUROTROPHIC FACTOR POLYMORPHISM [RCV000019045] Chr11:58624028 [GRCh38]
Chr11:58391501 [GRCh37]
Chr11:11q12.1
benign
GRCh38/hg38 11q11-12.1(chr11:55319519-58998777)x3 copy number gain See cases [RCV000142757] Chr11:55319519..58998777 [GRCh38]
Chr11:55086995..58766250 [GRCh37]
Chr11:54843571..58522826 [NCBI36]
Chr11:11q11-12.1
pathogenic
GRCh37/hg19 11p15.5-q25(chr11:230616-134938470) copy number gain See cases [RCV000511729] Chr11:230616..134938470 [GRCh37]
Chr11:11p15.5-q25
pathogenic
GRCh37/hg19 11p15.5-q25(chr11:230616-134938470)x3 copy number gain See cases [RCV000510881] Chr11:230616..134938470 [GRCh37]
Chr11:11p15.5-q25
pathogenic
GRCh37/hg19 11p11.12-q12.1(chr11:49313405-59008426)x3 copy number gain not provided [RCV000683370] Chr11:49313405..59008426 [GRCh37]
Chr11:11p11.12-q12.1
uncertain significance
GRCh37/hg19 11p15.5-q25(chr11:198510-134934063)x3 copy number gain not provided [RCV000737348] Chr11:198510..134934063 [GRCh37]
Chr11:11p15.5-q25
pathogenic
GRCh37/hg19 11p15.5-q25(chr11:70864-134938470)x3 copy number gain not provided [RCV000749874] Chr11:70864..134938470 [GRCh37]
Chr11:11p15.5-q25
pathogenic
NM_000614.4(CNTF):c.146A>G (p.Asn49Ser) single nucleotide variant not provided [RCV000947349] Chr11:58624065 [GRCh38]
Chr11:58391538 [GRCh37]
Chr11:11q12.1
benign
GRCh37/hg19 11q12.1(chr11:58237819-58800374)x3 copy number gain not provided [RCV001249328] Chr11:58237819..58800374 [GRCh37]
Chr11:11q12.1
not provided
Single allele deletion Intellectual disability [RCV001293382] Chr11:118359328..118372573 [GRCh37]
Chr11:11p15.3-q23.3
pathogenic

Additional Information

Database Acc Id Source(s)
AGR Gene HGNC:2169 AgrOrtholog
COSMIC CNTF COSMIC
Ensembl Genes ENSG00000242689 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSP00000355370 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENST00000361987 ENTREZGENE, UniProtKB/Swiss-Prot
GTEx ENSG00000242689 GTEx
HGNC ID HGNC:2169 ENTREZGENE
Human Proteome Map CNTF Human Proteome Map
InterPro 4_helix_cytokine-like_core UniProtKB/Swiss-Prot
  Ciliary_neurotrophic_fac_CNTF UniProtKB/Swiss-Prot
KEGG Report hsa:1270 UniProtKB/Swiss-Prot
NCBI Gene 1270 ENTREZGENE
OMIM 118945 OMIM
PANTHER PTHR15196 UniProtKB/Swiss-Prot
Pfam CNTF UniProtKB/Swiss-Prot
PharmGKB PA26683 PharmGKB
Superfamily-SCOP SSF47266 UniProtKB/Swiss-Prot
UniProt CNTF_HUMAN UniProtKB/Swiss-Prot, ENTREZGENE
UniProt Secondary B2RAB2 UniProtKB/Swiss-Prot