Ndnf (neuron-derived neurotrophic factor) - Rat Genome Database

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Advanced Search (OLGA)
Gene: Ndnf (neuron-derived neurotrophic factor) Mus musculus
Analyze
Symbol: Ndnf
Name: neuron-derived neurotrophic factor
RGD ID: 1332106
MGI Page MGI
Description: Enables heparin binding activity. Involved in gonadotrophin-releasing hormone neuronal migration to the hypothalamus; response to ischemia; and vascular wound healing. Acts upstream of or within extracellular matrix organization and positive regulation of cell-substrate adhesion. Located in extracellular matrix. Is expressed in several structures, including brain; embryo mesenchyme; intervertebral disc; lung; and molar. Human ortholog(s) of this gene implicated in hypogonadotropic hypogonadism. Orthologous to human NDNF (neuron derived neurotrophic factor).
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: A930038C07Rik; epide; epidermacan; fibronectin type-III domain-containing protein C4orf31 homolog
RGD Orthologs
Human
Rat
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCm39 - Mouse Genome Assembly GRCm39
Position:
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39665,648,595 - 65,689,307 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl665,648,574 - 65,689,310 (+)EnsemblGRCm39 Ensembl
GRCm38665,671,611 - 65,712,323 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl665,671,590 - 65,712,326 (+)EnsemblGRCm38mm10GRCm38
MGSCv37665,621,605 - 65,656,924 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36665,601,189 - 65,636,508 (+)NCBIMGSCv36mm8
Celera667,797,717 - 67,833,030 (+)NCBICelera
Cytogenetic Map6C1NCBI
cM Map630.29NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

Phenotype Annotations     Click to see Annotation Detail View

Mammalian Phenotype
References

References - curated
# Reference Title Reference Citation
1. Functional annotation of a full-length mouse cDNA collection. Kawai J, etal., Nature. 2001 Feb 8;409(6821):685-90.
2. Electronic Transfer of Homolog Data MGD and Homologene mouse data transfer
3. MGDs mouse GO annotations MGD data from the GO Consortium
4. Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs. Okazaki Y, etal., Nature. 2002 Dec 5;420(6915):563-73.
5. Mouse MP Annotation Import Pipeline RGD automated import pipeline
6. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
7. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
8. Database resources of the National Center for Biotechnology Information. Wheeler DL, etal., Nucleic Acids Res 2001 Jan 1;29(1):11-6.
Additional References at PubMed
PMID:10349636   PMID:11042159   PMID:11076861   PMID:12477932   PMID:16141072   PMID:16141073   PMID:18287559   PMID:18757743   PMID:19501082   PMID:20016822   PMID:21267068   PMID:21491433  
PMID:21873635   PMID:24154525   PMID:24706764   PMID:24952961   PMID:25654972   PMID:26238476   PMID:26727548   PMID:27224923   PMID:30104732   PMID:30269988   PMID:30392798   PMID:30413647  
PMID:30635555   PMID:30858601   PMID:31680851   PMID:31883645   PMID:32160552   PMID:32386544   PMID:33184213   PMID:33186530   PMID:33188733   PMID:33789083   PMID:34004146   PMID:34038743  
PMID:34220450   PMID:34314698   PMID:34387544   PMID:34478630   PMID:34686328   PMID:35051783   PMID:35926459   PMID:36046622   PMID:36378956   PMID:36550293   PMID:36774552   PMID:37015225  
PMID:37543035   PMID:38070510   PMID:38159590   PMID:38362542   PMID:38443186   PMID:38743567   PMID:38760574   PMID:39058591   PMID:39180750  


Genomics

Comparative Map Data
Ndnf
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39665,648,595 - 65,689,307 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl665,648,574 - 65,689,310 (+)EnsemblGRCm39 Ensembl
GRCm38665,671,611 - 65,712,323 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl665,671,590 - 65,712,326 (+)EnsemblGRCm38mm10GRCm38
MGSCv37665,621,605 - 65,656,924 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36665,601,189 - 65,636,508 (+)NCBIMGSCv36mm8
Celera667,797,717 - 67,833,030 (+)NCBICelera
Cytogenetic Map6C1NCBI
cM Map630.29NCBI
NDNF
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh384121,035,613 - 121,072,535 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl4121,035,613 - 121,073,021 (-)EnsemblGRCh38hg38GRCh38
GRCh374121,956,768 - 121,993,690 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 364122,176,232 - 122,213,123 (-)NCBINCBI36Build 36hg18NCBI36
Celera4119,341,856 - 119,378,753 (-)NCBICelera
Cytogenetic Map4q27NCBI
HuRef4117,683,742 - 117,720,651 (-)NCBIHuRef
CHM1_14121,933,274 - 121,970,187 (-)NCBICHM1_1
T2T-CHM13v2.04124,339,896 - 124,376,833 (-)NCBIT2T-CHM13v2.0
Ndnf
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8496,274,147 - 96,311,624 (+)NCBIGRCr8
mRatBN7.2494,944,392 - 94,981,871 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl494,944,360 - 94,981,873 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx4100,193,058 - 100,230,529 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0495,968,010 - 96,005,484 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0494,369,186 - 94,406,663 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0496,528,830 - 96,565,780 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl496,562,725 - 96,564,611 (+)NCBIRnor6.0rn6Rnor6.0
Rnor_5.04161,312,929 - 161,350,269 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4495,313,453 - 95,350,122 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1495,362,576 - 95,593,810 (+)NCBI
Celera489,680,807 - 89,717,405 (+)NCBICelera
Cytogenetic Map4q31NCBI
Ndnf
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495542819,552,493 - 19,587,712 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495542819,552,493 - 19,587,712 (+)NCBIChiLan1.0ChiLan1.0
NDNF
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v23118,827,117 - 118,864,569 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan14119,105,165 - 119,148,571 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v04113,242,800 - 113,283,834 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.14124,379,629 - 124,422,793 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl4124,386,606 - 124,422,793 (-)Ensemblpanpan1.1panPan2
NDNF
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11919,009,966 - 19,053,047 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1919,036,372 - 19,049,937 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1919,232,899 - 19,275,734 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.01919,136,515 - 19,179,608 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl1919,136,294 - 19,177,150 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.11919,095,810 - 19,138,637 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01919,367,085 - 19,409,920 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01919,845,970 - 19,888,691 (+)NCBIUU_Cfam_GSD_1.0
Ndnf
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440530166,494,805 - 66,525,931 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_004936662594,331 - 624,980 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_004936662593,848 - 624,974 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
NDNF
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl8102,996,281 - 103,088,230 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.18103,047,783 - 103,094,800 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.28110,382,585 - 110,544,736 (+)NCBISscrofa10.2Sscrofa10.2susScr3
NDNF
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1768,320,045 - 68,356,644 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl768,320,690 - 68,356,577 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366603747,281,797 - 47,324,186 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Ndnf
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247771,035,991 - 1,072,996 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046247771,036,389 - 1,072,271 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:762
Count of miRNA genes:504
Interacting mature miRNAs:578
Transcripts:ENSMUST00000054351, ENSMUST00000169795
Prediction methods: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 (GRCm39)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
4142271Egq8_mearly growth QTL 8 (mouse)Not determined450382396633110Mouse
1301266Lmr4_mleishmaniasis resistance 4 (mouse)Not determined64209335876093500Mouse
12910785Pwgrq16_mpost-weaning growth rate QTL 16 (mouse)64380374777788506Mouse
11252142Mom12_mModifier of Min 12 (mouse)63387226167872400Mouse
4140983Srilp_msleep response to influenza, light phase (mouse)Not determined4870349075424693Mouse
12910798Pwgrq5_mpre-weaning growth rate QTL 5 (mouse)64380374777788506Mouse
1300767Aliq4_macute lung injury QTL 4 (mouse)Not determined63627333270273435Mouse
4142259Tabw2_mtally ho associated body weight 2 (mouse)Not determined46912919136400690Mouse
25314319Histh6_mhistamine hypersensitivity 6 (mouse)648696934125336963Mouse
4142126W3q3_mweight 3 weeks QTL 3 (mouse)Not determined450382396633110Mouse
14746995Manh60_mmandible shape 60 (mouse)63720266271202662Mouse
12910807Pwbwq11_mpost-weaning body weight QTL 11 (mouse)64380374777788506Mouse
25314320Histh5_mhistamine hypersensitivity 5 (mouse)648696934148351498Mouse
1301254Skts11_mskin tumor susceptibility 11 (mouse)Not determined65115613485156284Mouse
1357442Dbts1_mdiabetes 1 (mouse)Not determined61823414773364675Mouse
12910802Pwbwq12_mpost-weaning body weight QTL 12 (mouse)64380374777788506Mouse
4141094Hrtr1_mheart rate 1 (mouse)Not determined3674146370741463Mouse
1300618Pgia19_mproteoglycan induced arthritis 19 (mouse)Not determined64529099387403016Mouse
12910809Pwbwq10_mpost-weaning body weight QTL 10 (mouse)64380374777788506Mouse
12910820Ogrq3_moverall growth rate QTL 3 (mouse)64380374777788506Mouse
26884414Bzwq12_mbi-zygomatic width QTL 12, 16 week (mouse)63400000139076998Mouse
4142361W10q11_mweight 10 weeks QTL 11 (mouse)Not determined450382396633110Mouse
4142232W6q4_mweight 6 weeks QTL 4 (mouse)Not determined450382396633110Mouse
10412213Sxbq2_mSGC/Knj cross B6 QTL 2 (mouse)Not determined61991268571299759Mouse
4141454Obrq4_mobesity resistance QTL 4 (mouse)Not determined3170349965703611Mouse
13208564Bmiq7_mbody mass index QTL 7 (mouse)62499999979976983Mouse
26884441Sklq3_mskull length QTL 3, 5 week (mouse)6760000080576983Mouse
10412119Stv_mstriatal volumne (mouse)Not determined660026991100026967Mouse
1300959Lxw2_mlupus BXSB x NZW 2 (mouse)Not determined63387226167872400Mouse
1558977Skmw10_mskeletal muscle weight 10 (mouse)Not determined65842456692424693Mouse
1301962Eila2_methanol induced locomotor activity 2 (mouse)Not determined648703490125333748Mouse
4141028Mclr_mmethylcholanthrene lymphoma resistance (mouse)Not determined5435041188356155Mouse
1301326Trbv4c2_mT cell receptor beta variable 4 (mouse)Not determined64086823071356155Mouse
10043972Obq28_mobesity QTL 28 (mouse)Not determined65851741692517416Mouse
1300556Cia6_mcollagen induced arthritis QTL 6 (mouse)Not determined6446488487403016Mouse
1558984Cplaq9_mcircadian period of locomotor activity 9 (mouse)Not determined63864656092584431Mouse
10412157Fl1n_mfatty liver 1 in NSY (mouse)Not determined645290993128811995Mouse
25440480Moaq2_mmodifier of alien QTL 2 (mouse)63050001117476961Mouse
1357683Igf1sl1_mIGF-1 serum levels 1 (mouse)Not determined652138693116132228Mouse
15039373Adip28_madiposity 28 (mouse)65628519490285194Mouse
4141782Mrdq5_mmodifier of retinal degeneration QTL 5 (mouse)Not determined3282758578215957Mouse
15039375Bw41_mbody weight QTL 41 (mouse)65628519490285194Mouse
1301369Im4_mimmunoregulatory 4 (mouse)Not determined66346172197461888Mouse
12880424V25Dq4_mvitamin D inactive form serum level QTL 4 (mouse)64157698575576985Mouse
12880425V25Dq5_mvitamin D inactive form serum level QTL 5 (mouse)63267698066676980Mouse
11040600Lmr4c_mleishmaniasis resistance 4c (mouse)64209335876093500Mouse
11040601Lmr4a_mleishmaniasis resistance 4a (mouse)64209335876093500Mouse
11533915Mts4_mmammary tumor susceptibility 4 (mouse)64209335876093500Mouse
10043885Cia6c_mcollagen induced arthritis QTL 6c (mouse)Not determined64444280571096451Mouse
1357539Bsbob3_mBSB obesity 3 (mouse)Not determined63644845670448576Mouse
1301740Bwq2_mbody weight QTL 2 (mouse)Not determined66003466394034782Mouse


Expression

RNA-SEQ Expression


Sequence


Ensembl Acc Id: ENSMUST00000054351   ⟹   ENSMUSP00000051297
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl665,648,574 - 65,689,310 (+)Ensembl
GRCm38.p6 Ensembl665,671,590 - 65,712,326 (+)Ensembl
Ensembl Acc Id: ENSMUST00000169795
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl665,678,414 - 65,680,424 (+)Ensembl
GRCm38.p6 Ensembl665,701,430 - 65,703,440 (+)Ensembl
RefSeq Acc Id: NM_172399   ⟹   NP_765987
RefSeq Status: VALIDATED
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39665,648,595 - 65,683,914 (+)NCBI
GRCm38665,671,611 - 65,706,930 (+)NCBI
MGSCv37665,621,605 - 65,656,924 (+)RGD
Celera667,797,717 - 67,833,030 (+)RGD
cM Map6 ENTREZGENE
Sequence:
RefSeq Acc Id: XM_006506528   ⟹   XP_006506591
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39665,654,128 - 65,689,307 (+)NCBI
GRCm38665,676,480 - 65,712,323 (+)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_765987 (Get FASTA)   NCBI Sequence Viewer  
  XP_006506591 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAH47154 (Get FASTA)   NCBI Sequence Viewer  
  BAC26349 (Get FASTA)   NCBI Sequence Viewer  
  BAC33925 (Get FASTA)   NCBI Sequence Viewer  
  EDK98778 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSMUSP00000051297
  ENSMUSP00000051297.5
GenBank Protein Q8C119 (Get FASTA)   NCBI Sequence Viewer  
RefSeq Acc Id: NP_765987   ⟸   NM_172399
- Peptide Label: precursor
- UniProtKB: Q80VN3 (UniProtKB/Swiss-Prot),   Q8BWV6 (UniProtKB/Swiss-Prot),   Q8C119 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006506591   ⟸   XM_006506528
- Peptide Label: isoform X1
- UniProtKB: Q80VN3 (UniProtKB/Swiss-Prot),   Q8BWV6 (UniProtKB/Swiss-Prot),   Q8C119 (UniProtKB/Swiss-Prot)
- Sequence:
Ensembl Acc Id: ENSMUSP00000051297   ⟸   ENSMUST00000054351
Protein Domains
Fibronectin type-III

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q8C119-F1-model_v2 AlphaFold Q8C119 1-568 view protein structure

Promoters
RGD ID:6838795
Promoter ID:MM_KWN:46242
Type:CpG-Island
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:BoneMarrow_0Hour,   BoneMarrow_2Hour,   BoneMarrow_4Hour,   Brain,   Lung,   MEF_B4
Transcripts:NM_172399
Position:
Mouse AssemblyChrPosition (strand)Source
MGSCv36665,621,424 - 65,621,924 (+)MPROMDB
RGD ID:6889896
Promoter ID:EPDNEW_M8399
Type:multiple initiation site
Name:Ndnf_1
Description:Mus musculus neuron-derived neurotrophic factor , 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
GRCm38665,671,611 - 65,671,671EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene MGI:1915419 AgrOrtholog
Ensembl Genes ENSMUSG00000049001 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSMUST00000054351 ENTREZGENE
  ENSMUST00000054351.6 UniProtKB/Swiss-Prot
Gene3D-CATH 2.60.40.10 UniProtKB/Swiss-Prot
InterPro FN3_dom UniProtKB/Swiss-Prot
  FN3_sf UniProtKB/Swiss-Prot
  Ig-like_fold UniProtKB/Swiss-Prot
  NDNF UniProtKB/Swiss-Prot
  NDNF_C UniProtKB/Swiss-Prot
KEGG Report mmu:68169 UniProtKB/Swiss-Prot
MGD MGI:1915419 ENTREZGENE
NCBI Gene 68169 ENTREZGENE
PANTHER PROTEIN NDNF UniProtKB/Swiss-Prot
  PTHR14619 UniProtKB/Swiss-Prot
Pfam DUF2369 UniProtKB/Swiss-Prot
  NDNF_C UniProtKB/Swiss-Prot
PhenoGen Ndnf PhenoGen
SMART FN3 UniProtKB/Swiss-Prot
Superfamily-SCOP SSF49265 UniProtKB/Swiss-Prot
UniProt NDNF_MOUSE UniProtKB/Swiss-Prot
  Q80VN3 ENTREZGENE
  Q8BWV6 ENTREZGENE
  Q8C119 ENTREZGENE
UniProt Secondary Q80VN3 UniProtKB/Swiss-Prot
  Q8BWV6 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2012-09-25 Ndnf  neuron-derived neurotrophic factor  A930038C07Rik  RIKEN cDNA A930038C07 gene  Symbol and/or name change 5135510 APPROVED