Ntf3 (neurotrophin 3) - Rat Genome Database

Name: Ntf3
Creator: Rat Genome Database
License: Creative Commons CC BY 4.0
Keywords: Rat Gene RGD Genome

Gene: Ntf3 (neurotrophin 3) Ictidomys tridecemlineatus

Analyze

Symbol:

Ntf3

Name:

neurotrophin 3

RGD ID:

12692307

Description:

ENCODES a protein that exhibits nerve growth factor binding (ortholog); INVOLVED IN axon guidance (ortholog); brain development (ortholog); enteric nervous system development (ortholog); ASSOCIATED WITH alcohol use disorder (ortholog); Alcohol-Related Disorders (ortholog); Alzheimer's disease (ortholog); FOUND IN cytoplasmic vesicle (ortholog)

Type:

protein-coding

RefSeq Status:

MODEL

Previously known as:

neurotrophin-3

RGD Orthologs

Alliance Genes

More Info

more info ...

More Info

Species	Gene symbol and name	Data Source	Assertion derived from	less info ...
Orthologs ¹				less info ...
Homo sapiens (human):	NTF3 (neurotrophin 3)	NCBI	Ortholog
Mus musculus (house mouse):	Ntf3 (neurotrophin 3)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Rattus norvegicus (Norway rat):	Ntf3 (neurotrophin 3)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chinchilla lanigera (long-tailed chinchilla):	Ntf3 (neurotrophin 3)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Pan paniscus (bonobo/pygmy chimpanzee):	NTF3 (neurotrophin 3)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Canis lupus familiaris (dog):	NTF3 (neurotrophin 3)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Sus scrofa (pig):	NTF3 (neurotrophin 3)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chlorocebus sabaeus (green monkey):	NTF3 (neurotrophin 3)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Heterocephalus glaber (naked mole-rat):	Ntf3 (neurotrophin 3)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline

Latest Assembly:

SpeTri2.0 - Squirrel SpeTri2.0 Assembly

Position:

Squirrel Assembly	Chr	Position (strand)	Source	Genome Browsers
Squirrel Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HiC_Itri_2	NW_024404945	103,495,858 - 103,555,782 (-)	NCBI		HiC_Itri_2
SpeTri2.0 Ensembl	NW_004936709	2,163,334 - 2,223,552 (-)	Ensembl	SpeTri2.0	SpeTri2.0 Ensembl
SpeTri2.0	NW_004936709	2,163,510 - 2,223,429 (-)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

alcohol use disorder (ISO)

Alcohol-Related Disorders (ISO)

Alzheimer's disease (ISO)

asthma (ISO)

atrial heart septal defect 1 (ISO)

autistic disorder (ISO)

borna disease (ISO)

chronic obstructive pulmonary disease (ISO)

diabetic neuropathy (ISO)

Down syndrome (ISO)

epilepsy with generalized tonic-clonic seizures (ISO)

episodic ataxia type 1 (ISO)

genetic disease (ISO)

Hearing Loss (ISO)

Hirschsprung's disease (ISO)

hydrocephalus (ISO)

Hyperalgesia (ISO)

Hyperphosphatemic Familial Tumoral Calcinosis 1 (ISO)

lymphoproliferative syndrome 2 (ISO)

Nerve Degeneration (ISO)

pulmonary sarcoidosis (ISO)

schizophrenia (ISO)

Spinal Cord Injuries (ISO)

status epilepticus (ISO)

tetralogy of Fallot (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

axon guidance (ISO)

brain development (ISO)

cell surface receptor protein tyrosine kinase signaling pathway (IEA)

enteric nervous system development (ISO)

epidermis development (ISO)

generation of neurons (ISO)

glial cell fate determination (ISO)

induction of positive chemotaxis (IEA)

mechanoreceptor differentiation (ISO)

memory (IEA)

modulation of chemical synaptic transmission (IEA,ISO)

myelination (ISO)

negative regulation of neuron apoptotic process (IEA,ISO)

negative regulation of peptidyl-tyrosine phosphorylation (IEA)

nerve development (IEA,ISO)

nerve growth factor signaling pathway (IEA)

nervous system development (ISO)

neuromuscular synaptic transmission (ISO)

neuron apoptotic process (ISO)

neuron development (ISO)

neuron projection morphogenesis (IEA)

peripheral nervous system development (IEA,ISO)

positive chemotaxis (IEA)

positive regulation of cell migration (IEA)

positive regulation of cell population proliferation (IEA)

positive regulation of glial cell differentiation (ISO)

positive regulation of peptidyl-serine phosphorylation (IEA)

positive regulation of peptidyl-tyrosine phosphorylation (IEA)

positive regulation of receptor internalization (IEA)

positive regulation of transcription by RNA polymerase II (ISO)

regulation of apoptotic process (IEA,ISO)

regulation of neuron apoptotic process (ISO)

regulation of neuron differentiation (IEA)

response to immobilization stress (ISO)

smooth muscle cell differentiation (ISO)

Cellular Component

axon (IEA)

cytoplasmic vesicle (ISO)

dendrite (IEA)

extracellular region (IEA)

extracellular space (IEA)

membrane (IEA)

synaptic vesicle (IEA)

Molecular Function

chemoattractant activity (IEA)

growth factor activity (IEA)

nerve growth factor binding (ISO)

nerve growth factor receptor binding (IEA)

neurotrophin receptor binding (IEA)

protein binding (ISO)

References

Additional References at PubMed

PMID:30032202

Genomics

Comparative Map Data

Ntf3
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)

Squirrel Assembly	Chr	Position (strand)	Source	Genome Browsers
Squirrel Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HiC_Itri_2	NW_024404945	103,495,858 - 103,555,782 (-)	NCBI		HiC_Itri_2
SpeTri2.0 Ensembl	NW_004936709	2,163,334 - 2,223,552 (-)	Ensembl	SpeTri2.0	SpeTri2.0 Ensembl
SpeTri2.0	NW_004936709	2,163,510 - 2,223,429 (-)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

NTF3
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38	12	5,430,332 - 5,495,299 (+)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38.p14 Ensembl	12	5,432,108 - 5,521,536 (+)	Ensembl	GRCh38		hg38	GRCh38
GRCh37	12	5,541,274 - 5,604,465 (+)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	12	5,411,541 - 5,474,726 (+)	NCBI	NCBI36	Build 36	hg18	NCBI36
Build 34	12	5,473,526 - 5,474,725	NCBI
Celera	12	7,162,184 - 7,225,194 (+)	NCBI		Celera
Cytogenetic Map	12	p13.31	NCBI
HuRef	12	5,455,606 - 5,458,036 (+)	NCBI		HuRef
CHM1_1	12	5,540,527 - 5,604,287 (+)	NCBI		CHM1_1
T2T-CHM13v2.0	12	5,437,400 - 5,502,089 (+)	NCBI		T2T-CHM13v2.0

Ntf3
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	6	126,078,375 - 126,143,703 (-)	NCBI	GRCm39	GRCm39	mm39
GRCm39 Ensembl	6	126,078,375 - 126,143,873 (-)	Ensembl		GRCm39 Ensembl
GRCm38	6	126,101,412 - 126,166,772 (-)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	6	126,101,412 - 126,166,910 (-)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	6	126,051,430 - 126,116,762 (-)	NCBI	GRCm37	MGSCv37	mm9	NCBIm37
MGSCv36	6	126,067,031 - 126,130,540 (-)	NCBI		MGSCv36	mm8
Celera	6	127,765,447 - 127,832,752 (-)	NCBI		Celera
Cytogenetic Map	6	F3	NCBI
cM Map	6	60.45	NCBI

Ntf3
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	4	160,601,161 - 160,670,623 (-)	NCBI		GRCr8
mRatBN7.2	4	158,914,984 - 158,984,453 (-)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	4	158,914,957 - 158,984,596 (-)	Ensembl		mRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx	4	165,144,795 - 165,214,257 (-)	NCBI	Rnor_SHR	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	4	160,927,698 - 160,997,163 (-)	NCBI	Rnor_SHRSP	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	4	159,561,745 - 159,631,144 (-)	NCBI	Rnor_WKY	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	4	158,636,883 - 158,705,886 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	4	158,636,884 - 158,705,886 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	4	225,638,801 - 225,707,719 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	4	162,435,781 - 162,506,961 (-)	NCBI	RGSC3.4	RGSC_v3.4	rn4	RGSC3.4
RGSC_v3.1	4	162,680,717 - 162,751,897 (-)	NCBI
Celera	4	147,640,921 - 147,710,546 (-)	NCBI		Celera
Cytogenetic Map	4	q42	NCBI

Ntf3
(Chinchilla lanigera - long-tailed chinchilla)

Chinchilla Assembly	Chr	Position (strand)	Source	Genome Browsers
Chinchilla Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChiLan1.0 Ensembl	NW_004955413	3,207,123 - 3,273,491 (+)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955413	3,207,669 - 3,273,371 (+)	NCBI	ChiLan1.0	ChiLan1.0

NTF3
(Pan paniscus - bonobo/pygmy chimpanzee)

Bonobo Assembly	Chr	Position (strand)	Source	Genome Browsers
Bonobo Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
NHGRI_mPanPan1-v2	10	10,982,176 - 11,046,479 (+)	NCBI		NHGRI_mPanPan1-v2
NHGRI_mPanPan1	12	10,978,933 - 11,043,237 (+)	NCBI		NHGRI_mPanPan1
Mhudiblu_PPA_v0	12	5,551,734 - 5,615,981 (+)	NCBI	Mhudiblu_PPA_v0	Mhudiblu_PPA_v0	panPan3
PanPan1.1	12	5,470,093 - 5,534,300 (+)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	12	5,530,508 - 5,533,989 (+)	Ensembl	panpan1.1		panPan2

NTF3
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1	27	39,383,017 - 39,454,613 (-)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
CanFam3.1 Ensembl	27	39,383,152 - 39,454,601 (-)	Ensembl	CanFam3.1		canFam3	CanFam3.1
Dog10K_Boxer_Tasha	27	7,231,693 - 7,233,370 (+)	NCBI		Dog10K_Boxer_Tasha
ROS_Cfam_1.0	27	39,739,752 - 39,811,227 (-)	NCBI		ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl	27	39,739,747 - 39,811,226 (-)	Ensembl		ROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1	27	39,608,720 - 39,679,940 (-)	NCBI		UMICH_Zoey_3.1
UNSW_CanFamBas_1.0	27	39,650,338 - 39,721,747 (-)	NCBI		UNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0	27	6,639,885 - 6,711,187 (+)	NCBI		UU_Cfam_GSD_1.0

NTF3
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	5	65,052,519 - 65,123,788 (-)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	5	65,052,608 - 65,122,645 (-)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	5	67,204,186 - 67,204,959 (+)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

NTF3
(Chlorocebus sabaeus - green monkey)

Green Monkey Assembly	Chr	Position (strand)	Source	Genome Browsers
Green Monkey Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChlSab1.1	11	5,477,208 - 5,542,404 (+)	NCBI	ChlSab1.1	ChlSab1.1	chlSab2
Vero_WHO_p1.0	NW_023666063	2,690,949 - 2,765,784 (-)	NCBI	Vero_WHO_p1.0	Vero_WHO_p1.0

Ntf3
(Heterocephalus glaber - naked mole-rat)

Naked Mole-Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Naked Mole-Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HetGla_female_1.0 Ensembl	NW_004624860	2,416,503 - 2,479,225 (+)	Ensembl	HetGla_female_1.0	HetGla_female_1.0 Ensembl	hetGla2
HetGla 1.0	NW_004624860	2,416,448 - 2,479,216 (+)	NCBI	HetGla_female_1.0	HetGla 1.0	hetGla2

Expression

Sequence

Nucleotide Sequences


RefSeq Transcripts	XM_005338366	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	JAESOR010000004	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

RefSeq Acc Id:

ENSSTOT00000030017 ⟹ ENSSTOP00000018090

Type:

CODING

Position:

Squirrel Assembly	Chr	Position (strand)	Source
SpeTri2.0 Ensembl	NW_004936709	2,163,334 - 2,223,552 (-)	Ensembl

RefSeq Acc Id:

XM_005338366 ⟹ XP_005338423

Type:

CODING

Position:

Squirrel Assembly	Chr	Position (strand)	Source
HiC_Itri_2	NW_024404945	103,495,858 - 103,555,782 (-)	NCBI
SpeTri2.0	NW_004936709	2,163,510 - 2,223,429 (-)	NCBI

Sequence:

show sequence

CGGGGGCGGGCTCCGCGGCGCGTAAGGGGTTAAGGCGCTGAGCGCGGAGCCATCTGGCCGGGTT
GGCTGGTTATAACCGCGCAGATTATGTTCACGGGACTCAGAGTTGAAGGCTCCTCTCCTTACCG
AGCAGCTCTGCGCACCGCCCTGAGAGAGAGCCCGGCGCAACTTTCTTCCCCTCTTCTTTCTTTC
TTCTCTCATTTTCCCCCTGCTGGGTAGTGGCTGCGGCGGGGTGGGGGGGACTTTGAATGACCCA
GCTCACGTCTATCTTTCTCTTCATGTCGACGTCCCTGGAAATAGTCATACGGATGCCATGGTTA
CTTCTGCCACGATCTTACAGGTGAACAAGGTGATGTCCATCTTGTTTTATGTGATATTTCTCGC
TTATCTCCGTGGCATCCAAGGTAACAACATGGATCAAAGGAATTTGCCGGAAGACTCACTCAAC
TCCCTGATTATTAAGCTGATCCAGGCGGATATTTTGAAAAACAAGCTCTCCAAGCAGATGGTGG
ATGTTAAAGAAAATTACCAGAACGTCCTGCCGAAAGCAGAGGCAGCCCGAGAGCCGGAGCAGGG
AGAACCTGCCAGGTCAGAATTCCAGCCAATGATTGCGACAGACACCGAATTGCTGCGACAACAG
AGACGCTACAGTTCCCCCCGAGTCCTGCTAAGCGACAGTACCCCCTTGGAGCCTCCTCCCTTGT
ATCTCATGGAGGATTACGTGGGCAACCCCGTGGTGGCCAACAGAACGTCACGGCGGAAACGGTA
TGCAGAGCATAAGAGTCACCGGGGAGAGTACTCTGTGTGTGACAGTGAGAGTCTGTGGGTGACC
GACAAGTCGTCGGCCATCGACATTCGGGGACACCAGGTCACGGTGCTGGGGGAGATCAAAACCG
GCAACTCTCCCGTCAAACAATATTTTTATGAAACGAGATGTAAAGAAGCCAGGCCAGTCAAAAA
CGGTTGCAGGGGGATCGATGACAAACACTGGAACTCTCAGTGCAAAACGTCCCAAACCTACGTC
CGAGCACTGACTTCAGAAAACAACAAACTCGTAGGCTGGCGCTGGATACGAATAGACACTTCCT
GTGTGTGTGCCTTGTCGAGAAAAATCGGAAGAACATGAATTGGCATCTCTCCCCATATATAAAT
TATTACTTTAAATTATATGATATGCATGTAGCATATAAATGTTTATATTGTTTTTATATATTAT
AAGTTGACCTTTATTTATTAAACTTCAGCAACCCTACAGTATATAAGCTTTTTTCTCAATAAAG
TCAGTGTGCTTGCCTCCCCCCAGGCCTCTCCCATCTGTTAATCTTGTTTTGTGATCTGGCTCTC
AGGAGCCTTTCTGTAAAATCTGTGTACACCAGTACTTTGCATTCAGTATTGTCAAGGCCATGAC
TGTCGCTTTAGTAAACTTGTTAAAATCA

hide sequence

Protein Sequences


Protein RefSeqs	XP_005338423	(Get FASTA)	NCBI Sequence Viewer
Ensembl Protein	ENSSTOP00000018090.1
GenBank Protein	KAG3292577	(Get FASTA)	NCBI Sequence Viewer

RefSeq Acc Id:

XP_005338423 ⟸ XM_005338366

- UniProtKB:

I3N144 (UniProtKB/TrEMBL)

- Sequence:

show sequence

MVTSATILQVNKVMSILFYVIFLAYLRGIQGNNMDQRNLPEDSLNSLIIKLIQADILKNKLSKQ
MVDVKENYQNVLPKAEAAREPEQGEPARSEFQPMIATDTELLRQQRRYSSPRVLLSDSTPLEPP
PLYLMEDYVGNPVVANRTSRRKRYAEHKSHRGEYSVCDSESLWVTDKSSAIDIRGHQVTVLGEI
KTGNSPVKQYFYETRCKEARPVKNGCRGIDDKHWNSQCKTSQTYVRALTSENNKLVGWRWIRID
TSCVCALSRKIGRT

hide sequence

RefSeq Acc Id:

ENSSTOP00000018090 ⟸ ENSSTOT00000030017

Protein Domains

Nerve growth factor-related

Additional Information

External Database Links

Database	Acc Id	Source(s)
Ensembl Genes	ENSSTOG00000021165	Ensembl, UniProtKB/TrEMBL
Ensembl Transcript	ENSSTOT00000030017.2	UniProtKB/TrEMBL
Gene3D-CATH	2.10.90.10	UniProtKB/TrEMBL
InterPro	Cystine-knot_cytokine	UniProtKB/TrEMBL
	Nerve_growth_factor-like	UniProtKB/TrEMBL
	Nerve_growth_factor-rel	UniProtKB/TrEMBL
	Nerve_growth_factor_CS	UniProtKB/TrEMBL
	Neurotrophin-3	UniProtKB/TrEMBL
	NTF3_N	UniProtKB/TrEMBL
NCBI Gene	Ntf3	ENTREZGENE
PANTHER	PTHR11589	UniProtKB/TrEMBL
	PTHR11589:SF4	UniProtKB/TrEMBL
Pfam	NGF	UniProtKB/TrEMBL
	NTF3_N	UniProtKB/TrEMBL
PIRSF	NGF	UniProtKB/TrEMBL
PRINTS	NEUROTROPHN3	UniProtKB/TrEMBL
	NGF	UniProtKB/TrEMBL
PROSITE	NGF_1	UniProtKB/TrEMBL
	NGF_2	UniProtKB/TrEMBL
SMART	NGF	UniProtKB/TrEMBL
Superfamily-SCOP	SSF57501	UniProtKB/TrEMBL
UniProt	I3N144	ENTREZGENE, UniProtKB/TrEMBL

Gene Annotator (Functional Annotation) unavailable	Gene Annotator (Annotation Distribution) unavailable	Variant Visualizer (Genomic Variants) unavailble Variant Visualizer (Genomic Variants) unavailable
Gene Annotator (Functional Annotation)	Gene Annotator (Annotation Distribution)	Variant Visualizer (Genomic Variants)

InterViewer (Protein-Protein Interactions) unavailable	Gviewer (Genome Viewer) unavailable	Variant Visualizer (Damaging Variants) unavailble Variant Visualizer (Damaging Variants) unavailable
InterViewer (Protein-Protein Interactions)	GViewer (Genome Viewer)	Variant Visualizer (Damaging Variants)

Gene Annotator (Annotation Comparison) unavailable	OLGA (Gene List Generator) unavailable
Gene Annotator (Annotation Comparison)	OLGA (Gene List Generator)	Excel (Download)

MOET (Multi-Ontology Enrichement) unavailable	GOLF (Gene-Ortholog Location Finder) unavailable
MOET (Multi-Ontology Enrichement)	GOLF (Gene-Ortholog Location Finder)

Imported Disease Annotations - ClinVar

Imported Disease Annotations - CTD

Imported Disease Annotations - MGI

Send us a Message

Imported Disease Annotations - ClinVar

Imported Disease Annotations - CTD

Imported Disease Annotations - MGI