Nefm (neurofilament medium chain) - Rat Genome Database

Send us a Message
Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Search RGD Grant Resources Citing RGD About Us Contact Us
Genes Variants Community Projects QTLs Strains Markers Genome Information Ontologies Cell Lines References Download Submit Data
OntoMate (Literature Search) JBrowse (Genome Browser) Synteny Browser (VCMap) Variant Visualizer Multi-Ontology Enrichment (MOET) Gene-Ortholog Location Finder (GOLF) InterViewer (Protein-Protein Interactions) PhenoMiner (Quatitative Phenotypes) Gene Annotator OLGA (Gene List Generator) AllianceMine GViewer (Genome Viewer)
Aging & Age-Related Disease Cancer & Neoplastic Disease Cardiovascular Disease Coronavirus Disease Developmental Disease Diabetes Hematologic Disease Immune & Inflammatory Disease Infectious Disease Liver Disease Neurological Disease Obesity & Metabolic Syndrome Renal Disease Respiratory Disease Sensory Organ Disease
Find Models   new Genetic Models Autism Models Rat PhenoMiner (Quantitative Phenotypes) Chinchilla PhenoMiner Expected Ranges (Quantitative Phenotype) PhenoMiner Term Comparison Hybrid Rat Diversity Panel Phenotypes Phenotypes in Other Animal Models Animal Husbandry Strain Medical Records Phylogenetics Strain Availability Calendar Rats 101 Submissions Photo Archive
Pathways
Rat Community Forum Directory of Rat Laboratories Video Tutorials News RGD Publications RGD Presentations Archive Nomenclature Guidelines Resource Links Laboratory Resources Employment Resources
Gene: Nefm (neurofilament medium chain) Ictidomys tridecemlineatus
Analyze
Symbol: Nefm
Name: neurofilament medium chain (Ensembl:neurofilament medium)
RGD ID: 12607176
Description: ENCODES a protein that exhibits protein-containing complex binding (ortholog); signaling receptor binding (ortholog); toxic substance binding (ortholog); INVOLVED IN axo-dendritic transport (ortholog); axon regeneration (ortholog); cellular response to estradiol stimulus (ortholog); ASSOCIATED WITH Alzheimer's disease (ortholog); amyotrophic lateral sclerosis (ortholog); congenital hypothyroidism (ortholog); FOUND IN axon (ortholog); cytoskeleton (ortholog); intermediate filament (ortholog)
Type: protein-coding
RefSeq Status: MODEL
Previously known as: neurofilament medium; neurofilament medium polypeptide; neurofilament medium, transcript variant X1; neurofilament medium, transcript variant X2; neurofilament, medium polypeptide
RGD Orthologs
Human
Mouse
Rat
Chinchilla
Bonobo
Dog
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: SpeTri2.0 - Squirrel SpeTri2.0 Assembly
Position:
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494310,410,240 - 10,415,458 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049367571,663,399 - 1,668,075 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049367571,662,905 - 1,668,707 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

References
Additional References at PubMed
PMID:22301074   PMID:30032202  


Genomics

Comparative Map Data
Nefm
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494310,410,240 - 10,415,458 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049367571,663,399 - 1,668,075 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049367571,662,905 - 1,668,707 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
NEFM
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38824,913,761 - 24,919,093 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl824,913,758 - 24,919,098 (+)EnsemblGRCh38hg38GRCh38
GRCh37824,771,274 - 24,776,606 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36824,827,179 - 24,832,511 (+)NCBINCBI36Build 36hg18NCBI36
Build 34824,827,211 - 24,832,511NCBI
Celera823,734,685 - 23,740,017 (+)NCBICelera
Cytogenetic Map8p21.2NCBI
HuRef823,315,978 - 23,321,310 (+)NCBIHuRef
CHM1_1824,973,582 - 24,978,914 (+)NCBICHM1_1
T2T-CHM13v2.0825,188,914 - 25,194,246 (+)NCBIT2T-CHM13v2.0
Nefm
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391468,356,994 - 68,362,453 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1468,320,039 - 68,362,295 (-)EnsemblGRCm39 Ensembl
GRCm381468,119,545 - 68,125,004 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1468,082,590 - 68,124,846 (-)EnsemblGRCm38mm10GRCm38
MGSCv371468,737,602 - 68,743,061 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361467,073,367 - 67,078,143 (-)NCBIMGSCv36mm8
Celera1465,887,284 - 65,892,688 (-)NCBICelera
Cytogenetic Map14D1NCBI
cM Map1435.46NCBI
Nefm
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81546,535,857 - 46,541,161 (-)NCBIGRCr8
mRatBN7.21542,360,449 - 42,365,753 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1542,360,454 - 42,365,755 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1544,225,130 - 44,230,434 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01545,375,350 - 45,380,655 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01543,820,704 - 43,826,010 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01544,855,307 - 44,860,604 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1544,855,310 - 44,860,604 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01546,736,787 - 46,741,632 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41547,698,371 - 47,703,350 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11547,714,153 - 47,719,121 (-)NCBI
Celera1542,015,992 - 42,021,311 (-)NCBICelera
Cytogenetic Map15p12NCBI
Nefm
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0NW_00495540347,920,408 - 47,926,922 (+)NCBIChiLan1.0ChiLan1.0
NEFM
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2743,421,006 - 43,426,459 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1819,155,199 - 19,160,653 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0824,181,335 - 24,186,701 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1821,097,646 - 21,103,263 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl821,098,005 - 21,107,468 (+)Ensemblpanpan1.1panPan2
NEFM
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12532,493,517 - 32,498,615 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2532,493,675 - 32,498,570 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2533,076,970 - 33,082,075 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.02532,692,550 - 32,697,657 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2532,692,550 - 32,697,640 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12532,647,982 - 32,653,102 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02532,497,397 - 32,502,517 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02532,663,548 - 32,668,651 (-)NCBIUU_Cfam_GSD_1.0
NEFM
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1148,955,346 - 8,967,211 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21410,117,172 - 10,122,612 (-)NCBISscrofa10.2Sscrofa10.2susScr3
NEFM
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1823,039,187 - 23,044,668 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl823,039,282 - 23,044,667 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366605219,128,898 - 19,136,687 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Nefm
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462475820,030,450 - 20,036,105 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2


Expression


Sequence


Reference Sequences
RefSeq Acc Id: ENSSTOT00000023482   ⟹   ENSSTOP00000015136
Type: CODING
Position:
Squirrel AssemblyChrPosition (strand)Source
SpeTri2.0 EnsemblNW_0049367571,663,399 - 1,668,075 (-)Ensembl
RefSeq Acc Id: XM_021719865   ⟹   XP_021575540
Type: CODING
Position:
Squirrel AssemblyChrPosition (strand)Source
HiC_Itri_2NW_02440494310,410,240 - 10,415,458 (-)NCBI
SpeTri2.0NW_0049367571,662,905 - 1,668,707 (-)NCBI
Sequence:
RefSeq Acc Id: XM_040292836   ⟹   XP_040148770
Type: CODING
Position:
Squirrel AssemblyChrPosition (strand)Source
HiC_Itri_2NW_02440494310,410,240 - 10,415,458 (-)NCBI
RefSeq Acc Id: XM_040292845   ⟹   XP_040148779
Type: CODING
Position:
Squirrel AssemblyChrPosition (strand)Source
HiC_Itri_2NW_02440494310,410,240 - 10,415,458 (-)NCBI
Protein Sequences
Protein RefSeqs XP_021575540 (Get FASTA)   NCBI Sequence Viewer  
  XP_040148770 (Get FASTA)   NCBI Sequence Viewer  
  XP_040148779 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSSTOP00000015136.2
GenBank Protein KAG3294352 (Get FASTA)   NCBI Sequence Viewer  
  KAG3294353 (Get FASTA)   NCBI Sequence Viewer  
Reference Protein Sequences
RefSeq Acc Id: XP_021575540   ⟸   XM_021719865
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_040148779   ⟸   XM_040292845
- Peptide Label: isoform X3
RefSeq Acc Id: XP_040148770   ⟸   XM_040292836
- Peptide Label: isoform X2
RefSeq Acc Id: ENSSTOP00000015136   ⟸   ENSSTOT00000023482
Protein Domains
IF rod


Additional Information

Database Acc Id Source(s)
Ensembl Genes ENSSTOG00000019862 Ensembl, UniProtKB/TrEMBL
Ensembl Transcript ENSSTOT00000023482.2 UniProtKB/TrEMBL
Gene3D-CATH 1.20.5.170 UniProtKB/TrEMBL
  Single helix bin UniProtKB/TrEMBL
  Vasodilator-stimulated phosphoprotein UniProtKB/TrEMBL
InterPro IF_conserved UniProtKB/TrEMBL
  IF_rod_dom UniProtKB/TrEMBL
  Intermed_filament_DNA-bd UniProtKB/TrEMBL
  Keratin_I UniProtKB/TrEMBL
NCBI Gene Nefm ENTREZGENE
PANTHER GLIAL FIBRILLARY ACIDIC PROTEIN UniProtKB/TrEMBL
  PTHR45652:SF3 UniProtKB/TrEMBL
Pfam Filament UniProtKB/TrEMBL
  Filament_head UniProtKB/TrEMBL
PRINTS TYPE1KERATIN UniProtKB/TrEMBL
PROSITE IF_ROD_1 UniProtKB/TrEMBL
  IF_ROD_2 UniProtKB/TrEMBL
SMART Filament UniProtKB/TrEMBL
Superfamily-SCOP Intermediate filament protein, coiled coil region UniProtKB/TrEMBL
UniProt I3MSP1_ICTTR UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2021-03-26 Nefm  neurofilament medium chain  Nefm  neurofilament medium  Symbol and/or name change 5135510 APPROVED