Nexmif (neurite extension and migration factor) - Rat Genome Database

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Gene: Nexmif (neurite extension and migration factor) Rattus norvegicus
Analyze
Symbol: Nexmif
Name: neurite extension and migration factor
RGD ID: 1561931
Description: Involved in negative regulation of cell adhesion and negative regulation of neuron migration. Predicted to be located in cytosol; midbody; and nucleoplasm. Predicted to be active in nucleus. Human ortholog(s) of this gene implicated in non-syndromic X-linked intellectual disability 98. Orthologous to human NEXMIF (neurite extension and migration factor); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 6-propyl-2-thiouracil; acrylamide.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: KIAA2022; KIDLIA; LOC302396; RGD1561931; similar to KIAA2022 protein; XLMR protein related to neurite extension; Xpn
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
GRCr8X73,153,786 - 73,284,943 (-)NCBIGRCr8
mRatBN7.2X69,088,076 - 69,219,253 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 EnsemblX69,088,076 - 69,112,930 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_UtxX70,597,183 - 70,622,041 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0X74,097,485 - 74,122,346 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0X71,658,669 - 71,683,534 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0X74,943,440 - 75,053,559 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX74,945,082 - 74,968,405 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0X75,748,099 - 75,852,569 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X92,073,589 - 92,081,623 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
CeleraX70,444,945 - 70,469,768 (-)NCBICelera
Cytogenetic MapXq22NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
cytosol  (IEA,ISO)
midbody  (IEA,ISO)
nucleoplasm  (IEA,ISO)
nucleus  (IBA)

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. XLMR protein related to neurite extension (Xpn/KIAA2022) regulates cell-cell and cell-matrix adhesion and migration. Magome T, etal., Neurochem Int. 2013 Nov;63(6):561-9. doi: 10.1016/j.neuint.2013.09.011. Epub 2013 Sep 24.
3. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
4. GOA pipeline RGD automated data pipeline
5. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
6. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:8889548   PMID:23615299   PMID:27822498  


Genomics

Comparative Map Data
Nexmif
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8X73,153,786 - 73,284,943 (-)NCBIGRCr8
mRatBN7.2X69,088,076 - 69,219,253 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 EnsemblX69,088,076 - 69,112,930 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_UtxX70,597,183 - 70,622,041 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0X74,097,485 - 74,122,346 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0X71,658,669 - 71,683,534 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0X74,943,440 - 75,053,559 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX74,945,082 - 74,968,405 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0X75,748,099 - 75,852,569 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X92,073,589 - 92,081,623 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
CeleraX70,444,945 - 70,469,768 (-)NCBICelera
Cytogenetic MapXq22NCBI
NEXMIF
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38X74,732,856 - 74,925,452 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 EnsemblX74,732,856 - 74,925,472 (-)EnsemblGRCh38hg38GRCh38
GRCh37X73,952,691 - 74,145,287 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36X73,870,137 - 74,061,709 (-)NCBINCBI36Build 36hg18NCBI36
CeleraX74,236,153 - 74,428,748 (-)NCBICelera
Cytogenetic MapXq13.3NCBI
HuRefX67,587,986 - 67,778,886 (-)NCBIHuRef
CHM1_1X73,845,555 - 74,038,181 (-)NCBICHM1_1
T2T-CHM13v2.0X73,166,463 - 73,359,096 (-)NCBIT2T-CHM13v2.0
Nexmif
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39X103,120,367 - 103,245,403 (-)NCBIGRCm39GRCm39mm39
GRCm39 EnsemblX103,121,040 - 103,244,791 (-)EnsemblGRCm39 Ensembl
GRCm38X104,076,761 - 104,201,783 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 EnsemblX104,077,434 - 104,201,185 (-)EnsemblGRCm38mm10GRCm38
MGSCv37X101,272,774 - 101,396,456 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36X100,285,909 - 100,403,904 (-)NCBIMGSCv36mm8
CeleraX90,976,514 - 91,092,555 (-)NCBICelera
Cytogenetic MapXDNCBI
cM MapX46.48NCBI
Nexmif
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_004955562780,189 - 968,083 (-)EnsemblChiLan1.0
ChiLan1.0NW_004955562780,172 - 786,049 (-)NCBIChiLan1.0ChiLan1.0
NEXMIF
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2X74,415,648 - 74,608,170 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1X74,419,979 - 74,611,783 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0X63,985,226 - 64,177,750 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1X74,107,799 - 74,292,323 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 EnsemblX74,107,799 - 74,114,635 (-)Ensemblpanpan1.1panPan2
NEXMIF
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1X57,986,884 - 58,120,453 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 EnsemblX57,992,476 - 58,013,478 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_TashaX49,165,913 - 49,299,478 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0X59,225,238 - 59,358,844 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 EnsemblX59,230,777 - 59,358,928 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1X56,945,135 - 57,078,689 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0X58,524,242 - 58,664,141 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0X58,131,656 - 58,265,221 (-)NCBIUU_Cfam_GSD_1.0
Nexmif
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2X43,790,406 - 43,907,835 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049366831,042,288 - 1,157,377 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049366831,041,739 - 1,157,382 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
NEXMIF
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 EnsemblX59,972,373 - 60,120,021 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1X59,967,712 - 60,013,938 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2X68,178,778 - 68,329,023 (-)NCBISscrofa10.2Sscrofa10.2susScr3
NEXMIF
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1X64,332,957 - 64,530,082 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 EnsemblX64,334,196 - 64,340,549 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366606717,196,621 - 17,395,597 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Nexmif
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248366,067,156 - 6,073,035 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046248365,907,848 - 6,075,518 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Nexmif
208 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:16
Count of miRNA genes:14
Interacting mature miRNAs:16
Transcripts:ENSRNOT00000035653
Prediction methods:Miranda, Pita, 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.


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
61430Cia18Collagen induced arthritis QTL 183.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)X14843113120568734Rat
1598837Memor13Memory QTL 133.2exploratory behavior trait (VT:0010471)difference between time of physical contact/close proximity of test subject and social stimulus during sample phase and test phase (CMO:0002678)X41052407146860749Rat
738035Stresp1Stress response QTL 14.960.000011stress-related behavior trait (VT:0010451)defensive burying - copingX41304447112935181Rat
61431Cia19Collagen induced arthritis QTL 194.4joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)X65612192120568734Rat

Markers in Region
RH36660  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2X69,088,791 - 69,088,866 (+)MAPPERmRatBN7.2
Rnor_6.0X74,944,156 - 74,944,230NCBIRnor6.0
Rnor_5.0X75,746,740 - 75,746,814UniSTSRnor5.0
RGSC_v3.4X92,070,106 - 92,070,180UniSTSRGSC3.4
CeleraX70,445,661 - 70,445,735UniSTS
Cytogenetic MapXq31UniSTS
C77370  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2X69,099,540 - 69,100,267 (+)MAPPERmRatBN7.2
Rnor_6.0X74,954,905 - 74,955,631NCBIRnor6.0
Rnor_5.0X75,757,489 - 75,758,215UniSTSRnor5.0
RGSC_v3.4X92,080,855 - 92,081,581UniSTSRGSC3.4
CeleraX70,456,380 - 70,457,106UniSTS
Cytogenetic MapXq31UniSTS


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 8 58 3 1
Low 24 10 2 9 2 3 3 16 35 34 10 3
Below cutoff 3 18 17 17 8 17 5 7 4 5

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000035653   ⟹   ENSRNOP00000036176
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 EnsemblX69,088,076 - 69,112,930 (-)Ensembl
Rnor_6.0 EnsemblX74,945,082 - 74,968,405 (-)Ensembl
RefSeq Acc Id: NM_001313815   ⟹   NP_001300744
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X73,153,786 - 73,178,639 (-)NCBI
mRatBN7.2X69,088,076 - 69,112,930 (-)NCBI
Rnor_6.0X74,943,440 - 74,968,405 (-)NCBI
CeleraX70,444,945 - 70,469,768 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039099590   ⟹   XP_038955518
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X73,153,786 - 73,284,943 (-)NCBI
mRatBN7.2X69,088,076 - 69,219,253 (-)NCBI
RefSeq Acc Id: XM_039099591   ⟹   XP_038955519
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X73,153,786 - 73,284,943 (-)NCBI
mRatBN7.2X69,088,076 - 69,219,253 (-)NCBI
RefSeq Acc Id: XM_039099592   ⟹   XP_038955520
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X73,153,786 - 73,284,943 (-)NCBI
mRatBN7.2X69,088,076 - 69,219,253 (-)NCBI
Reference Protein Sequences
RefSeq Acc Id: NP_001300744   ⟸   NM_001313815
- UniProtKB: D3ZGX1 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000036176   ⟸   ENSRNOT00000035653
RefSeq Acc Id: XP_038955520   ⟸   XM_039099592
- Peptide Label: isoform X1
- UniProtKB: D3ZGX1 (UniProtKB/Swiss-Prot)
RefSeq Acc Id: XP_038955518   ⟸   XM_039099590
- Peptide Label: isoform X1
- UniProtKB: D3ZGX1 (UniProtKB/Swiss-Prot)
RefSeq Acc Id: XP_038955519   ⟸   XM_039099591
- Peptide Label: isoform X1
- UniProtKB: D3ZGX1 (UniProtKB/Swiss-Prot)

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZGX1-F1-model_v2 AlphaFold D3ZGX1 1-1517 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:1561931 AgrOrtholog
BioCyc Gene G2FUF-1993 BioCyc
Ensembl Genes ENSRNOG00000021589 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOG00055026893 UniProtKB/Swiss-Prot
  ENSRNOG00060021206 UniProtKB/Swiss-Prot
  ENSRNOG00065016625 UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000035653 ENTREZGENE
  ENSRNOT00000035653.7 UniProtKB/Swiss-Prot
  ENSRNOT00055046447 UniProtKB/Swiss-Prot
  ENSRNOT00060036730 UniProtKB/Swiss-Prot
  ENSRNOT00065027699 UniProtKB/Swiss-Prot
InterPro DUF4683 UniProtKB/Swiss-Prot
  Nexmif UniProtKB/Swiss-Prot
KEGG Report rno:302396 UniProtKB/Swiss-Prot
NCBI Gene 302396 ENTREZGENE
PANTHER NEURITE EXTENSION AND MIGRATION FACTOR UniProtKB/Swiss-Prot
  PTHR46946 UniProtKB/Swiss-Prot
Pfam DUF4683 UniProtKB/Swiss-Prot
PhenoGen Nexmif PhenoGen
RatGTEx ENSRNOG00000021589 RatGTEx
  ENSRNOG00055026893 RatGTEx
  ENSRNOG00060021206 RatGTEx
  ENSRNOG00065016625 RatGTEx
UniProt D3ZGX1 ENTREZGENE, UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2017-06-20 Nexmif  neurite extension and migration factor  RGD1561931  similar to KIAA2022 protein  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 RGD1561931  similar to KIAA2022 protein   RGD1561931_predicted  similar to KIAA2022 protein (predicted)  'predicted' is removed 2292626 APPROVED
2006-03-07 RGD1561931_predicted  similar to KIAA2022 protein (predicted)  LOC302396  similar to KIAA2022 protein  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC302396  similar to KIAA2022 protein      Symbol and Name status set to provisional 70820 PROVISIONAL