Stmn3 (stathmin 3) - Rat Genome Database

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Gene: Stmn3 (stathmin 3) Rattus norvegicus
Analyze
Symbol: Stmn3
Name: stathmin 3
RGD ID: 3628
Description: Enables chaperone binding activity. Involved in cellular response to nerve growth factor stimulus. Located in cytosol; neuron projection; and perinuclear region of cytoplasm. Orthologous to human STMN3 (stathmin 3); INTERACTS WITH 1-naphthyl isothiocyanate; 2,3,7,8-tetrachlorodibenzodioxine; 2,3,7,8-Tetrachlorodibenzofuran.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: SCG10-like protein; scgn10 like-protein; Sclip; stathmin-3; stathmin-like 3
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
NCBI Annotation Information: Annotation category: partial on reference assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.23168,416,810 - 168,424,946 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl3168,416,810 - 168,425,056 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx3172,797,424 - 172,805,557 (-)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.03181,756,524 - 181,764,657 (-)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.03178,417,755 - 178,425,891 (-)NCBIRnor_WKY
Rnor_6.03176,808,016 - 176,816,108 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl3176,808,017 - 176,816,162 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.03180,518,142 - 180,526,234 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.43170,446,808 - 170,454,900 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.13170,352,844 - 170,359,534 (-)NCBI
Celera3164,161,529 - 164,169,621 (+)NCBICelera
Cytogenetic Map3q43NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
cytoplasm  (IBA,ISO,ISS)
cytosol  (IDA,ISO)
Golgi apparatus  (IEA,ISO)
growth cone  (IEA)
neuron projection  (IBA,IDA)
perinuclear region of cytoplasm  (IDA)

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. SCLIP, a microtubule-destabilizing factor, interacts with RasGRF1 and inhibits its ability to promote Rac activation and neurite outgrowth. Baldassa S, etal., J Biol Chem. 2007 Jan 26;282(4):2333-45. Epub 2006 Nov 29.
2. 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.
3. The stathmin phosphoprotein family: intracellular localization and effects on the microtubule network. Gavet O, etal., J Cell Sci 1998 Nov;111 ( Pt 22):3333-46.
4. Rat ISS GO annotations from GOA human gene data--August 2006 GOA data from the GO Consortium
5. Clusterin interacts with SCLIP (SCG10-like protein) and promotes neurite outgrowth of PC12 cells. Kang SW, etal., Exp Cell Res. 2005 Oct 1;309(2):305-15.
6. Electronic Transfer of LocusLink and RefSeq Data NCBI rat LocusLink and RefSeq merged data July 26, 2002
7. Differential, regional, and cellular expression of the stathmin family transcripts in the adult rat brain. Ozon S, etal., J Neurosci Res 1999 Jun 1;56(5):553-64.
8. GOA pipeline RGD automated data pipeline
9. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
10. Tentative Sequence Identification Numbers Tentative Sequence Data IDs. TIGR Gene Index, Rat Data
Additional References at PubMed
PMID:16401721   PMID:17145186   PMID:18632943   PMID:21471001   PMID:22577147   PMID:22871113   PMID:27869233  


Genomics

Comparative Map Data
Stmn3
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.23168,416,810 - 168,424,946 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl3168,416,810 - 168,425,056 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx3172,797,424 - 172,805,557 (-)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.03181,756,524 - 181,764,657 (-)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.03178,417,755 - 178,425,891 (-)NCBIRnor_WKY
Rnor_6.03176,808,016 - 176,816,108 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl3176,808,017 - 176,816,162 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.03180,518,142 - 180,526,234 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.43170,446,808 - 170,454,900 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.13170,352,844 - 170,359,534 (-)NCBI
Celera3164,161,529 - 164,169,621 (+)NCBICelera
Cytogenetic Map3q43NCBI
STMN3
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh382063,639,712 - 63,653,424 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl2063,639,705 - 63,657,682 (-)EnsemblGRCh38hg38GRCh38
GRCh372062,271,065 - 62,284,777 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 362061,741,505 - 61,755,224 (-)NCBINCBI36Build 36hg18NCBI36
Build 342061,741,504 - 61,755,224NCBI
Celera2058,951,675 - 58,965,521 (-)NCBICelera
Cytogenetic Map20q13.33NCBI
HuRef2059,001,022 - 59,018,614 (-)NCBIHuRef
CHM1_12062,172,106 - 62,186,629 (-)NCBICHM1_1
T2T-CHM13v2.02065,453,599 - 65,467,540 (-)NCBIT2T-CHM13v2.0
Stmn3
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm392180,948,252 - 180,956,293 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl2180,948,252 - 180,956,293 (-)EnsemblGRCm39 Ensembl
GRCm382181,306,459 - 181,314,500 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl2181,306,459 - 181,314,500 (-)EnsemblGRCm38mm10GRCm38
MGSCv372181,041,164 - 181,049,205 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv362181,235,866 - 181,243,907 (-)NCBIMGSCv36mm8
Celera2185,389,152 - 185,397,193 (-)NCBICelera
Cytogenetic Map2H4NCBI
Stmn3
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_004955528577,536 - 583,850 (+)EnsemblChiLan1.0
ChiLan1.0NW_004955528577,536 - 583,850 (+)NCBIChiLan1.0ChiLan1.0
STMN3
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.12061,567,262 - 61,580,178 (-)NCBIpanpan1.1PanPan1.1panPan2
STMN3
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12447,209,738 - 47,220,146 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2447,209,784 - 47,219,472 (-)EnsemblCanFam3.1canFam3CanFam3.1
ROS_Cfam_1.02448,348,857 - 48,359,203 (-)NCBIROS_Cfam_1.0
UMICH_Zoey_3.12447,193,781 - 47,204,121 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02447,318,649 - 47,328,993 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02448,056,725 - 48,067,074 (-)NCBIUU_Cfam_GSD_1.0
Stmn3
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024408640195,456,801 - 195,481,831 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_00493651410,906,732 - 10,912,960 (-)EnsemblSpeTri2.0
SpeTri2.0NW_00493651410,910,444 - 10,914,676 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
STMN3
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1762,600,455 - 62,609,018 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11762,600,450 - 62,609,851 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
STMN3
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12567,440 - 584,080 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl2573,912 - 584,276 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366605048,128,051 - 48,141,375 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Stmn3
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462474129,292,076 - 29,299,621 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462474129,292,321 - 29,299,623 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Stmn3
72 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:191
Count of miRNA genes:132
Interacting mature miRNAs:141
Transcripts:ENSRNOT00000018697
Prediction methods:Microtar, 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.


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1559282Emca5Estrogen-induced mammary cancer QTL 53.9mammary gland integrity trait (VT:0010552)percentage of study population developing mammary tumors during a period of time (CMO:0000948)343827364169034231Rat
631541Bp81Blood pressure QTL 814arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3124122556169034231Rat
1578656Vnigr2Vascular neointimal growth QTL 24.2artery morphology trait (VT:0002191)lesioned artery residual lumen area (CMO:0001417)3130656562169034231Rat
1578653Vnigr3Vascular neointimal growth QTL 33.1artery morphology trait (VT:0002191)artery neointimal hyperplastic lesion area (CMO:0001414)3130656562169034231Rat
9589106Insul23Insulin level QTL 2313.860.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)3131635904169034231Rat
2298477Eau4Experimental allergic uveoretinitis QTL 40.0011uvea integrity trait (VT:0010551)experimental autoimmune uveitis score (CMO:0001504)3137398739169034231Rat
8552952Pigfal13Plasma insulin-like growth factor 1 level QTL 13blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)3138799500169034231Rat
1298068Bp167Blood pressure QTL 1670.004arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3141074471169034231Rat
2317883Alcrsp26Alcohol response QTL 261.80.63response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)3145526770169034231Rat
8552791Vie2Viral induced encephalitis QTL 24.1brain integrity trait (VT:0010579)encephalitis incidence/prevalence measurement (CMO:0002361)3145956084169034231Rat
1300161Rf10Renal function QTL 103.57renal blood flow trait (VT:2000006)absolute change in renal vascular resistance (CMO:0001900)3161192952169034231Rat

Markers in Region
RH128377  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.23168,416,930 - 168,417,121 (+)MAPPERmRatBN7.2
Rnor_6.03176,808,133 - 176,808,323NCBIRnor6.0
Rnor_5.03180,518,259 - 180,518,449UniSTSRnor5.0
RGSC_v3.43170,446,925 - 170,447,115UniSTSRGSC3.4
Celera3164,169,314 - 164,169,504UniSTS
Cytogenetic Map3q43UniSTS


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 4
Medium 68 2
Low 3 15 32 16 16 16 8 8 2 12 28 9 8
Below cutoff 16 17 17 3 17 2 23 9 2

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000018697   ⟹   ENSRNOP00000018697
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl3168,416,815 - 168,424,931 (-)Ensembl
Rnor_6.0 Ensembl3176,808,121 - 176,816,162 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000079262   ⟹   ENSRNOP00000074686
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl3168,416,810 - 168,425,056 (-)Ensembl
Rnor_6.0 Ensembl3176,808,017 - 176,816,114 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000109405   ⟹   ENSRNOP00000089824
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl3168,416,810 - 168,419,949 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000109612   ⟹   ENSRNOP00000095748
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl3168,416,810 - 168,424,316 (-)Ensembl
RefSeq Acc Id: NM_024346   ⟹   NP_077322
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.23168,416,810 - 168,424,946 (-)NCBI
Rnor_6.03176,808,016 - 176,816,108 (-)NCBI
Rnor_5.03180,518,142 - 180,526,234 (-)NCBI
RGSC_v3.43170,446,808 - 170,454,900 (-)RGD
Celera3164,161,529 - 164,169,621 (+)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_001382074 (Get FASTA)   NCBI Sequence Viewer  
  NP_077322 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAF86617 (Get FASTA)   NCBI Sequence Viewer  
  EDL88728 (Get FASTA)   NCBI Sequence Viewer  
  EDL88729 (Get FASTA)   NCBI Sequence Viewer  
  Q9JHU6 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_077322   ⟸   NM_024346
- Sequence:
RefSeq Acc Id: ENSRNOP00000074686   ⟸   ENSRNOT00000079262
RefSeq Acc Id: ENSRNOP00000018697   ⟸   ENSRNOT00000018697
RefSeq Acc Id: ENSRNOP00000089824   ⟸   ENSRNOT00000109405
RefSeq Acc Id: ENSRNOP00000095748   ⟸   ENSRNOT00000109612
Protein Domains
SLD

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q9JHU6-F1-model_v2 AlphaFold Q9JHU6 1-180 view protein structure

Transcriptome

eQTL   View at Phenogen
WGCNA   View at Phenogen
Tissue/Strain Expression   View at Phenogen

Promoters
RGD ID:13692751
Promoter ID:EPDNEW_R3276
Type:multiple initiation site
Name:Stmn3_1
Description:stathmin 3
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.03176,816,129 - 176,816,189EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:3628 AgrOrtholog
BioCyc Gene G2FUF-46292 BioCyc
Ensembl Genes ENSRNOG00000013657 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000018697.4 UniProtKB/TrEMBL
  ENSRNOP00000074686.2 UniProtKB/TrEMBL
  ENSRNOP00000089824.1 UniProtKB/TrEMBL
  ENSRNOP00000095748.1 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000018697.7 UniProtKB/TrEMBL
  ENSRNOT00000079262.2 UniProtKB/TrEMBL
  ENSRNOT00000109405.1 UniProtKB/TrEMBL
  ENSRNOT00000109612.1 UniProtKB/TrEMBL
InterPro Stathmin-3 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Stathmin_CS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Stathmin_fam UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Stathmin_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:29246 UniProtKB/Swiss-Prot
NCBI Gene 29246 ENTREZGENE
PANTHER PTHR10104 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PTHR10104:SF17 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam Stathmin UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Stmn3 PhenoGen
PIRSF Stathmin UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PRINTS STATHMIN UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE STATHMIN_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  STATHMIN_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  STATHMIN_3 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF101494 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
TIGR TC229396
UniProt A0A0G2K8P5_RAT UniProtKB/TrEMBL
  A0A8I6A9I7_RAT UniProtKB/TrEMBL
  A0A8I6ANU3_RAT UniProtKB/TrEMBL
  D3ZI49 ENTREZGENE, UniProtKB/TrEMBL
  Q9JHU6 ENTREZGENE, UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2015-11-25 Stmn3  stathmin 3  Stmn3  stathmin-like 3  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2003-04-09 Stmn3  stathmin-like 3   Sclip  scgn10 like-protein  Symbol and Name updated 629477 APPROVED
2002-06-10 Sclip  scgn10 like-protein      Symbol and Name status set to approved 70586 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_cellular_localization membrane-associated, in part localized to the Golgi apparatus 61521
gene_cellular_localization membrane-associated, in part localized to the Golgi apparatus 61528
gene_domains shares a COOH-terminal stathmin-like domain with a regulatory region containing one or several of the stathmin phosphorylation sites and an interaction subdomain with a putative coiled-coil forming an a-helical structure 61521
gene_domains shares a COOH-terminal stathmin-like domain with a regulatory region containing one or several of the stathmin phosphorylation sites and an interaction subdomain with a putative coiled-coil forming an a-helical structure 61528
gene_expression exclusively expressed in the nervous system, equally found in neonatal as well as in adult brain 61521
gene_expression exclusively expressed in the nervous system, equally found in neonatal as well as in adult brain 61528
gene_process may be involved in functions of mature cells of the nervous system 61521
gene_process may be involved in functions of mature cells of the nervous system 61528
gene_product member of the stathmin family of phosphoproteins involved in intracellular signaling 61521