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Gene: Spin4 (spindlin family, member 4) Rattus norvegicus

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Symbol:

Spin4

Name:

spindlin family, member 4

RGD ID:

1564004

Description:

Predicted to enable histone H3K4me3 reader activity. Predicted to be involved in negative regulation of cell population proliferation and positive regulation of canonical Wnt signaling pathway. Predicted to be located in chromatin; cytoplasm; and nucleus. Orthologous to human SPIN4 (spindlin family member 4); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; bisphenol A; thioacetamide.

Type:

protein-coding

RefSeq Status:

INFERRED

Previously known as:

AABR07038930.1; LOC299038; RGD1564004; similar to RIKEN cDNA 9630042H07 gene; spindlin-4

RGD Orthologs

Alliance Orthologs

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):	SPIN4 (spindlin family member 4)	HGNC	HomoloGene, NCBI, Panther
Mus musculus (house mouse):	Spin4 (spindlin family, member 4)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chinchilla lanigera (long-tailed chinchilla):	Spin4 (spindlin family member 4)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Pan paniscus (bonobo/pygmy chimpanzee):	SPIN4 (spindlin family member 4)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Canis lupus familiaris (dog):	SPIN4 (spindlin family member 4)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Ictidomys tridecemlineatus (thirteen-lined ground squirrel):	Spin4 (spindlin family member 4)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Sus scrofa (pig):	SPIN4 (spindlin family member 4)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chlorocebus sabaeus (green monkey):	SPIN4 (spindlin family member 4)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Heterocephalus glaber (naked mole-rat):	Spin4 (spindlin family member 4)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Rattus rattus (black rat):	Spin4 (spindlin family member 4)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Alliance orthologs ³
Mus musculus (house mouse):	Spin4 (spindlin family, member 4)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Homo sapiens (human):	SPIN4 (spindlin family member 4)	Alliance	DIOPT (Ensembl Compara\|HGNC\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Homo sapiens (human):	SPIN4 (spindlin family member 4)	Alliance	DIOPT (HGNC)
Danio rerio (zebrafish):	zmp:0000000521	Alliance	DIOPT (Ensembl Compara\|PANTHER)
Danio rerio (zebrafish):	spinb (spindlin b)	Alliance	DIOPT (Ensembl Compara\|PANTHER)

Latest Assembly:

GRCr8 - GRCr8 Assembly

Position:

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	X	63,898,338 - 63,902,427 (-)	NCBI	GRCr8	GRCr8		GRCr8
GRCr8 Ensembl	X	63,900,148 - 63,903,811 (-)	Ensembl				GRCr8
mRatBN7.2	X	59,888,728 - 59,892,817 (-)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	X	59,891,581 - 59,892,330 (-)	Ensembl				mRatBN7.2
UTH_Rnor_SHR_Utx	X	61,359,427 - 61,363,518 (-)	NCBI	UTH_Rnor_SHR_Utx	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	X	64,859,949 - 64,864,040 (-)	NCBI	UTH_Rnor_SHRSP_BbbUtx_1.0	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	X	62,438,155 - 62,442,244 (-)	NCBI	UTH_Rnor_WKY_Bbb_1.0	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	X	64,217,074 - 64,221,225 (-)	NCBI	Rnor_6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	X	64,219,933 - 64,220,593 (-)	NCBI			rn6	Rnor6.0
Rnor_5.0	X	65,118,212 - 65,123,811 (-)	NCBI	Rnor_5.0	Rnor_5.0	rn5
RGSC_v3.4	X	82,564,580 - 82,565,329 (-)	NCBI	RGSC_v3.4	RGSC_v3.4	rn4
Celera	X	60,320,231 - 60,324,382 (-)	NCBI		Celera
Cytogenetic Map	X	q22	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

Lui-Jee-Baron syndrome (ISO)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

(-)-demecolcine (ISO)

1,2-dichloroethane (ISO)

17beta-estradiol (ISO)

2,3,7,8-tetrachlorodibenzodioxine (EXP,ISO)

2-hydroxypropanoic acid (ISO)

2-methylcholine (ISO)

aflatoxin B1 (ISO)

all-trans-retinoic acid (ISO)

arsane (ISO)

arsenic atom (ISO)

azathioprine (ISO)

benzo[a]pyrene (ISO)

benzo[a]pyrene diol epoxide I (ISO)

bisphenol A (EXP,ISO)

butanal (ISO)

calcitriol (ISO)

carbon nanotube (ISO)

cobalt dichloride (ISO)

copper atom (ISO)

copper(0) (ISO)

coumestrol (ISO)

crocidolite asbestos (ISO)

cyclosporin A (ISO)

cytarabine (ISO)

Dibutyl phosphate (ISO)

dorsomorphin (ISO)

doxorubicin (ISO)

endosulfan (ISO)

Enterolactone (ISO)

ethyl methanesulfonate (ISO)

formaldehyde (ISO)

levonorgestrel (ISO)

manganese atom (ISO)

manganese(0) (ISO)

manganese(II) chloride (ISO)

methyl methanesulfonate (ISO)

mono(2-ethylhexyl) phthalate (ISO)

okadaic acid (ISO)

pentanal (ISO)

pirinixic acid (ISO)

potassium chromate (ISO)

quercetin (ISO)

quinolin-8-ol (ISO)

rac-lactic acid (ISO)

resorcinol (ISO)

resveratrol (ISO)

SB 431542 (ISO)

sodium arsenate (ISO)

sodium arsenite (ISO)

sunitinib (ISO)

testosterone (ISO)

testosterone undecanoate (ISO)

tetrachloromethane (ISO)

thioacetamide (EXP)

thiram (ISO)

titanium dioxide (ISO)

trichostatin A (ISO)

trimellitic anhydride (ISO)

triphenyl phosphate (ISO)

urethane (ISO)

valproic acid (ISO)

vincristine (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

chromatin organization (IEA)

gamete generation (IEA)

negative regulation of cell population proliferation (ISO)

positive regulation of canonical Wnt signaling pathway (ISO)

Cellular Component

chromatin (ISO)

cytoplasm (ISO)

nucleus (ISO)

Molecular Function

histone H3K4me3 reader activity (ISO)

protein binding (ISO)

References

References - curated

#	Reference Title	Reference Citation
1.	Data Import for Chemical-Gene Interactions	RGD automated import pipeline for gene-chemical interactions

Additional References at PubMed

PMID:29061846

Genomics

Comparative Map Data

Spin4
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	X	63,898,338 - 63,902,427 (-)	NCBI	GRCr8	GRCr8		GRCr8
GRCr8 Ensembl	X	63,900,148 - 63,903,811 (-)	Ensembl				GRCr8
mRatBN7.2	X	59,888,728 - 59,892,817 (-)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	X	59,891,581 - 59,892,330 (-)	Ensembl				mRatBN7.2
UTH_Rnor_SHR_Utx	X	61,359,427 - 61,363,518 (-)	NCBI	UTH_Rnor_SHR_Utx	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	X	64,859,949 - 64,864,040 (-)	NCBI	UTH_Rnor_SHRSP_BbbUtx_1.0	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	X	62,438,155 - 62,442,244 (-)	NCBI	UTH_Rnor_WKY_Bbb_1.0	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	X	64,217,074 - 64,221,225 (-)	NCBI	Rnor_6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	X	64,219,933 - 64,220,593 (-)	NCBI			rn6	Rnor6.0
Rnor_5.0	X	65,118,212 - 65,123,811 (-)	NCBI	Rnor_5.0	Rnor_5.0	rn5
RGSC_v3.4	X	82,564,580 - 82,565,329 (-)	NCBI	RGSC_v3.4	RGSC_v3.4	rn4
Celera	X	60,320,231 - 60,324,382 (-)	NCBI		Celera
Cytogenetic Map	X	q22	NCBI

SPIN4
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38	X	63,347,228 - 63,351,332 (-)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38.p14 Ensembl	X	63,347,228 - 63,351,332 (-)	Ensembl			hg38	GRCh38
GRCh37	X	62,567,107 - 62,571,211 (-)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	X	62,483,832 - 62,487,943 (-)	NCBI	Build 36	Build 36	hg18	NCBI36
Celera	X	62,913,949 - 62,918,060 (-)	NCBI		Celera
Cytogenetic Map	X	q11.1	NCBI
HuRef	X	56,393,952 - 56,398,063 (-)	NCBI		HuRef
CHM1_1	X	62,459,711 - 62,463,822 (-)	NCBI		CHM1_1
T2T-CHM13v2.0	X	61,772,497 - 61,776,601 (-)	NCBI		T2T-CHM13v2.0

Spin4
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	X	94,066,113 - 94,070,288 (-)	NCBI	GRCm39	GRCm39	mm39
GRCm39 Ensembl	X	94,066,116 - 94,070,288 (-)	Ensembl		GRCm39 Ensembl		GRCm39
GRCm38	X	95,022,507 - 95,026,682 (-)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	X	95,022,510 - 95,026,682 (-)	Ensembl			mm10	GRCm38
MGSCv37	X	92,217,846 - 92,222,021 (-)	NCBI	MGSCv37	MGSCv37	mm9	NCBIm37
MGSCv36	X	91,225,229 - 91,229,401 (-)	NCBI		MGSCv36	mm8
Celera	X	82,046,345 - 82,050,536 (-)	NCBI		Celera
Cytogenetic Map	X	C3	NCBI
cM Map	X	41.83	NCBI

Spin4
(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_004955475	3,970,481 - 3,971,230 (-)	Ensembl
ChiLan1.0	NW_004955475	3,967,813 - 3,971,725 (-)	NCBI	ChiLan1.0	ChiLan1.0

SPIN4
(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	X	62,898,091 - 63,113,996 (-)	NCBI		NHGRI_mPanPan1-v2
NHGRI_mPanPan1	X	62,900,023 - 63,117,594 (-)	NCBI		NHGRI_mPanPan1
Mhudiblu_PPA_v0	X	52,489,880 - 52,494,902 (-)	NCBI	Mhudiblu_PPA_v0	Mhudiblu_PPA_v0	panPan3
PanPan1.1	X	62,502,776 - 62,506,934 (-)	NCBI	PanPan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	X	62,505,610 - 62,506,359 (-)	Ensembl			panPan2	panpan1.1

SPIN4
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1	X	48,805,292 - 48,809,546 (-)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
CanFam3.1 Ensembl	X	48,808,215 - 48,808,964 (-)	Ensembl			canFam3	CanFam3.1
Dog10K_Boxer_Tasha	X	39,675,781 - 39,680,076 (+)	NCBI	Dog10K_Boxer_Tasha	Dog10K_Boxer_Tasha

Spin4
(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	X	53,602,203 - 53,606,366 (+)	NCBI		HiC_Itri_2
SpeTri2.0 Ensembl	NW_004936635	4,368,491 - 4,369,240 (+)	Ensembl		SpeTri2.0 Ensembl
SpeTri2.0	NW_004936635	4,367,956 - 4,369,768 (+)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

SPIN4
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	X	49,976,950 - 49,981,084 (-)	Ensembl			susScr11	Sscrofa11.1
Sscrofa11.1	X	49,976,956 - 49,981,312 (-)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1

SPIN4
(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	X	53,601,474 - 53,605,617 (-)	NCBI	ChlSab1.1	ChlSab1.1	chlSab2
ChlSab1.1 Ensembl	X	53,604,335 - 53,605,081 (-)	Ensembl		ChlSab1.1 Ensembl	chlSab2	Vervet-AGM
Vero_WHO_p1.0	NW_023666083	820,332 - 824,461 (-)	NCBI	Vero_WHO_p1.0	Vero_WHO_p1.0

Spin4
(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_004624898	3,525,469 - 3,526,218 (+)	Ensembl		HetGla_female_1.0 Ensembl	hetGla2	HetGla_female_1.0 Ensembl
HetGla 1.0	NW_004624898	3,524,809 - 3,528,954 (+)	NCBI	HetGla 1.0	HetGla 1.0	hetGla2

Spin4
(Rattus rattus - black rat)

Black Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Black Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Rrattus_CSIRO_v1	X	53,367,397 - 53,369,654 (+)	NCBI		Rrattus_CSIRO_v1

Variants

Variants in Spin4
9 total Variants

miRNA Target Status (No longer updated)

Predicted Target Of

	Summary Value
Count of predictions:	135
Count of miRNA genes:	107
Interacting mature miRNAs:	111
Transcripts:	ENSRNOT00000058100
Prediction methods:	Microtar, 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 (GRCr8)

The following QTLs overlap with this region.

RGD ID	Symbol	Name	LOD	P Value	Trait	Sub Trait	Chr	Start	Stop	Species
738035	Stresp1	Stress response QTL 1	4.96	0.000011	stress-related behavior trait (VT:0010451)	defensive burying - coping	X	45182909	117740458	Rat
70221	Bp56	Blood pressure QTL 56	4.9		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	X	61035856	67175160	Rat
1598837	Memor13	Memory QTL 13	3.2		exploratory behavior trait (VT:0010471)	difference between duration of physical contact or close proximity of test subject and social stimulus during sample phase and test phase (CMO:0002678)	X	44930883	89930883	Rat

Expression

RNA-SEQ Expression

Click on a value in the shaded box below the category label to view a detailed expression data table for that system.

Download All Expressed Objects for this Gene

alimentary part of gastrointestinal system	appendage	circulatory system	ectoderm	hemolymphoid system	mesenchyme	mesoderm	musculoskeletal system	nervous system	renal system	reproductive system	sensory system	visual system
7	1	18	26	10	80	38	11	25	35	32	12	12

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_001401117	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_008758444	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	JAXUCZ010000021	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Ensembl Acc Id:

ENSRNOT00000058100 ⟹ ENSRNOP00000097234

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	X	59,891,581 - 59,892,330 (-)	Ensembl

Ensembl Acc Id:

ENSRNOT00000136053 ⟹ ENSRNOP00000104082

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8 Ensembl	X	63,900,148 - 63,903,811 (-)	Ensembl

RefSeq Acc Id:

NM_001401117 ⟹ NP_001388046

RefSeq Status:

INFERRED

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8	X	63,898,338 - 63,902,427 (-)	NCBI
mRatBN7.2	X	59,888,728 - 59,892,817 (-)	NCBI

Protein Sequences


Protein RefSeqs	NP_001388046	(Get FASTA)	NCBI Sequence Viewer
Ensembl Protein	ENSRNOP00000104082
	ENSRNOP00000104082.1

Ensembl Acc Id:

ENSRNOP00000097234 ⟸ ENSRNOT00000058100

RefSeq Acc Id:	NP_001388046 ⟸ NM_001401117
- UniProtKB:	A0A8I6ASA7 (UniProtKB/TrEMBL)

Ensembl Acc Id:

ENSRNOP00000104082 ⟸ ENSRNOT00000136053

Transcriptome

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

Additional Information

External Database Links

Database	Acc Id	Source(s)
AGR Gene	RGD:1564004	AgrOrtholog
BioCyc Gene	G2FUF-2215	BioCyc
Ensembl Genes	ENSRNOG00000038169	Ensembl
	ENSRNOG00000077287	Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript	ENSRNOT00000136053	ENTREZGENE
	ENSRNOT00000136053.1	UniProtKB/TrEMBL
NCBI Gene	299038	ENTREZGENE
PhenoGen	Spin4	PhenoGen
RatGTEx	ENSRNOG00000038169	RatGTEx
	ENSRNOG00000077287	RatGTEx
UniProt	A0A8I6ASA7	ENTREZGENE
	A0ABK0LFI7_RAT	UniProtKB/TrEMBL

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2022-06-02	Spin4	spindlin family, member 4	AABR07038930.1		Data merged from RGD:15004280	737654	PROVISIONAL
2019-11-08	AABR07038930.1				Symbol and Name status set to provisional	45752	PROVISIONAL
2008-03-06	Spin4	spindlin family, member 4	RGD1564004_predicted	similar to RIKEN cDNA 9630042H07 gene (predicted)	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2006-03-07	RGD1564004_predicted	similar to RIKEN cDNA 9630042H07 gene (predicted)	LOC299038	similar to RIKEN cDNA 9630042H07 gene	Symbol and Name status set to approved	1299863	APPROVED
2006-02-09	LOC299038	similar to RIKEN cDNA 9630042H07 gene			Symbol and Name status set to provisional	70820	PROVISIONAL

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)

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Imported Disease Annotations - OMIM