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Gene: Silc1 (sciatic injury induced lincRNA upregulator of SOX11) Rattus norvegicus

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Symbol:

Silc1

Name:

sciatic injury induced lincRNA upregulator of SOX11

RGD ID:

2318102

Description:

Orthologous to human SILC1 (sciatic injury induced lincRNA upregulator of SOX11); INTERACTS WITH aflatoxin B1 (ortholog); benzo[a]pyrene (ortholog); bisphenol A (ortholog).

Type:

ncrna

RefSeq Status:

MODEL

Previously known as:

LOC100362486; small nuclear ribonucleoprotein D3

RGD Orthologs

Human

Mouse

Alliance Orthologs

More Info

more info ...

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	6	49,534,980 - 49,553,789 (-)	NCBI	GRCr8	GRCr8		GRCr8
mRatBN7.2	6	43,805,709 - 43,825,284 (-)	NCBI	mRatBN7.2	mRatBN7.2
Rnor_6.0	6	46,433,302 - 46,451,961 (-)	NCBI	Rnor_6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_5.0	6	55,146,951 - 55,165,611 (-)	NCBI	Rnor_5.0	Rnor_5.0	rn5
RGSC_v3.4	6	45,059,313 - 45,059,658 (-)	NCBI	RGSC_v3.4	RGSC_v3.4	rn4
Celera	6	43,057,837 - 43,076,509 (-)	NCBI		Celera
Cytogenetic Map	6	q16	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Annotation Click to see Annotation Detail View

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

aflatoxin B1 (ISO)

benzo[a]pyrene (ISO)

bisphenol A (ISO)

sodium arsenite (ISO)

triclosan (ISO)

References

Genomics

Comparative Map Data

Silc1
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	6	49,534,980 - 49,553,789 (-)	NCBI	GRCr8	GRCr8		GRCr8
mRatBN7.2	6	43,805,709 - 43,825,284 (-)	NCBI	mRatBN7.2	mRatBN7.2
Rnor_6.0	6	46,433,302 - 46,451,961 (-)	NCBI	Rnor_6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_5.0	6	55,146,951 - 55,165,611 (-)	NCBI	Rnor_5.0	Rnor_5.0	rn5
RGSC_v3.4	6	45,059,313 - 45,059,658 (-)	NCBI	RGSC_v3.4	RGSC_v3.4	rn4
Celera	6	43,057,837 - 43,076,509 (-)	NCBI		Celera
Cytogenetic Map	6	q16	NCBI

SILC1
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38	2	5,932,687 - 5,980,218 (+)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38.p14 Ensembl	2	5,932,543 - 6,060,570 (+)	Ensembl			hg38	GRCh38
GRCh37	2	6,072,819 - 6,120,350 (+)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	2	6,027,379 - 6,030,779 (+)	NCBI	Build 36	Build 36	hg18	NCBI36
Celera	2	5,986,934 - 6,034,463 (+)	NCBI		Celera
Cytogenetic Map	2	p25.2	NCBI
HuRef	2	5,916,929 - 5,964,447 (+)	NCBI		HuRef
CHM1_1	2	6,002,188 - 6,049,718 (+)	NCBI		CHM1_1
T2T-CHM13v2.0	2	5,954,658 - 6,002,183 (+)	NCBI		T2T-CHM13v2.0

Silc1
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	12	27,190,795 - 27,210,515 (-)	NCBI	GRCm39	GRCm39	mm39
GRCm39 Ensembl	12	27,086,808 - 27,211,001 (-)	Ensembl		GRCm39 Ensembl		GRCm39
GRCm38	12	27,140,796 - 27,160,516 (-)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	12	27,050,950 - 27,160,633 (-)	Ensembl			mm10	GRCm38
MGSCv37	12	27,825,661 - 27,845,176 (-)	NCBI	MGSCv37	MGSCv37	mm9	NCBIm37
MGSCv36	12	27,727,070 - 27,746,901 (-)	NCBI		MGSCv36	mm8
Celera	12	28,616,919 - 28,636,766 (-)	NCBI		Celera
Cytogenetic Map	12	A2	NCBI
cM Map	12	9.86	NCBI

Variants

Variants in Silc1
69 total Variants

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
9590290	Uminl2	Urine mineral level QTL 2	3.96	0.001	urine mineral amount (VT:0015086)	urine electrolyte level (CMO:0000593)	6	44510974	89510974	Rat
8693632	Alc27	Alcohol consumption QTL 27	2.2	0.791	drinking behavior trait (VT:0001422)	calculated ethanol drink intake rate (CMO:0001615)	6	40052411	56848866	Rat
634318	Bw118	Body weight QTL 118	3.55		abdominal fat pad mass (VT:1000711)	abdominal fat pad weight (CMO:0000088)	6	39028659	63457441	Rat
10401812	Kidm54	Kidney mass QTL 54			kidney mass (VT:0002707)	both kidneys wet weight (CMO:0000085)	6	20097635	65097635	Rat
634307	Bp141	Blood pressure QTL 141	4		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	6	40957564	85957564	Rat
1331743	Uae28	Urinary albumin excretion QTL 28	4.5		urine albumin amount (VT:0002871)	urine albumin level (CMO:0000130)	6	45153786	90153786	Rat
8552910	Pigfal5	Plasma insulin-like growth factor 1 level QTL 5	4.3		blood insulin-like growth factor amount (VT:0010479)	plasma insulin-like growth factor 1 level (CMO:0001299)	6	22653889	67653889	Rat
10401800	Kidm49	Kidney mass QTL 49			kidney mass (VT:0002707)	both kidneys wet weight (CMO:0000085)	6	20097635	65097635	Rat
1331779	Rf38	Renal function QTL 38	2.876		kidney blood vessel physiology trait (VT:0100012)	absolute change in renal vascular resistance (CMO:0001900)	6	31185002	76185002	Rat
737827	Hcar11	Hepatocarcinoma resistance QTL 11	4.4		liver integrity trait (VT:0010547)	liver tumorous lesion number (CMO:0001068)	6	46050607	116278722	Rat
724513	Uae14	Urinary albumin excretion QTL 14	6.5		urine albumin amount (VT:0002871)	urine albumin excretion rate (CMO:0000757)	6	46047353	91047353	Rat
2293839	Kiddil2	Kidney dilation QTL 2	4.8		kidney pelvis morphology trait (VT:0004194)	hydronephrosis severity score (CMO:0001208)	6	26618314	86868070	Rat
1576309	Emca7	Estrogen-induced mammary cancer QTL 7	4		mammary gland integrity trait (VT:0010552)	mammary tumor number (CMO:0000343)	6	20859430	113082285	Rat
9590140	Scort4	Serum corticosterone level QTL 4	14.49	0.001	blood corticosterone amount (VT:0005345)	plasma corticosterone level (CMO:0001173)	6	44510974	89510974	Rat
2301964	Bp323	Blood pressure QTL 323	4.3		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	6	1	86868070	Rat
9590306	Scort18	Serum corticosterone level QTL 18	2.88	0.001	blood corticosterone amount (VT:0005345)	plasma corticosterone level (CMO:0001173)	6	44510974	89510974	Rat
1578665	Bss16	Bone structure and strength QTL 16	4.4		femur morphology trait (VT:0000559)	bone trabecular cross-sectional area (CMO:0002311)	6	33328841	78328841	Rat
2293841	Kiddil4	Kidney dilation QTL 4	4.4		kidney pelvis morphology trait (VT:0004194)	hydronephrosis severity score (CMO:0001208)	6	26618314	86868070	Rat
1641898	Colcr4	Colorectal carcinoma resistance QTL4	3.71	0.0007	intestine integrity trait (VT:0010554)	well differentiated malignant colorectal tumor surface area measurement (CMO:0002077)	6	30937632	75937632	Rat
1578668	Bmd14	Bone mineral density QTL 14	3.8		femur mineral mass (VT:0010011)	total volumetric bone mineral density (CMO:0001728)	6	33328841	78328841	Rat
6893340	Cm77	Cardiac mass QTL 77	0.26	0.57	heart mass (VT:0007028)	heart weight to body weight ratio (CMO:0000074)	6	39028659	86867923	Rat
70199	Coreg1	Compensatory renal growth QTL 1	11.8		kidney mass (VT:0002707)	compensatory renal growth score (CMO:0001894)	6	14599473	63457687	Rat
2301972	Bp325	Blood pressure QTL 325	4.8		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	6	16089372	61967788	Rat
1354664	Slep2	Serum leptin concentration QTL 2	4.49		blood leptin amount (VT:0005667)	serum leptin level (CMO:0000780)	6	22288257	67288257	Rat
1300143	Rf14	Renal function QTL 14	2.92		renal blood flow trait (VT:2000006)	absolute change in renal blood flow rate (CMO:0001168)	6	40163183	85163183	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

circulatory system	ectoderm	hemolymphoid system	mesenchyme	mesoderm	nervous system	renal system	reproductive system	sensory system	visual system
5	14	2	14	7	14	7	3	11	11

Sequence

Nucleotide Sequences


RefSeq Transcripts	XR_347139	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XR_354716	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	JAXUCZ010000006	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

RefSeq Acc Id:

XR_354716

Type:

NON-CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8	6	49,534,980 - 49,553,789 (-)	NCBI
mRatBN7.2	6	43,805,709 - 43,825,284 (-)	NCBI
Rnor_6.0	6	46,433,302 - 46,451,961 (-)	NCBI
Rnor_5.0	6	55,146,951 - 55,165,611 (-)	NCBI

Sequence:

show sequence

CACTTTGCTCTAAGTGATGGCTTCCCTTTAGCTGGCACATTTTGCAGGGGTTGGTTGCGCGCAG
CTTGGGGCATGAGCATTGTGGCATTGTGGGACGTTGTTTCAGCCTGCGACTTGAGGGTTATGAG
CTCGGGGAAGAGACAGTTAAAGCTTCCTCGCACCAGCAAGATGAGTTGTACCACAGCGCTCATG
CCAAGGTCAGCAGTCTGAGTGGAGCTGAGACACTTAATGCCCGTTCCAAGCAGTGCCAAGCACC
TCTGGAAGCCCCTGCCTAGGACCCCAAATTTAGATTCATGCTGCAGTCTGGAGAGTGTTCTGAC
GGCTGCCGGGCTACAGGGAAAAGCACACTGCACACTGCCTCTGAAACGAGACAGAGCTCTCCAG
GCTGGGAGTCTGAGGAAGCCGGACCTGAGCAGCGCTAGTCAGGGGAAAGAGAAGCCCAGTTCAC
CATTGGCCATCAGGGTCCAGGAGCATCACTTCCTTTATCCAGCACCCTATCTCTGTGACATGTG
AAGAAACCAGTCCATTTTCCAATGGCAAAACCGAGCTCACATACACCATATTCTTCAATGTCTG
TCCTTCTACCAGTTGGATCTGTTTTCTTTTGTAGTTCTGGGCACTTTTCAAGACTCTGTTGACT
AAATCTTAAAGGAGTGTTGATAATGCAATTCATAAACTGGCTTTCTGAGCTATTATGATGCCTT
TTCCTCTCTTTGTGACCAAGAACATCTACTCTCTTGCCTTTGAAGATCCATGAGGTTTTAAAAT
CATGAGACCCAAGGCAGAAGTGTCCAGGCAACTGGGAGCCAAGTCTAGCTGCTGCACTTGAAAG
CCAGGACTTGACTGGAGAGAACGCAGTAGAGGTAAAGATTCTGTGAGTGCGTTTGGACCATGAG
AATAATGTGTCTTCGTACAAGACAATGGGTGGCTGATTTTTGATGCCTCCTGGGTTACTGTTTG
GTGAACTCTGAAATACCCACTCTGCTCACACACAGGGTCACAGAAGACATGGGTATATTGAGCA
CACTGGTACTAGGGTCAACAGTGAGCTGACGCTATGTGCAGATGAACCTCTCTGTTTCTACTGG
AGCCATCATTCAATGGACAGAAAGGATTTGGGTGTTGGACTCATCTCTGATACATCCTGTCTGC
AGGGATAGAAAGTATTCCTGGGGAACATCGAAGCTGAAGAAACTACAGCTTTTCTTTCGAGTCT
GGATTATTCTGAACCACATGGAATTACAATCAAGTCCGGGATGAGTGGCTCAAAGCCTGGCTAT
GACCGAGGGAACGGAAGACAAATTGGGATCATATTTTATTCAACCAAGAGAAATGGAATCCAGC
AGAGTAAATTTCATGTTCTCTGGAAATATGTCCTGTTAATGTTATTATTGAGAAGAAGCACAGA
CAACACAGTCTTCCAGGCAAGGAAGAGAAGGAGATGTGACCTTGGCTTTGTGAGCTGTGGCAGG
GAGGGACCCAGAATGATAGTGAAGGTCTCTGGAAGCTTCCAAACAAACAAGTGTGGGTGTCTTT
TGTCAGATCCCTGAGAGTGGGTGGGGCAGAAGACTTGCTGTGTTTTCTGTGGATAAATACACAA
AACGATTTATTACTGCAACACAAGCAGGCTACAATACACTTCATACATTTCTTTGGTTTTAACA
A

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Additional Information

External Database Links

Database	Acc Id	Source(s)
AGR Gene	RGD:2318102	AgrOrtholog
BioCyc Gene	G2FUF-37987	BioCyc
NCBI Gene	100362486	ENTREZGENE
PhenoGen	Silc1	PhenoGen
RNAcentral	URS0000CD0332	RNACentral

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2023-04-28	Silc1	sciatic injury induced lincRNA upregulator of SOX11	LOC100362486	small nuclear ribonucleoprotein D3	Name and Symbol changed	629549	APPROVED
2010-05-05	LOC100362486	small nuclear ribonucleoprotein D3			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)

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

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