LUM (lumican) - Rat Genome Database

Name: LUM
Creator: Rat Genome Database
License: Creative Commons CC BY 4.0
Keywords: Rat Gene RGD Genome

Gene: LUM (lumican) Pan paniscus

Analyze

Symbol:

LUM

Name:

lumican

RGD ID:

11971426

Description:

ENCODES a protein that exhibits collagen binding (inferred); INVOLVED IN cartilage development (ortholog); positive regulation of transcription by RNA polymerase II (ortholog); response to growth factor (ortholog); ASSOCIATED WITH Arterial Occlusive Diseases (ortholog); carotid artery disease (ortholog); coronary artery disease (ortholog); FOUND IN extracellular matrix (inferred); extracellular region (inferred); extracellular space (inferred)

Type:

protein-coding

RefSeq Status:

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):	LUM (lumican)	NCBI	Ortholog
Mus musculus (house mouse):	Lum (lumican)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Rattus norvegicus (Norway rat):	Lum (lumican)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chinchilla lanigera (long-tailed chinchilla):	Lum (lumican)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Canis lupus familiaris (dog):	LUM (lumican)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Ictidomys tridecemlineatus (thirteen-lined ground squirrel):	Lum (lumican)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Sus scrofa (pig):	LUM (lumican)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chlorocebus sabaeus (green monkey):	LUM (lumican)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Heterocephalus glaber (naked mole-rat):	Lum (lumican)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline

Latest Assembly:

Mhudiblu_PPA_v0 - Bonobo Mhudiblu_PPA_v0 Assembly

Position:

Bonobo Assembly	Chr	Position (strand)	Source	Genome Browsers
Bonobo Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
NHGRI_mPanPan1-v2	10	99,136,692 - 99,144,880 (-)	NCBI		NHGRI_mPanPan1-v2
NHGRI_mPanPan1	12	99,133,086 - 99,141,066 (-)	NCBI		NHGRI_mPanPan1
Mhudiblu_PPA_v0	12	88,636,825 - 88,644,665 (-)	NCBI	Mhudiblu_PPA_v0	Mhudiblu_PPA_v0	panPan3
PanPan1.1	12	91,952,277 - 91,960,388 (-)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	12	91,952,277 - 91,960,388 (-)	Ensembl	panpan1.1		panPan2

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

Arterial Occlusive Diseases (ISO)

carotid artery disease (ISO)

coronary artery disease (ISO)

Ehlers-Danlos syndrome classic type 1 (ISO)

Experimental Liver Cirrhosis (ISO)

facioscapulohumeral muscular dystrophy (ISO)

Fibrosis (ISO)

liver cirrhosis (ISO)

Myocardial Reperfusion Injury (ISO)

pancreatic cancer (ISO)

Spinal Cord Injuries (ISO)

ureteral obstruction (ISO)

varicose veins (ISO)

Wounds and Injuries (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

cartilage development (ISO)

positive regulation of transcription by RNA polymerase II (IEA,ISO)

positive regulation of transforming growth factor beta1 production (IEA)

response to growth factor (ISO)

response to organic cyclic compound (ISO)

Cellular Component

extracellular matrix (IEA)

extracellular region (IEA)

extracellular space (IEA)

fibrillar collagen trimer (IEA)

Molecular Function

collagen binding (IEA)

protein binding (ISO)

References

Additional References at PubMed

PMID:22301074	PMID:30032202

Genomics

Comparative Map Data

LUM
(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	10	99,136,692 - 99,144,880 (-)	NCBI		NHGRI_mPanPan1-v2
NHGRI_mPanPan1	12	99,133,086 - 99,141,066 (-)	NCBI		NHGRI_mPanPan1
Mhudiblu_PPA_v0	12	88,636,825 - 88,644,665 (-)	NCBI	Mhudiblu_PPA_v0	Mhudiblu_PPA_v0	panPan3
PanPan1.1	12	91,952,277 - 91,960,388 (-)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	12	91,952,277 - 91,960,388 (-)	Ensembl	panpan1.1		panPan2

LUM
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38	12	91,102,629 - 91,111,494 (-)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38.p14 Ensembl	12	91,102,629 - 91,111,494 (-)	Ensembl	GRCh38		hg38	GRCh38
GRCh37	12	91,496,406 - 91,505,271 (-)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	12	90,021,363 - 90,029,673 (-)	NCBI	NCBI36	Build 36	hg18	NCBI36
Build 34	12	89,999,795 - 90,007,762	NCBI
Celera	12	91,168,384 - 91,176,693 (-)	NCBI		Celera
Cytogenetic Map	12	q21.33	NCBI
HuRef	12	88,565,018 - 88,573,311 (-)	NCBI		HuRef
CHM1_1	12	91,462,214 - 91,470,560 (-)	NCBI		CHM1_1
T2T-CHM13v2.0	12	91,080,108 - 91,088,974 (-)	NCBI		T2T-CHM13v2.0

Lum
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	10	97,401,363 - 97,408,565 (+)	NCBI	GRCm39	GRCm39	mm39
GRCm39 Ensembl	10	97,400,990 - 97,408,565 (+)	Ensembl		GRCm39 Ensembl
GRCm38	10	97,565,501 - 97,572,703 (+)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	10	97,565,128 - 97,572,703 (+)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	10	97,028,135 - 97,035,337 (+)	NCBI	GRCm37	MGSCv37	mm9	NCBIm37
MGSCv36	10	96,995,518 - 97,002,392 (+)	NCBI		MGSCv36	mm8
Celera	10	99,536,481 - 99,543,683 (+)	NCBI		Celera
Cytogenetic Map	10	C3	NCBI
cM Map	10	50.32	NCBI

Lum
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	7	34,245,323 - 34,252,510 (+)	NCBI		GRCr8
mRatBN7.2	7	32,358,990 - 32,365,794 (+)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	7	32,358,614 - 32,365,793 (+)	Ensembl		mRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx	7	34,326,157 - 34,332,958 (+)	NCBI	Rnor_SHR	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	7	36,514,385 - 36,521,189 (+)	NCBI	Rnor_SHRSP	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	7	36,248,713 - 36,255,514 (+)	NCBI	Rnor_WKY	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	7	38,820,058 - 38,826,862 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	7	38,819,771 - 38,826,862 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	7	38,861,407 - 38,868,211 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	7	35,083,480 - 35,090,284 (+)	NCBI	RGSC3.4	RGSC_v3.4	rn4	RGSC3.4
RGSC_v3.1	7	35,103,750 - 35,110,554 (+)	NCBI
Celera	7	29,396,589 - 29,403,393 (+)	NCBI		Celera
Cytogenetic Map	7	q13	NCBI

Lum
(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_004955405	28,298,988 - 28,308,054 (-)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955405	28,299,966 - 28,307,982 (-)	NCBI	ChiLan1.0	ChiLan1.0

LUM
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1	15	31,792,872 - 31,800,444 (-)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
CanFam3.1 Ensembl	15	31,793,233 - 31,800,912 (-)	Ensembl	CanFam3.1		canFam3	CanFam3.1
Dog10K_Boxer_Tasha	15	32,247,441 - 32,254,994 (-)	NCBI		Dog10K_Boxer_Tasha
ROS_Cfam_1.0	15	32,449,009 - 32,456,782 (-)	NCBI		ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl	15	32,449,009 - 32,456,645 (-)	Ensembl		ROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1	15	31,741,534 - 31,749,085 (-)	NCBI		UMICH_Zoey_3.1
UNSW_CanFamBas_1.0	15	31,805,190 - 31,812,738 (-)	NCBI		UNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0	15	32,098,606 - 32,106,158 (-)	NCBI		UU_Cfam_GSD_1.0

Lum
(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	NW_024404945	28,380,086 - 28,387,678 (+)	NCBI		HiC_Itri_2
SpeTri2.0 Ensembl	NW_004936507	7,846,681 - 7,855,455 (-)	Ensembl	SpeTri2.0	SpeTri2.0 Ensembl
SpeTri2.0	NW_004936507	7,847,761 - 7,855,311 (-)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

LUM
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	5	91,748,885 - 91,757,598 (+)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	5	91,748,871 - 91,756,381 (+)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	5	96,175,872 - 96,183,382 (+)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

LUM
(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	11	86,510,824 - 86,519,008 (-)	NCBI	ChlSab1.1	ChlSab1.1	chlSab2
ChlSab1.1 Ensembl	11	86,509,722 - 86,519,010 (-)	Ensembl	ChlSab1.1	ChlSab1.1 Ensembl	chlSab2
Vero_WHO_p1.0	NW_023666037	158,664,710 - 158,672,984 (+)	NCBI	Vero_WHO_p1.0	Vero_WHO_p1.0

Lum
(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_004624750	15,553,383 - 15,559,408 (+)	Ensembl	HetGla_female_1.0	HetGla_female_1.0 Ensembl	hetGla2
HetGla 1.0	NW_004624750	15,553,400 - 15,560,746 (+)	NCBI	HetGla_female_1.0	HetGla 1.0	hetGla2

Expression

Sequence

Nucleotide Sequences


RefSeq Transcripts	XM_003823402	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	JARIFH020000010	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

RefSeq Acc Id:

ENSPPAT00000031123 ⟹ ENSPPAP00000008487

Type:

CODING

Position:

Bonobo Assembly	Chr	Position (strand)	Source
PanPan1.1 Ensembl	12	91,952,277 - 91,960,388 (-)	Ensembl

RefSeq Acc Id:

XM_003823402 ⟹ XP_003823450

Type:

CODING

Position:

Bonobo Assembly	Chr	Position (strand)	Source
NHGRI_mPanPan1-v2	10	99,136,692 - 99,144,880 (-)	NCBI
NHGRI_mPanPan1	12	99,133,086 - 99,141,066 (-)	NCBI
Mhudiblu_PPA_v0	12	88,636,825 - 88,644,665 (-)	NCBI
PanPan1.1	12	91,952,277 - 91,960,388 (-)	NCBI

Sequence:

show sequence

GAGCACATTGCACTTAATTGTTGCCACAGCCACAGATGTAAAGAGGCTTGTAAGAAAAATGTTC
TCACAGTGAGCTTCCTTATTTGAAGCAGGACTCAATTCTTGGTTAAAAGCTATGGTATTTGAGC
TAGTTAAACACATATCTCTCTCCCATTCCATAGGGAATGAGCTGGGCTGTCCTTTCTCCCCACG
TTCACCTGCACTTCGTTAGAGAGCAGTGTTCACATGCCACACCACAAGATCCCCACAATGACAT
AGCTCCATTCAGAGACTGGCGTGACTGGGCTGGGTCTCCCCACCCCCCTTCAGCTCTTGTATCA
CTCAGAATCTGGCAGCCAGTTCCGTCCTGACAGAGTTTACAGCATATATTGGTGGATTCTTGTC
CATAGTGCATCTGCTTTAAGAATTAACGAAAGCAGTGTCAAGACAGTAAGGATTCAAACCATTT
GCCAAAAATGAGTCTAAGTGCATTTACTCTCTTCCTGGCATTGATTGGTGGTACCAGTGGCCAG
TACTATGATTATGATTTTCCCCTATCAATTTATGGGCAATCATCACCAAACTGTGCACCAGAAT
GTAACTGCCCTGAAAGCTACCCAAGTGCCATGTACTGTGATGAGCTGAAATTGAAAAGTGTACC
AATGGTGCCTCCTGGAATCAAGTATCTTTACCTTAGGAATAACCAGATTGACCATATTGATGAA
AAGGCCTTTGAGAATGTAACTGATCTGCAGTGGCTCATTCTAGATCACAACCTTCTAGAAAACT
CCAAGATAAAAGGGAGAGTTTTCTCTAAATTGAAACAACTGAAGAAGCTGCATATAAACCACAA
CAACCTGACAGAGTCTGTGGGCCCACTTCCCAAATCTCTGGAGGATCTGCAGCTTACTCATAAC
AAGATCACAAAGCTGGGCTCTTTTGAAGGATTGGTAAACCTGACCTTCATCCATCTCCAACACA
ATCGGCTGAAAGAGGATGCTGTTTCAGCTGCTTTTAAAGGTCTTAAATCACTCGAATACCTTGA
CTTGAGCTTCAATCAGATAGCCAAACTGCCTTCTGGTCTCCCTGTCTCTCTTCTAACTCTCTAC
TTAGACAACAATAAGATCAGCAACATCCCTGATGAGTATTTCAAGCGTTTTAATGCATTGCAGT
ATCTGCGTTTATCTCACAACGAACTGGCTGATAGTGGAATACCTGGAAATTCTTTCAATGTGTC
ATCACTGGTTGAGCTGGATCTGTCCTATAACAAGCTTAAAAACATACCAACTGTCAATGAAAAC
CTTGAAAACTATTACCTGGAGGTCAATCAACTTGAGAAGTTTGACGTAAAGAGCTTCTGCAAGA
TCCTGGGGCCATTATCCTACTCCAAGATCAAGCATTTGCGTTTGGATGGCAATCGCATCTCAGA
AACCAGTCTTCCACCGGATATGTATGAATGTCTACGTGTTGCTAACGAAGTCACTCTTAATTAA
TATCTGTATCCTGGAACGATATTTTATGGTTATGTTTTTCTGTGTGTCAGTTTTCATAGTATCC
ATATTTTATTACTGTTTATTACTTCCATGAATTTTAAAATCTGAGGGAAATGTTTTGTAAACAT
TTATTTTTTTTAAAGAAAAGATGAAAGGCAGGCCTATTTCATCACAAGAACACACACATATACA
CGAATAGACATCAAACTCAATGCTTTATTTGTAAATTTAGTGTTTTTTTATTTCTACTGTCAAA
TGATGTGCAAAACCCTTTACTGGTTGCATGGAAATCAGCCAAGTTTTATAATCCTTAAATCTTA
ATGTGCCCCAAAGCTTGGATTAAATACATATGGATGTTTACTCTCTTGCACCAAATTATCTTGA
TACGTTCAAATTTGTCTGGTTAAAAAATAGGTGGTAGATATTGAGGCCAAGAATATTGCAAAAT
ACATGAAGCCTCATGCACTTAAAGAAGTATTTTTAGAATAAGAATTTGCATACTTACCTAGTGA
AACTTTTCTAGAATTATTTTTCACTCTAAGTCATGTATGTTTCTCTTTGATTATTTGCATGTTA
TGTTTAATAAGCTACTAGCAAAATAAAACATAGCAAATGGCA

hide sequence

Protein Sequences


Protein RefSeqs	XP_003823450	(Get FASTA)	NCBI Sequence Viewer
Ensembl Protein	ENSPPAP00000008487
	ENSPPAP00000008487.1

RefSeq Acc Id:

XP_003823450 ⟸ XM_003823402

- UniProtKB:

A0A2R8ZXH3 (UniProtKB/TrEMBL)

- Sequence:

show sequence

MSLSAFTLFLALIGGTSGQYYDYDFPLSIYGQSSPNCAPECNCPESYPSAMYCDELKLKSVPMV
PPGIKYLYLRNNQIDHIDEKAFENVTDLQWLILDHNLLENSKIKGRVFSKLKQLKKLHINHNNL
TESVGPLPKSLEDLQLTHNKITKLGSFEGLVNLTFIHLQHNRLKEDAVSAAFKGLKSLEYLDLS
FNQIAKLPSGLPVSLLTLYLDNNKISNIPDEYFKRFNALQYLRLSHNELADSGIPGNSFNVSSL
VELDLSYNKLKNIPTVNENLENYYLEVNQLEKFDVKSFCKILGPLSYSKIKHLRLDGNRISETS
LPPDMYECLRVANEVTLN

hide sequence

RefSeq Acc Id:

ENSPPAP00000008487 ⟸ ENSPPAT00000031123

Protein Domains

LRRNT

Additional Information

External Database Links

Database	Acc Id	Source(s)
Ensembl Genes	ENSPPAG00000027479	Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript	ENSPPAT00000031123.1	UniProtKB/TrEMBL
Gene3D-CATH	3.80.10.10	UniProtKB/TrEMBL
InterPro	Leu-rich_rpt	UniProtKB/TrEMBL
	Leu-rich_rpt_typical-subtyp	UniProtKB/TrEMBL
	LRR_dom_sf	UniProtKB/TrEMBL
	LRRNT	UniProtKB/TrEMBL
KEGG Report	pps:100970142	UniProtKB/TrEMBL
NCBI Gene	LUM	ENTREZGENE
PANTHER	AGAP008170-PA	UniProtKB/TrEMBL
	PTHR45712:SF6	UniProtKB/TrEMBL
Pfam	LRR_1	UniProtKB/TrEMBL
	LRR_8	UniProtKB/TrEMBL
	LRRNT	UniProtKB/TrEMBL
PRINTS	LEURICHRPT	UniProtKB/TrEMBL
PROSITE	LRR	UniProtKB/TrEMBL
SMART	LRR_BAC	UniProtKB/TrEMBL
	LRR_SD22	UniProtKB/TrEMBL
	LRR_TYP	UniProtKB/TrEMBL
	LRRNT	UniProtKB/TrEMBL
Superfamily-SCOP	L domain-like	UniProtKB/TrEMBL
UniProt	A0A2R8ZXH3	ENTREZGENE, UniProtKB/TrEMBL

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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