LUM (lumican) - Rat Genome Database

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Gene: LUM (lumican) Sus scrofa
Analyze
Symbol: LUM
Name: lumican
RGD ID: 14081955
Description: ENCODES a protein that exhibits collagen binding (inferred); extracellular matrix structural constituent conferring compression resistance (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: VALIDATED
RGD Orthologs
Human
Mouse
Rat
Chinchilla
Bonobo
Dog
Squirrel
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: Sscrofa11.1 - Pig Sscrofa11.1 Assembly
Position:
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl591,748,885 - 91,757,598 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1591,748,871 - 91,756,381 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2596,175,872 - 96,183,382 (+)NCBISscrofa10.2Sscrofa10.2susScr3
JBrowse: View Region in Genome Browser (JBrowse)
Model


References
Additional References at PubMed
PMID:14681463   PMID:17145712   PMID:17407547   PMID:22301074   PMID:30032202  


Genomics

Comparative Map Data
LUM
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl591,748,885 - 91,757,598 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1591,748,871 - 91,756,381 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2596,175,872 - 96,183,382 (+)NCBISscrofa10.2Sscrofa10.2susScr3
LUM
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381291,102,629 - 91,111,494 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1291,102,629 - 91,111,494 (-)EnsemblGRCh38hg38GRCh38
GRCh371291,496,406 - 91,505,271 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361290,021,363 - 90,029,673 (-)NCBINCBI36Build 36hg18NCBI36
Build 341289,999,795 - 90,007,762NCBI
Celera1291,168,384 - 91,176,693 (-)NCBICelera
Cytogenetic Map12q21.33NCBI
HuRef1288,565,018 - 88,573,311 (-)NCBIHuRef
CHM1_11291,462,214 - 91,470,560 (-)NCBICHM1_1
T2T-CHM13v2.01291,080,108 - 91,088,974 (-)NCBIT2T-CHM13v2.0
Lum
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391097,401,363 - 97,408,565 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1097,400,990 - 97,408,565 (+)EnsemblGRCm39 Ensembl
GRCm381097,565,501 - 97,572,703 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1097,565,128 - 97,572,703 (+)EnsemblGRCm38mm10GRCm38
MGSCv371097,028,135 - 97,035,337 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361096,995,518 - 97,002,392 (+)NCBIMGSCv36mm8
Celera1099,536,481 - 99,543,683 (+)NCBICelera
Cytogenetic Map10C3NCBI
cM Map1050.32NCBI
Lum
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8734,245,323 - 34,252,510 (+)NCBIGRCr8
mRatBN7.2732,358,990 - 32,365,794 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl732,358,614 - 32,365,793 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx734,326,157 - 34,332,958 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0736,514,385 - 36,521,189 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0736,248,713 - 36,255,514 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0738,820,058 - 38,826,862 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl738,819,771 - 38,826,862 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0738,861,407 - 38,868,211 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4735,083,480 - 35,090,284 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1735,103,750 - 35,110,554 (+)NCBI
Celera729,396,589 - 29,403,393 (+)NCBICelera
Cytogenetic Map7q13NCBI
Lum
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495540528,298,988 - 28,308,054 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495540528,299,966 - 28,307,982 (-)NCBIChiLan1.0ChiLan1.0
LUM
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21099,136,692 - 99,144,880 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11299,133,086 - 99,141,066 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01288,636,825 - 88,644,665 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11291,952,277 - 91,960,388 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1291,952,277 - 91,960,388 (-)Ensemblpanpan1.1panPan2
LUM
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11531,792,872 - 31,800,444 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1531,793,233 - 31,800,912 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1532,247,441 - 32,254,994 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.01532,449,009 - 32,456,782 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl1532,449,009 - 32,456,645 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.11531,741,534 - 31,749,085 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01531,805,190 - 31,812,738 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01532,098,606 - 32,106,158 (-)NCBIUU_Cfam_GSD_1.0
Lum
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494528,380,086 - 28,387,678 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365077,846,681 - 7,855,455 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049365077,847,761 - 7,855,311 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
LUM
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11186,510,824 - 86,519,008 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1186,509,722 - 86,519,010 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_023666037158,664,710 - 158,672,984 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Lum
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462475015,553,383 - 15,559,408 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462475015,553,400 - 15,560,746 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in LUM
255 total Variants

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 hemolymphoid system musculoskeletal system nervous system renal system reproductive system respiratory system
High
Medium 10 4 3 2 3 1
Low 3 1 23 2
Below cutoff 1

Sequence


RefSeq Acc Id: ENSSSCT00000001000   ⟹   ENSSSCP00000000978
Type: CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.1 Ensembl591,748,885 - 91,757,598 (+)Ensembl
RefSeq Acc Id: NM_001243339   ⟹   NP_001230268
RefSeq Status: VALIDATED
Type: CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.1591,748,871 - 91,756,381 (+)NCBI
Sequence:
RefSeq Acc Id: NP_001230268   ⟸   NM_001243339
- Peptide Label: precursor
- UniProtKB: F1SQ09 (UniProtKB/TrEMBL),   A0A4X1SG78 (UniProtKB/TrEMBL),   A0A8D1H059 (UniProtKB/TrEMBL),   A0A8D0XMM8 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSSSCP00000000978   ⟸   ENSSSCT00000001000
Protein Domains
LRRNT


Additional Information

Database Acc Id Source(s)
Ensembl Genes ENSSSCG00000000916 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
  ENSSSCG00005018295 UniProtKB/TrEMBL
  ENSSSCG00015065886 UniProtKB/TrEMBL
  ENSSSCG00030058998 UniProtKB/TrEMBL
  ENSSSCG00040008308 UniProtKB/TrEMBL
  ENSSSCG00045007942 UniProtKB/TrEMBL
  ENSSSCG00050064705 UniProtKB/TrEMBL
  ENSSSCG00060058274 UniProtKB/TrEMBL
  ENSSSCG00070000706 UniProtKB/TrEMBL
Ensembl Transcript ENSSSCT00000001000 ENTREZGENE
  ENSSSCT00000001000.5 UniProtKB/TrEMBL
  ENSSSCT00005028877.1 UniProtKB/TrEMBL
  ENSSSCT00005028903.1 UniProtKB/TrEMBL
  ENSSSCT00015088331.1 UniProtKB/TrEMBL
  ENSSSCT00030082334.1 UniProtKB/TrEMBL
  ENSSSCT00040010862.1 UniProtKB/TrEMBL
  ENSSSCT00045013320.1 UniProtKB/TrEMBL
  ENSSSCT00045013342.1 UniProtKB/TrEMBL
  ENSSSCT00050088092.1 UniProtKB/TrEMBL
  ENSSSCT00060079460.1 UniProtKB/TrEMBL
  ENSSSCT00060079467.1 UniProtKB/TrEMBL
  ENSSSCT00070001314.1 UniProtKB/TrEMBL
  ENSSSCT00070001319.1 UniProtKB/TrEMBL
  ENSSSCT00070001322.1 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 ssc:100152607 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 A0A4X1SG78 ENTREZGENE
  A0A8D0XMM8 ENTREZGENE, UniProtKB/TrEMBL
  A0A8D1H059 ENTREZGENE, UniProtKB/TrEMBL
  F1SQ09 ENTREZGENE, UniProtKB/TrEMBL
UniProt Secondary A0A4X1SG78 UniProtKB/TrEMBL
VGNC ID VGNC:89894 ENTREZGENE