Ldoc1 (LDOC1, regulator of NFKB signaling) - Rat Genome Database

Send us a Message
Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Search RGD Grant Resources Citing RGD About Us Contact Us
Genes Variants Community Projects QTLs Strains Markers Genome Information Ontologies Cell Lines References Download Submit Data
OntoMate (Literature Search) JBrowse (Genome Browser) Synteny Browser (VCMap) Variant Visualizer Multi-Ontology Enrichment (MOET) Gene-Ortholog Location Finder (GOLF) InterViewer (Protein-Protein Interactions) PhenoMiner (Quatitative Phenotypes) Gene Annotator OLGA (Gene List Generator) AllianceMine GViewer (Genome Viewer)
Aging & Age-Related Disease Cancer & Neoplastic Disease Cardiovascular Disease Coronavirus Disease Developmental Disease Diabetes Hematologic Disease Immune & Inflammatory Disease Infectious Disease Liver Disease Neurological Disease Obesity & Metabolic Syndrome Renal Disease Respiratory Disease Sensory Organ Disease
Find Models Genetic Models Autism Models Rat PhenoMiner (Quantitative Phenotypes) Chinchilla PhenoMiner Expected Ranges (Quantitative Phenotype) PhenoMiner Term Comparison Hybrid Rat Diversity Panel Phenotypes Phenotypes in Other Animal Models Animal Husbandry Strain Medical Records Phylogenetics Strain Availability Calendar Rats 101 Submissions Photo Archive
Pathways
Rat Community Forum Directory of Rat Laboratories Video Tutorials News RGD Publications RGD Presentations Archive Nomenclature Guidelines Resource Links Laboratory Resources Employment Resources
Advanced Search (OLGA)
Gene: Ldoc1 (LDOC1, regulator of NFKB signaling) Rattus norvegicus
Analyze
Symbol: Ldoc1
Name: LDOC1, regulator of NFKB signaling
RGD ID: 1565644
Description: Predicted to be involved in cellular response to lipopolysaccharide and cellular response to muramyl dipeptide. Predicted to act upstream of or within maternal placenta development and maternal process involved in parturition. Predicted to be located in nucleolus and nucleoplasm. Orthologous to human LDOC1 (LDOC1 regulator of NFKB signaling); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; bis(2-ethylhexyl) phthalate; bisphenol A.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: leucine zipper down-regulated in cancer 1; leucine zipper, down-regulated in cancer 1; LOC367956; NEWGENE_1565644; RGD1565644; similar to leucine zipper, down-regulated in cancer 1
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8X144,837,879 - 145,110,607 (+)NCBIGRCr8
mRatBN7.2X139,965,509 - 140,074,355 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 EnsemblX139,965,509 - 140,074,355 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_UtxX142,150,266 - 142,259,092 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0X145,691,249 - 145,800,064 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0X143,246,943 - 143,355,782 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0X144,699,737 - 144,778,947 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX144,807,392 - 144,807,829 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0X144,715,836 - 144,835,379 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X147,294,439 - 147,294,882 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
CeleraX135,996,966 - 136,075,293 (+)NCBICelera
Cytogenetic MapXq36NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
nucleolus  (ISO)
nucleoplasm  (ISO)
nucleus  (IEA)

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. 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.
2. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:25468940   PMID:27812135  


Genomics

Comparative Map Data
Ldoc1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8X144,837,879 - 145,110,607 (+)NCBIGRCr8
mRatBN7.2X139,965,509 - 140,074,355 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 EnsemblX139,965,509 - 140,074,355 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_UtxX142,150,266 - 142,259,092 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0X145,691,249 - 145,800,064 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0X143,246,943 - 143,355,782 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0X144,699,737 - 144,778,947 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX144,807,392 - 144,807,829 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0X144,715,836 - 144,835,379 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X147,294,439 - 147,294,882 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
CeleraX135,996,966 - 136,075,293 (+)NCBICelera
Cytogenetic MapXq36NCBI
LDOC1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38X141,173,235 - 141,177,129 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 EnsemblX141,111,605 - 141,177,129 (-)EnsemblGRCh38hg38GRCh38
GRCh37X140,267,420 - 140,271,314 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36X140,097,596 - 140,098,976 (-)NCBINCBI36Build 36hg18NCBI36
Build 34X139,995,452 - 139,996,830NCBI
CeleraX140,808,897 - 140,810,277 (+)NCBICelera
Cytogenetic MapXq27.1NCBI
HuRefX129,731,182 - 129,732,563 (-)NCBIHuRef
CHM1_1X140,181,056 - 140,182,436 (-)NCBICHM1_1
T2T-CHM13v2.0X139,490,611 - 139,494,505 (-)NCBIT2T-CHM13v2.0
Ldoc1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39X60,753,217 - 60,754,556 (+)NCBIGRCm39GRCm39mm39
GRCm39 EnsemblX60,753,103 - 60,754,561 (+)EnsemblGRCm39 Ensembl
GRCm38X61,709,611 - 61,710,950 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 EnsemblX61,709,497 - 61,710,955 (+)EnsemblGRCm38mm10GRCm38
MGSCv37X58,962,791 - 58,964,125 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36X57,970,279 - 57,971,615 (+)NCBIMGSCv36mm8
CeleraX48,141,460 - 48,142,412 (+)NCBICelera
Cytogenetic MapXA5NCBI
cM MapX34.57NCBI
Ldoc1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_004955539127,887 - 128,324 (+)EnsemblChiLan1.0
ChiLan1.0NW_004955539127,705 - 129,147 (+)NCBIChiLan1.0ChiLan1.0
LDOC1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2X140,665,044 - 140,666,509 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1X140,668,645 - 140,670,112 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0X130,368,487 - 130,369,951 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1X140,707,249 - 140,708,712 (-)NCBIpanpan1.1PanPan1.1panPan2
LDOC1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1X111,065,937 - 111,067,337 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 EnsemblX111,066,055 - 111,066,498 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_TashaX96,895,390 - 96,896,819 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0X113,058,785 - 113,060,204 (+)NCBIROS_Cfam_1.0
UMICH_Zoey_3.1X110,184,459 - 110,185,873 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0X112,375,065 - 112,376,494 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0X112,050,253 - 112,051,667 (+)NCBIUU_Cfam_GSD_1.0
Ldoc1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2X109,128,585 - 109,132,857 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365136,485,442 - 6,485,882 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049365136,481,758 - 6,486,018 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
LDOC1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 EnsemblX115,579,486 - 115,584,357 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1X115,580,622 - 115,583,129 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2X131,903,739 - 131,906,205 (+)NCBISscrofa10.2Sscrofa10.2susScr3
LDOC1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1X116,385,602 - 116,387,045 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 EnsemblX116,385,790 - 116,386,230 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366606553,806,893 - 53,808,336 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Ldoc1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248085,435,503 - 5,435,940 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046248085,434,695 - 5,436,099 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Ldoc1
455 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:144
Count of miRNA genes:120
Interacting mature miRNAs:125
Transcripts:ENSRNOT00000004529
Prediction methods:Microtar, Miranda, Rnahybrid
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
1598856Memor1Memory QTL 11.9exploratory behavior trait (VT:0010471)total horizontal distance resulting from voluntary locomotion in an experimental apparatus (CMO:0001443)X103312877148312877Rat
1598809Memor15Memory QTL 154.4exploratory behavior trait (VT:0010471)difference between time of physical contact/close proximity of test subject and social stimulus during sample phase and test phase (CMO:0002678)X103312877148312877Rat
738025Stresp3Stress response QTL 34.610.0066stress-related behavior trait (VT:0010451)defensive burying - approachX100567703150256146Rat
634346Insul4Insulin level QTL 40blood insulin amount (VT:0001560)serum insulin level (CMO:0000358)X126975089152453651Rat
10059603Bw174Body weight QTL 1743.40.025body mass (VT:0001259)body weight (CMO:0000012)X113937816152453651Rat
1598837Memor13Memory QTL 133.2exploratory behavior trait (VT:0010471)difference between time of physical contact/close proximity of test subject and social stimulus during sample phase and test phase (CMO:0002678)X41052407146860749Rat


Expression


Sequence


Ensembl Acc Id: ENSRNOT00000004529   ⟹   ENSRNOP00000004529
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 EnsemblX139,965,517 - 140,074,318 (+)Ensembl
Rnor_6.0 EnsemblX144,807,392 - 144,807,829 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000114336   ⟹   ENSRNOP00000088006
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 EnsemblX139,965,509 - 140,074,355 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000118280   ⟹   ENSRNOP00000097817
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 EnsemblX139,965,509 - 140,074,272 (+)Ensembl
RefSeq Acc Id: NM_001402267   ⟹   NP_001389196
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X145,001,767 - 145,110,601 (+)NCBI
mRatBN7.2X139,965,509 - 140,074,355 (+)NCBI
RefSeq Acc Id: XM_039100224   ⟹   XP_038956152
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X145,001,771 - 145,110,607 (+)NCBI
mRatBN7.2X139,965,513 - 140,074,355 (+)NCBI
RefSeq Acc Id: XM_063280184   ⟹   XP_063136254
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X144,837,879 - 145,110,607 (+)NCBI
RefSeq Acc Id: XM_063280185   ⟹   XP_063136255
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X145,044,100 - 145,110,607 (+)NCBI
RefSeq Acc Id: XM_063280186   ⟹   XP_063136256
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X145,044,101 - 145,110,607 (+)NCBI
RefSeq Acc Id: XP_038956152   ⟸   XM_039100224
- Peptide Label: isoform X1
- UniProtKB: D3ZTE6 (UniProtKB/TrEMBL)
Ensembl Acc Id: ENSRNOP00000004529   ⟸   ENSRNOT00000004529
Ensembl Acc Id: ENSRNOP00000097817   ⟸   ENSRNOT00000118280
Ensembl Acc Id: ENSRNOP00000088006   ⟸   ENSRNOT00000114336
RefSeq Acc Id: NP_001389196   ⟸   NM_001402267
- Peptide Label: precursor
- UniProtKB: D3ZTE6 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_063136254   ⟸   XM_063280184
- Peptide Label: isoform X1
- UniProtKB: D3ZTE6 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_063136255   ⟸   XM_063280185
- Peptide Label: isoform X1
- UniProtKB: D3ZTE6 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_063136256   ⟸   XM_063280186
- Peptide Label: isoform X1
- UniProtKB: D3ZTE6 (UniProtKB/TrEMBL)
Protein Domains
DUF4939

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZTE6-F1-model_v2 AlphaFold D3ZTE6 1-146 view protein structure

Transcriptome

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


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1565644 AgrOrtholog
BioCyc Gene G2FUF-859 BioCyc
Ensembl Genes ENSRNOG00000003409 Ensembl, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000004529.4 UniProtKB/TrEMBL
  ENSRNOT00000114336.1 UniProtKB/TrEMBL
  ENSRNOT00000118280.1 UniProtKB/TrEMBL
InterPro DUF4939 UniProtKB/TrEMBL
  LDOC1-rel UniProtKB/TrEMBL
NCBI Gene 367956 ENTREZGENE
PANTHER CCHC-TYPE DOMAIN-CONTAINING PROTEIN-RELATED UniProtKB/TrEMBL
  PTHR15503 UniProtKB/TrEMBL
Pfam DUF4939 UniProtKB/TrEMBL
PhenoGen Ldoc1 PhenoGen
RatGTEx ENSRNOG00000003409 RatGTEx
UniProt D3ZTE6 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2021-03-09 Ldoc1  LDOC1, regulator of NFKB signaling  NEWGENE_1565644  leucine zipper down-regulated in cancer 1  Data merged from RGD:11505382 737654 PROVISIONAL
2017-04-05 Ldoc1  LDOC1, regulator of NFKB signaling  Ldoc1  leucine zipper, down-regulated in cancer 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2016-08-02 NEWGENE_1565644  leucine zipper down-regulated in cancer 1      Symbol and Name status set to provisional 70820 PROVISIONAL
2008-03-07 Ldoc1  leucine zipper, down-regulated in cancer 1  RGD1565644_predicted  similar to leucine zipper, down-regulated in cancer 1 (predicted)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-03-07 RGD1565644_predicted  similar to leucine zipper, down-regulated in cancer 1 (predicted)  LOC367956  similar to leucine zipper, down-regulated in cancer 1  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC367956  similar to leucine zipper, down-regulated in cancer 1      Symbol and Name status set to provisional 70820 PROVISIONAL