Ldb1 (LIM domain binding 1) - Rat Genome Database

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Gene: Ldb1 (LIM domain binding 1) Heterocephalus glaber
Analyze
Symbol: Ldb1
Name: LIM domain binding 1
RGD ID: 18903106
Description: ENCODES a protein that exhibits DNA binding (ortholog); transcription coregulator activity (ortholog); INVOLVED IN anterior/posterior axis specification (ortholog); cell adhesion (ortholog); cellular component assembly (ortholog); ASSOCIATED WITH genetic disease (ortholog); nail-patella syndrome (ortholog); FOUND IN beta-catenin-TCF complex (inferred); cell leading edge (inferred); chromatin (inferred)
Type: protein-coding
RefSeq Status: MODEL
Previously known as: LIM domain-binding protein 1
RGD Orthologs
Human
Mouse
Rat
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Alliance Genes
More Info more info ...
Latest Assembly: HetGla 1.0 - Naked Mole-Rat female 1.0 Assembly
Position:
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248311,571,942 - 1,584,775 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046248311,573,058 - 1,584,861 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2
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

References
Additional References at PubMed
PMID:30032202  


Genomics

Comparative Map Data
Ldb1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248311,571,942 - 1,584,775 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046248311,573,058 - 1,584,861 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2
LDB1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh3810102,102,088 - 102,121,442 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl10102,106,489 - 102,120,368 (-)EnsemblGRCh38hg38GRCh38
GRCh3710103,866,246 - 103,880,125 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 3610103,857,307 - 103,864,692 (-)NCBINCBI36Build 36hg18NCBI36
Build 3410103,857,316 - 103,864,692NCBI
Celera1097,608,243 - 97,621,137 (-)NCBICelera
Cytogenetic Map10q24.32NCBI
HuRef1097,499,399 - 97,512,291 (-)NCBIHuRef
CHM1_110104,150,870 - 104,163,764 (-)NCBICHM1_1
T2T-CHM13v2.010102,987,097 - 103,006,358 (-)NCBIT2T-CHM13v2.0
Ldb1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391946,019,963 - 46,036,584 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1946,020,009 - 46,033,653 (-)EnsemblGRCm39 Ensembl
GRCm381946,031,525 - 46,048,145 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1946,031,570 - 46,045,214 (-)EnsemblGRCm38mm10GRCm38
MGSCv371946,107,084 - 46,119,701 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361946,085,905 - 46,092,932 (-)NCBIMGSCv36mm8
Celera1946,795,488 - 46,808,103 (-)NCBICelera
Cytogenetic Map19C3NCBI
cM Map1938.75NCBI
Ldb1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81254,813,161 - 254,838,931 (-)NCBIGRCr8
mRatBN7.21244,864,168 - 244,890,007 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1244,877,173 - 244,890,013 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1253,021,407 - 253,028,952 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01259,716,387 - 259,723,937 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01252,368,592 - 252,376,144 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01265,772,729 - 265,798,442 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1265,785,409 - 265,798,167 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01273,215,566 - 273,228,637 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41251,253,305 - 251,260,850 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11251,513,919 - 251,527,836 (-)NCBI
Celera1240,683,703 - 240,691,248 (-)NCBICelera
Cytogenetic Map1q54NCBI
Ldb1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554858,229,517 - 8,241,142 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554858,229,517 - 8,242,003 (+)NCBIChiLan1.0ChiLan1.0
LDB1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v28113,988,310 - 114,006,857 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan110113,998,222 - 114,012,133 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01098,707,470 - 98,722,771 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.110102,176,744 - 102,191,745 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl10102,179,757 - 102,184,047 (-)Ensemblpanpan1.1panPan2
LDB1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12814,646,409 - 14,658,324 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2814,646,056 - 14,658,548 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2814,818,513 - 14,830,424 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.02815,119,475 - 15,131,392 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2815,118,375 - 15,131,637 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12814,664,778 - 14,676,690 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02814,704,089 - 14,716,005 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02814,836,486 - 14,848,625 (-)NCBIUU_Cfam_GSD_1.0
Ldb1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440721332,111,411 - 32,125,588 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049366003,714,095 - 3,728,815 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049366003,714,630 - 3,728,813 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
LDB1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl14113,113,179 - 113,126,816 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.114113,114,302 - 113,126,455 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.214122,967,114 - 122,979,261 (-)NCBISscrofa10.2Sscrofa10.2susScr3
LDB1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1995,102,312 - 95,153,029 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl995,138,424 - 95,153,179 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366604856,236,189 - 56,248,919 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0


Expression


Sequence


Reference Sequences
RefSeq Acc Id: ENSHGLT00000003070   ⟹   ENSHGLP00000003016
Type: CODING
Position:
Naked Mole-Rat AssemblyChrPosition (strand)Source
HetGla_female_1.0 EnsemblNW_0046248311,571,942 - 1,584,471 (-)Ensembl
RefSeq Acc Id: ENSHGLT00000003071   ⟹   ENSHGLP00000003017
Type: CODING
Position:
Naked Mole-Rat AssemblyChrPosition (strand)Source
HetGla_female_1.0 EnsemblNW_0046248311,572,880 - 1,584,775 (-)Ensembl
RefSeq Acc Id: ENSHGLT00000003072   ⟹   ENSHGLP00000003018
Type: CODING
Position:
Naked Mole-Rat AssemblyChrPosition (strand)Source
HetGla_female_1.0 EnsemblNW_0046248311,574,356 - 1,576,676 (-)Ensembl
RefSeq Acc Id: XM_004866385   ⟹   XP_004866442
Type: CODING
Position:
Naked Mole-Rat AssemblyChrPosition (strand)Source
HetGla 1.0NW_0046248311,573,058 - 1,584,441 (-)NCBI
RefSeq Acc Id: XM_004866386   ⟹   XP_004866443
Type: CODING
Position:
Naked Mole-Rat AssemblyChrPosition (strand)Source
HetGla 1.0NW_0046248311,573,058 - 1,584,441 (-)NCBI
RefSeq Acc Id: XM_013066152   ⟹   XP_012921606
Type: CODING
Position:
Naked Mole-Rat AssemblyChrPosition (strand)Source
HetGla 1.0NW_0046248311,573,058 - 1,584,861 (-)NCBI
RefSeq Acc Id: XM_013066153   ⟹   XP_012921607
Type: CODING
Position:
Naked Mole-Rat AssemblyChrPosition (strand)Source
HetGla 1.0NW_0046248311,573,058 - 1,579,218 (-)NCBI
Protein Sequences
Protein RefSeqs XP_004866442 (Get FASTA)   NCBI Sequence Viewer  
  XP_004866443 (Get FASTA)   NCBI Sequence Viewer  
  XP_012921606 (Get FASTA)   NCBI Sequence Viewer  
  XP_012921607 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSHGLP00000003016
  ENSHGLP00000003017
  ENSHGLP00100016354
GenBank Protein JAO00103 (Get FASTA)   NCBI Sequence Viewer  
Reference Protein Sequences
RefSeq Acc Id: XP_012921606   ⟸   XM_013066152
- Peptide Label: isoform X2
- UniProtKB: A0A0P6K509 (UniProtKB/TrEMBL),   G5CAG6 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_004866443   ⟸   XM_004866386
- Peptide Label: isoform X3
- UniProtKB: G5CAG6 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_004866442   ⟸   XM_004866385
- Peptide Label: isoform X1
- UniProtKB: A0A0P6K509 (UniProtKB/TrEMBL),   G5CAG6 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_012921607   ⟸   XM_013066153
- Peptide Label: isoform X4
- UniProtKB: G5CAG6 (UniProtKB/TrEMBL)
RefSeq Acc Id: ENSHGLP00000003016   ⟸   ENSHGLT00000003070
RefSeq Acc Id: ENSHGLP00000003018   ⟸   ENSHGLT00000003072
RefSeq Acc Id: ENSHGLP00000003017   ⟸   ENSHGLT00000003071


Additional Information

Database Acc Id Source(s)
Ensembl Genes ENSHGLG00000002254 Ensembl, ENTREZGENE
  ENSHGLG00100012074 UniProtKB/TrEMBL
Ensembl Transcript ENSHGLT00000003070 ENTREZGENE
  ENSHGLT00000003071 ENTREZGENE
  ENSHGLT00100016533 UniProtKB/TrEMBL
Gene3D-CATH Cysteine Rich Protein UniProtKB/TrEMBL
InterPro LID UniProtKB/TrEMBL
  LIM-bd/SEUSS UniProtKB/TrEMBL
KEGG Report hgl:101706605 UniProtKB/TrEMBL
NCBI Gene Ldb1 ENTREZGENE
PANTHER PTHR10378 UniProtKB/TrEMBL
  PTHR10378:SF7 UniProtKB/TrEMBL
Pfam LID UniProtKB/TrEMBL
  LIM_bind UniProtKB/TrEMBL
PROSITE LID UniProtKB/TrEMBL
UniProt A0A0P6K509 ENTREZGENE, UniProtKB/TrEMBL
  G5CAG6 ENTREZGENE, UniProtKB/TrEMBL