Lin54 (lin-54 DREAM MuvB core complex component) - Rat Genome Database
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Gene: Lin54 (lin-54 DREAM MuvB core complex component) Rattus norvegicus
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Symbol: Lin54
Name: lin-54 DREAM MuvB core complex component
RGD ID: 1311361
Description: Predicted to have RNA polymerase II transcription regulatory region sequence-specific DNA binding activity. Predicted to be involved in regulation of transcription, DNA-templated. Predicted to localize to nucleus. Orthologous to human LIN54 (lin-54 DREAM MuvB core complex component); INTERACTS WITH bisphenol A; cadmium dichloride; cobalt dichloride.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: lin-54 homolog (C. elegans); LOC305171; protein lin-54 homolog; RGD1311361; similar to hypothetical protein
Orthologs:
Homo sapiens (human) : LIN54 (lin-54 DREAM MuvB core complex component)  HGNC  Alliance
Mus musculus (house mouse) : Lin54 (lin-54 homolog (C. elegans))  MGI  Alliance
Chinchilla lanigera (long-tailed chinchilla) : Lin54 (lin-54 DREAM MuvB core complex component)
Pan paniscus (bonobo/pygmy chimpanzee) : LIN54 (lin-54 DREAM MuvB core complex component)
Canis lupus familiaris (dog) : LIN54 (lin-54 DREAM MuvB core complex component)
Ictidomys tridecemlineatus (thirteen-lined ground squirrel) : Lin54 (lin-54 DREAM MuvB core complex component)
Sus scrofa (pig) : LIN54 (lin-54 DREAM MuvB core complex component)
Chlorocebus sabaeus (African green monkey) : LIN54 (lin-54 DREAM MuvB core complex component)
Heterocephalus glaber (naked mole-rat) : Lin54 (lin-54 DREAM MuvB core complex component)
more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rnor_6.01410,770,072 - 10,828,115 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1410,786,399 - 10,828,106 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01410,717,462 - 10,775,710 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41410,398,080 - 10,439,960 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11410,383,795 - 10,439,950 (+)NCBI
Celera149,254,128 - 9,295,581 (+)NCBICelera
Cytogenetic Map14p22NCBI
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

Biological Process

Cellular Component
nucleus  (IBA)

References

Additional References at PubMed
PMID:12477932  


Genomics

Comparative Map Data
Lin54
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rnor_6.01410,770,072 - 10,828,115 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1410,786,399 - 10,828,106 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01410,717,462 - 10,775,710 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41410,398,080 - 10,439,960 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11410,383,795 - 10,439,950 (+)NCBI
Celera149,254,128 - 9,295,581 (+)NCBICelera
Cytogenetic Map14p22NCBI
LIN54
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl482,909,973 - 83,012,926 (-)EnsemblGRCh38hg38GRCh38
GRCh38482,924,603 - 83,012,951 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh37483,845,756 - 83,934,097 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36484,065,151 - 84,151,006 (-)NCBINCBI36hg18NCBI36
Celera481,136,312 - 81,224,592 (-)NCBI
Cytogenetic Map4q21.22NCBI
HuRef479,586,333 - 79,674,722 (-)NCBIHuRef
CHM1_1483,822,194 - 83,910,603 (-)NCBICHM1_1
Lin54
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm395100,589,892 - 100,648,506 (-)NCBI
GRCm385100,442,033 - 100,500,639 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl5100,441,918 - 100,500,639 (-)EnsemblGRCm38mm10GRCm38
MGSCv375100,871,052 - 100,929,658 (-)NCBIGRCm37mm9NCBIm37
MGSCv365100,682,502 - 100,740,941 (-)NCBImm8
Celera597,767,830 - 97,826,649 (-)NCBICelera
Cytogenetic Map5E4NCBI
Lin54
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554746,613,661 - 6,660,899 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554746,600,766 - 6,660,904 (+)NCBIChiLan1.0ChiLan1.0
LIN54
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1447,045,043 - 47,131,091 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl447,046,277 - 47,131,091 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0441,192,653 - 41,278,730 (+)NCBIMhudiblu_PPA_v0panPan3
LIN54
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 Ensembl326,878,187 - 6,941,268 (-)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.1326,876,111 - 6,940,754 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Lin54
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_0049367381,568,786 - 1,643,500 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
LIN54
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl8135,330,917 - 135,398,269 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.18135,330,868 - 135,398,274 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.28144,625,750 - 144,693,415 (+)NCBISscrofa10.2Sscrofa10.2susScr3
LIN54
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1 Ensembl731,326,174 - 31,404,045 (-)Ensembl
ChlSab1.1731,323,792 - 31,406,194 (-)NCBI
Lin54
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462490012,511 - 66,582 (-)NCBI

Position Markers
D16S2625  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01410,820,681 - 10,821,108NCBIRnor6.0
Rnor_5.01410,768,276 - 10,768,703UniSTSRnor5.0
RGSC_v3.41410,432,526 - 10,432,953UniSTSRGSC3.4
Celera149,288,147 - 9,288,574UniSTS
Cytogenetic Map14p22UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2300159Bmd61Bone mineral density QTL 615.30.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)14127597761Rat
2300183Bmd60Bone mineral density QTL 605.70.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)14127597761Rat
619619Rf4Renal disease susceptibility QTL 44.10.002total urine protein amount (VT:0000032)urine protein excretion rate to body weight ratio (CMO:0001099)14134403399Rat
9589814Gluco67Glucose level QTL 674.540.001blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)14141333960Rat
7411573Bw139Body weight QTL 1394.70.001body mass (VT:0001259)body weight gain (CMO:0000420)14141333960Rat
634352Apr6Acute phase response QTL 63.7blood interleukin-6 amount (VT:0008595)plasma interleukin-6 level (CMO:0001927)14142766285Rat
71115Niddm15Non-insulin dependent diabetes mellitus QTL 154.8blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)14222782512680613Rat
70204Niddm20Non-insulin dependent diabetes mellitus QTL 205.10.000008blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)14222782519230541Rat
2293089Iddm31Insulin dependent diabetes mellitus QTL 314.7blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)14483323319909932Rat
2293089Iddm31Insulin dependent diabetes mellitus QTL 314.7blood glucose amount (VT:0000188)age at onset/diagnosis of type 1 diabetes mellitus (CMO:0001140)14483323319909932Rat
1300114Srn2Serum renin concentration QTL 23.27blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)14483323323004027Rat
70195Mcs8Mammary carcinoma susceptibility QTL 84.28mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)14483323326466248Rat
1331740Bw26Body weight QTL 263.028body mass (VT:0001259)body weight (CMO:0000012)14483323333040042Rat
1581500Renag1Renal agenesis QTL 1kidney development trait (VT:0000527)percentage of study population developing unilateral renal agenesis during a period of time (CMO:0000940)14975643572854397Rat
1358296Ael3Aortic elastin QTL 33.70.00051aorta elastin amount (VT:0003905)aortic elastin141053997755539977Rat
2302045Pia39Pristane induced arthritis QTL 394.90.001blood immunoglobulin amount (VT:0002460)serum immunoglobulin G2a level (CMO:0002116)141053997755539977Rat
731183Pia20Pristane induced arthritis QTL 203.55joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)141072926861873323Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:670
Count of miRNA genes:298
Interacting mature miRNAs:381
Transcripts:ENSRNOT00000003006
Prediction methods:Microtar, Miranda, Rnahybrid, Targetscan
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.


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 exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 2 26 27 18 16 18 70 21 35 8
Low 1 17 30 23 3 23 8 11 4 14 6 3 8
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000003006   ⟹   ENSRNOP00000003006
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1410,786,399 - 10,828,106 (+)Ensembl
RefSeq Acc Id: NM_001100564   ⟹   NP_001094034
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01410,786,399 - 10,828,115 (+)NCBI
Rnor_5.01410,717,462 - 10,775,710 (+)NCBI
RGSC_v3.41410,398,080 - 10,439,960 (+)RGD
Celera149,254,128 - 9,295,581 (+)RGD
Sequence:
RefSeq Acc Id: XM_006250657   ⟹   XP_006250719
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01410,770,801 - 10,828,115 (+)NCBI
Rnor_5.01410,717,462 - 10,775,710 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006250658   ⟹   XP_006250720
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01410,770,072 - 10,828,115 (+)NCBI
Rnor_5.01410,717,462 - 10,775,710 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006250659   ⟹   XP_006250721
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01410,772,068 - 10,828,115 (+)NCBI
Rnor_5.01410,717,462 - 10,775,710 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006250661   ⟹   XP_006250723
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01410,770,072 - 10,828,115 (+)NCBI
Rnor_5.01410,717,462 - 10,775,710 (+)NCBI
Sequence:
RefSeq Acc Id: XM_008770022   ⟹   XP_008768244
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01410,770,801 - 10,828,115 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017599168   ⟹   XP_017454657
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01410,772,068 - 10,828,115 (+)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_001094034   ⟸   NM_001100564
- UniProtKB: Q641Z1 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006250720   ⟸   XM_006250658
- Peptide Label: isoform X2
- UniProtKB: Q641Z1 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006250723   ⟸   XM_006250661
- Peptide Label: isoform X4
- Sequence:
RefSeq Acc Id: XP_006250719   ⟸   XM_006250657
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_006250721   ⟸   XM_006250659
- Peptide Label: isoform X2
- UniProtKB: Q641Z1 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_008768244   ⟸   XM_008770022
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: XP_017454657   ⟸   XM_017599168
- Peptide Label: isoform X4
- Sequence:
RefSeq Acc Id: ENSRNOP00000003006   ⟸   ENSRNOT00000003006
Protein Domains
CRC

Transcriptome

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


Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN/SsN (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Buf/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
F344/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
FHH/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
GH/OmrMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/Ox (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LE/Stm (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
M520/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MHS/Gib (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
SBH/Ygl (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHRSP/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1311361 AgrOrtholog
Ensembl Genes ENSRNOG00000002203 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSRNOP00000003006 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000003006 ENTREZGENE, UniProtKB/Swiss-Prot
IMAGE_CLONE IMAGE:7131638 IMAGE-MGC_LOAD
  IMAGE:7441982 IMAGE-MGC_LOAD
InterPro CRC UniProtKB/Swiss-Prot
  Lin-54_fam UniProtKB/Swiss-Prot
  Tesmin/TSO1-like_CXC UniProtKB/Swiss-Prot
KEGG Report rno:305171 UniProtKB/Swiss-Prot
MGC_CLONE MGC:116098 IMAGE-MGC_LOAD
  MGC:95188 IMAGE-MGC_LOAD
NCBI Gene 305171 ENTREZGENE
PANTHER PTHR12446 UniProtKB/Swiss-Prot
Pfam TCR UniProtKB/Swiss-Prot
PhenoGen Lin54 PhenoGen
PROSITE CRC UniProtKB/Swiss-Prot
SMART CXC UniProtKB/Swiss-Prot
UniGene Rn.24111 ENTREZGENE
UniProt LIN54_RAT UniProtKB/Swiss-Prot, ENTREZGENE
UniProt Secondary Q4FZV6 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2014-07-23 Lin54  lin-54 DREAM MuvB core complex component  Lin54  lin-54 homolog (C. elegans)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-09-12 Lin54  lin-54 homolog (C. elegans)  RGD1311361  similar to hypothetical protein  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-12-06 RGD1311361  similar to hypothetical protein  RGD1311361_predicted  similar to hypothetical protein (predicted)  Symbol and Name updated 1559027 APPROVED
2005-01-20 RGD1311361_predicted  similar to hypothetical protein (predicted)  LOC305171_predicted    Symbol and Name status set to approved 1331353 APPROVED
2005-01-12 LOC305171_predicted  similar to hypothetical protein (predicted)      Symbol and Name status set to provisional 70820 PROVISIONAL