Gdap10 Gene Detail

Summary

• Symbol
  Gdap10
• Name
  ganglioside-induced differentiation-associated-protein 10
• Synonyms
  Gdap10

• Feature Type
  lncRNA gene
• IDs
  MGI:1338008
  NCBI Gene: 100504486
• Alliance
  gene page
• Candidate for QTL
  1 QTL

Location &
Maps

• Sequence Map
  Chr12:32874115-32876918 bp, + strand

  From NCBI annotation of GRCm39
  

• View this region in JBrowse
  

• Genome Browsers
  Ensembl | UCSC | NCBI

• Genetic Map
  Chromosome 12, 13.75 cM
• Mapping Data
  2 experiments

Strain
Comparison

• SNPs within 2kb
  203 from dbSNP Build 142
• Strain Annotations
  1

Strain	Gene Model ID	Feature Type	Coordinates
C57BL/6J	MGI_C57BL6J_1338008	lncRNA gene	Chr12:32874115-32876918 (+)
129S1/SvImJ	no annotation
A/J	no annotation
AKR/J	no annotation
BALB/cJ	no annotation
C3H/HeJ	no annotation
C57BL/6NJ	no annotation
CAROLI/EiJ	no annotation
CAST/EiJ	no annotation
CBA/J	no annotation
DBA/2J	no annotation
FVB/NJ	no annotation
LP/J	no annotation
NOD/ShiLtJ	no annotation
NZO/HlLtJ	no annotation
PWK/PhJ	no annotation
SPRET/EiJ	no annotation
WSB/EiJ	no annotation

Gene Ontology
(GO)
Classifications

• All GO Annotations
  1
• GO References
  1

Expression

• Assay Results
  10
• Tissues
  5
• cDNA Data
  18
• Literature Summary
  1

Tissue x Stage Matrix

• Other Mouse Links
  GEO

Sequences &
Gene Models

• All Sequences
  7
• RefSeq
  1
• UniProt
  2

• NCBI Gene
  100504486

Representative Sequences			Length	Strain/Species
genomic	100504486	NCBI Gene Model | MGI Sequence Detail	2804	C57BL/6J
transcript	NR_045032	RefSeq | MGI Sequence Detail	2804	C57BL/6
polypeptide	O88744	UniProt | EBI | MGI Sequence Detail	128	Not Applicable

Protein
Information

• UniProt
  2 Sequences

Molecular
Reagents

• All nucleic 19

  cDNA 18

  Primer pair 1

  
  

  Microarray probesets 2

References

• Summaries
  All 14

  Developmental Gene Expression 1

  Gene Ontology 1
• Earliest
  J:54635 Liu H, et al., Isolation of 10 differentially expressed cDNAs in differentiated Neuro2a cells induced through controlled expression of the GD3 synthase gene. J Neurochem. 1999 May;72(5):1781-90
• Latest
  J:244215 Suzuki M, et al., Genetic dissection of the fatty liver QTL Fl1sa by using congenic mice and identification of candidate genes in the liver and epididymal fat. BMC Genet. 2016 Nov 17;17(1):145

Gdap10 is Candidate Gene for:

QTL	Genetic Location*	Genome Location (GRCm39)	Reference	QTL Note
Fl1sa	Chr12, 13.69 cM		J:244215	Nonalcoholic fatty liver disease (NAFLD) is a multifactorial disease caused by interactions between environmental and genetic factors. It was previously determined that SMXA-5 mice develop severe fatty liver on a high fat diet, although parental SM/J and A/J mice were resistant to fatty liver. Quantitative trait analysis using (SM/J x SMxA-5)F2 intercrossed mice identified a significant QTL, Fl1sa (fatty liver 1 in SMXA), for liver weight, liver triglyceride and total lipid content on centromere-53.06 Mb of mouse Chromosome 12. The A/J allele at Fl1sa was associated with the fatty liver. [J:124974] In a subsequent study using the livers from A/J-Chr 12 consomic and A/J mice that were fed a high fat diet three candidate genes were identified, Iah1, Rrm2 and Prkd1 using DNA microarray analysis. [J: 240255] The goal of the current study was to narrow the previously identified Fl1sa region by genetic dissection using novel congenic mice to identify candidate genes within the narrowed Fl1sa region. Two strains of congenic mice, A.SM-(centromere - D12Mit85)/J (R2) and A.SM-(D12Mit85-D12Mit112)/J (R3), were constructed from parental A/J and A/JChr 12 . Microsatellite markers and SNPs were used for the genotyping of R2 and R3 genomic DNA. Physical positions were taken from GRCm38.P4. The lipid accumulation in the respective livers was analyzed. As the liver triglyceride content in R2 and R3 congenic mice was significantly lower than in A/J mice. Male A/J, A/J-Chr12, R2 and R3 mice were fed standard chow until 6 weeks of age and thereafter fed a high fat diet from 6 to 13 weeks of age. At 13 weeks of age all mice were sacrificed after a 4 hour fast. The liver and white adipose tissue (subcutaneous fat, epididymal fat, mesenteric fat and retroperitoneal fat) were harvested and weighed. Blood sample were collected to measure serum lipids. Serum triglyceride, cholesterol and hepatic triglyceride content were measured. Whole transcripts from epididymal fats were measured using a Mouse Genome ST 2.0 array. Liver triglyceride content was significantly lower in A/J-Chr 12, R2 and R3 mice compared with that of A/J mice. Liver triglyceride and liver total lipid in R2 and R3 mice showed intermediate values between those of A/J and A/J-Chr 12 mice. The results suggested that the genes responsible for fatty liver existed in the SM/J region in strain R2 (centromere-29.20 Mb) and in the SM/J region in strain R3 (29.20-46.75 Mb) of Chromosome 12, Fig 1. Subsequently, in both of the narrowed Fl1sa regions microarray analysis of liver and epididymal fat from A/J and A/J-Chr 12 mice was performed in an attempt to identify candidate genes. Significant differences in gene expression levels in epididymal fat analysis were confirmed in 6 candidate genes: Ntsr2, Zfp125, Gdap10, Nrcam, Stxbp6 and Nova1 between the two strains.

*cM position of peak correlated region/marker