Rassf4 Gene Detail

Summary

• Symbol
  Rassf4
• Name
  Ras association (RalGDS/AF-6) domain family member 4
• Synonyms
  3830411C14Rik

• Feature Type
  protein coding gene
• IDs
  MGI:2386853
  NCBI Gene: 213391
• Alliance
  gene page
• Transcription Start Sites
  34 TSS
• Candidate for QTL
  2 QTL

Location &
Maps

• Sequence Map
  Chr6:116609969-116650797 bp, - strand

  From NCBI annotation of GRCm39
  

• View this region in JBrowse
  

• Genome Browsers
  Ensembl | UCSC | NCBI

• Genetic Map
  Chromosome 6, 53.83 cM
• Mapping Data
  3 experiments

Strain
Comparison

• SNPs within 2kb
  1543 from dbSNP Build 142
• Strain Annotations
  18

Strain	Gene Model ID	Feature Type	Coordinates
C57BL/6J	MGI_C57BL6J_2386853	protein coding gene	Chr6:116609969-116650913 (-)
129S1/SvImJ	MGP_129S1SvImJ_G0031174	protein coding gene	Chr6:119319427-119368302 (-)
A/J	MGP_AJ_G0031144	protein coding gene	Chr6:114749067-114793366 (-)
AKR/J	MGP_AKRJ_G0031074	protein coding gene	Chr6:117830625-117877801 (-)
BALB/cJ	MGP_BALBcJ_G0031154	protein coding gene	Chr6:114545624-114590721 (-)
C3H/HeJ	MGP_C3HHeJ_G0030554	protein coding gene	Chr6:66420058-66461384 (+)
C57BL/6NJ	MGP_C57BL6NJ_G0031612	protein coding gene	Chr6:122393169-122433600 (-)
CAROLI/EiJ	MGP_CAROLIEiJ_G0028777	protein coding gene	Chr6:111753926-111794589 (-)
CAST/EiJ	MGP_CASTEiJ_G0030261	protein coding gene	Chr6:118215426-118257795 (-)
CBA/J	MGP_CBAJ_G0030838	protein coding gene	Chr6:127204871-127248324 (-)
DBA/2J	MGP_DBA2J_G0030994	protein coding gene	Chr6:113665116-113707648 (-)
FVB/NJ	MGP_FVBNJ_G0030946	protein coding gene	Chr6:112841076-112881650 (-)
LP/J	MGP_LPJ_G0031072	protein coding gene	Chr6:119349701-119393841 (-)
NOD/ShiLtJ	MGP_NODShiLtJ_G0030980	protein coding gene	Chr6:131352855-131399213 (-)
NZO/HlLtJ	MGP_NZOHlLtJ_G0031641	protein coding gene	Chr6:117864582-117911151 (-)
PWK/PhJ	MGP_PWKPhJ_G0029977	protein coding gene	Chr6:112681017-112722889 (-)
SPRET/EiJ	MGP_SPRETEiJ_G0029805	protein coding gene	Chr6:116605904-116648893 (-)
WSB/EiJ	MGP_WSBEiJ_G0030344	protein coding gene	Chr6:118139357-118181939 (-)

Homology

• Human Ortholog
  RASSF4, Ras association domain family member 4

• Vertebrate Orthologs
  3

Vertebrate Orthology Source

Alliance of Genome Resources

• Human Ortholog
  RASSF4, Ras association domain family member 4
  
• Synonyms
  AD037
• Links
  HGNC:20793

  NCBI Gene ID: 83937

  neXtProt AC: NX_Q9H2L5

  UniProt: Q9H2L5

  
  
• Chr Location
  10q11.21; chr10:44959407-44995891 (+)  GRCh38

---

• MGI Vertebrate Homology
  Rassf4 stringent orthology
  1 human;1 mouse;1 rat;1 zebrafish
  
• HCOP
  vertebrate homology predictions: RASSF4
• Gene Tree
  Rassf4
  

Mutations,
Alleles, and
Phenotypes

• Phenotype Summary
  4 phenotype references
  

• All Mutations and Alleles
  6
• Endonuclease-mediated
  3
• Targeted
  3
• Incidental Mutations
  Mutagenetix , APF
• Find Mice (IMSR)
  26 strains or lines available

Gene Ontology
(GO)
Classifications

• All GO Annotations
  2
• GO References
  2

Expression

• Assay Results
  842
• Tissues
  17
• cDNA Data
  86
• Literature Summary
  2

Images

Tissue x Stage Matrix

• Other Mouse Links
  Allen Institute
  GEO
  Expression Atlas
• Other Vertebrate Links
  Xenbase rassf4

Sequences &
Gene Models

• All Sequences
  58
• RefSeq
  4
• UniProt
  3
• CCDS
  CCDS20460.1

• Ensembl
  ENSMUSG00000042129 (Evidence)
• NCBI Gene
  213391

Representative Sequences			Length	Strain/Species
genomic	213391	NCBI Gene Model | MGI Sequence Detail	40829	C57BL/6J
transcript	NM_178045	RefSeq | MGI Sequence Detail	6370	C57BL/6
polypeptide	Q8CB96	UniProt | EBI | MGI Sequence Detail	322	Not Applicable

Protein
Information

• UniProt
  3 Sequences
• Protein Ontology
  PR:000013765 Ras association domain-containing protein 4
  (term hierarchy)
• InterPro Domains
  IPR000159 Ras-associating domain
  IPR033614 Ras association domain-containing protein 1-6
  IPR033622 Ras association domain-containing protein 4, RA domain
  IPR011524 SARAH domain
  IPR029071 Ubiquitin-like domain superfamily

Molecular
Reagents

• All nucleic 89

  cDNA 88

  Other 1

  
  

  Microarray probesets 5

Other
Accession IDs

MGI:1917929, MGI:2141449

References

• Summaries
  All 32

  Developmental Gene Expression 2

  Gene Ontology 2

  Phenotypes 4
• Earliest
  J:65060 Kawai J, et al., Functional annotation of a full-length mouse cDNA collection. Nature. 2001 Feb 8;409(6821):685-90
• Latest
  J:326541 Cyagen Biosciences Inc., Cyagen Biosciences Website. 2022;

TSS for Rassf4:

(View these features in JBrowse)

Transcription Start Site	Location	Distance from Gene 5'-end
Tssr62609	Chr6:116650751-116650814 (-)	14 bp
Tssr62608	Chr6:116650732-116650750 (-)	56 bp
Tssr62607	Chr6:116649400-116649428 (-)	1,383 bp
Tssr62606	Chr6:116648368-116648391 (-)	2,417 bp
Tssr62605	Chr6:116645362-116645376 (-)	5,428 bp
Tssr62604	Chr6:116645328-116645352 (-)	5,457 bp
Tssr62603	Chr6:116642912-116642924 (-)	7,879 bp
Tssr62602	Chr6:116636471-116636489 (-)	14,317 bp
Tssr62601	Chr6:116634514-116634528 (-)	16,276 bp
Tssr62600	Chr6:116634449-116634475 (-)	16,335 bp
Tssr62599	Chr6:116634374-116634414 (-)	16,403 bp
Tssr62598	Chr6:116634321-116634370 (-)	16,451 bp
Tssr62597	Chr6:116634159-116634184 (-)	16,625 bp
Tssr62596	Chr6:116634106-116634148 (-)	16,670 bp
Tssr62595	Chr6:116633898-116633948 (-)	16,874 bp
Tssr62594	Chr6:116633697-116633729 (-)	17,084 bp
Tssr62593	Chr6:116633456-116633468 (-)	17,335 bp
Tssr62592	Chr6:116633289-116633302 (-)	17,501 bp
Tssr62591	Chr6:116632434-116632457 (-)	18,351 bp
Tssr62585	Chr6:116622185-116622208 (-)	28,600 bp
Tssr62584	Chr6:116622116-116622142 (-)	28,668 bp
Tssr62583	Chr6:116618692-116618708 (-)	32,097 bp
Tssr62582	Chr6:116618414-116618443 (-)	32,368 bp
Tssr62581	Chr6:116617278-116617304 (-)	33,506 bp
Tssr62580	Chr6:116614833-116614855 (-)	35,953 bp
Tssr62579	Chr6:116614780-116614811 (-)	36,001 bp
Tssr62578	Chr6:116614283-116614299 (-)	36,506 bp
Tssr62577	Chr6:116613907-116613929 (-)	36,879 bp
Tssr62576	Chr6:116611903-116611921 (-)	38,885 bp
Tssr62575	Chr6:116610775-116610789 (-)	40,015 bp
Tssr62574	Chr6:116610528-116610556 (-)	40,255 bp
Tssr62573	Chr6:116610370-116610376 (-)	40,424 bp
Tssr62572	Chr6:116610305-116610316 (-)	40,486 bp
Tssr62571	Chr6:116610266-116610277 (-)	40,525 bp

Rassf4 is Candidate Gene for:

QTL	Genetic Location*	Genome Location (GRCm39)	Reference	QTL Note
Hdlq24	Chr6, 74.64 cM		J:133501	SNP analysis, mRNA microarray analysis and protein expression difference analysis were used to narrow the QTL intervals of 9 previously identified QTLs for HDL cholesterol (Hdlq1, Hdlq20, Hdlq24), gallstone susceptibility (Lith17, Lith19, Lith21) and obesity (Obwq3, Obwq4, Obwq5). This methodology identified a manageable list of potential candidate genes for each QTL. A panel of 130,000 SNPs for SM/J and NZB/BlNJ reduced the QTL intervals by 40%-72%. Liver mRNA analysis identified 10 genes differentially expressed between SM/J and NZB/BlNJ strains and this finding was confirmed using TaqMan RT-PCR assays. Mass spectrometry analysis of liver proteins identified 45 proteins displaying differential expression between SM/J andNZB/BlNJ. On mouse Chromosome 1, Apoa2 (92.6 cM), Fh1, and Hsd11b1 were identified as potential candidate genes for Hdlq20 at 96 cM. Apoa2 was identified based on protein expression and SNP coding sequence differences. Apoa2 displays up-regulation in NZB/BlNJ liver proteins comparedto SM/J. Fh1 displays gene coding sequence differences and decreased protein expression in NZB/BlNJ livers compared to SM/J. Hsd11b1 was identified based on decreased protein expression in NZB/BlNJ. On mouse Chromosome 5, Acads (65 cM) and Scarb1 (68 cM)were identified as potential candidate genes for Hdlq1 (70 cM) and Lith17 (60 cM). Acads was identified on the basis of decreased protein expression in NZB/BlNJ livers compared to SM/J, as well as coding sequence differences. Scarb1 displays coding regionsequence differences and decreased liver mRNA expression in NZB/BlNJ. Scarb1 is located more closely to Hdlq1 and decreased Scarb1 mRNA expression was observed for this QTL. On mouse Chromosome 6, Pparg (52.7 cM), Rassf4 and Adipor2 (60.7 cM) were identified as potential candidate genes for Hdlq24 (66 cM) and Obwq3 (42 cM). Pparg displays coding sequences differences between NZB/BlNJ and SM/J while Rassf4 displays decreased liver mRNA expression in NZB/BlNJ animals. Adipor2 displays increased liver mRNAexpression in NZB/BlNJ and gene coding sequence differences. Ndufa9 was identified as a QTL for Hdlq24 on the basis of decreased liver protein expression in NZB/BlNJ and coding sequence differences. On mouse Chromosome 8,Slc10a2 (2 cM) was identifiedasa potential candidate gene for Lith19 (0 cM) on the basis of increased liver mRNA expression in NZB/BlNJ animals compared to SM/J. On mouse Chromosome 10, Ctgf (17 cM) was identified as a potential candidate gene for Lith21 (24 cM)on the basis of decreased liver mRNA expression in NZB/BlNJ animals compared to SM/J and gene coding sequences differences. On mouse Chromosome 17, Pgc (30 cM) was identified as a potential candidate for Obwq4 (32 cM).Pgc displays coding sequence differences between NZB/BlNJand SM/J. Atrnl1 was identified as a candidate for Obwq5 (52 cM) on chromosome 19. Atrnl1 displays increased liver mRNA expression in NZB/BlNJ animals compared to SM/J.
Obwq3	Chr6, 49.71 cM		J:133501	SNP analysis, mRNA microarray analysis and protein expression difference analysis were used to narrow the QTL intervals of 9 previously identified QTLs for HDL cholesterol (Hdlq1, Hdlq20, Hdlq24), gallstone susceptibility (Lith17, Lith19, Lith21) and obesity (Obwq3, Obwq4, Obwq5). This methodology identified a manageable list of potential candidate genes for each QTL. A panel of 130,000 SNPs for SM/J and NZB/BlNJ reduced the QTL intervals by 40%-72%. Liver mRNA analysis identified 10 genes differentially expressed between SM/J and NZB/BlNJ strains and this finding was confirmed using TaqMan RT-PCR assays. Mass spectrometry analysis of liver proteins identified 45 proteins displaying differential expression between SM/J andNZB/BlNJ. On mouse Chromosome 1, Apoa2 (92.6 cM), Fh1, and Hsd11b1 were identified as potential candidate genes for Hdlq20 at 96 cM. Apoa2 was identified based on protein expression and SNP coding sequence differences. Apoa2 displays up-regulation in NZB/BlNJ liver proteins comparedto SM/J. Fh1 displays gene coding sequence differences and decreased protein expression in NZB/BlNJ livers compared to SM/J. Hsd11b1 was identified based on decreased protein expression in NZB/BlNJ. On mouse Chromosome 5, Acads (65 cM) and Scarb1 (68 cM)were identified as potential candidate genes for Hdlq1 (70 cM) and Lith17 (60 cM). Acads was identified on the basis of decreased protein expression in NZB/BlNJ livers compared to SM/J, as well as coding sequence differences. Scarb1 displays coding regionsequence differences and decreased liver mRNA expression in NZB/BlNJ. Scarb1 is located more closely to Hdlq1 and decreased Scarb1 mRNA expression was observed for this QTL. On mouse Chromosome 6, Pparg (52.7 cM), Rassf4 and Adipor2 (60.7 cM) were identified as potential candidate genes for Hdlq24 (66 cM) and Obwq3 (42 cM). Pparg displays coding sequences differences between NZB/BlNJ and SM/J while Rassf4 displays decreased liver mRNA expression in NZB/BlNJ animals. Adipor2 displays increased liver mRNAexpression in NZB/BlNJ and gene coding sequence differences. Ndufa9 was identified as a QTL for Hdlq24 on the basis of decreased liver protein expression in NZB/BlNJ and coding sequence differences. On mouse Chromosome 8,Slc10a2 (2 cM) was identifiedasa potential candidate gene for Lith19 (0 cM) on the basis of increased liver mRNA expression in NZB/BlNJ animals compared to SM/J. On mouse Chromosome 10, Ctgf (17 cM) was identified as a potential candidate gene for Lith21 (24 cM)on the basis of decreased liver mRNA expression in NZB/BlNJ animals compared to SM/J and gene coding sequences differences. On mouse Chromosome 17, Pgc (30 cM) was identified as a potential candidate for Obwq4 (32 cM).Pgc displays coding sequence differences between NZB/BlNJand SM/J. Atrnl1 was identified as a candidate for Obwq5 (52 cM) on chromosome 19. Atrnl1 displays increased liver mRNA expression in NZB/BlNJ animals compared to SM/J.

*cM position of peak correlated region/marker