Saa4 (serum amyloid A4) - Rat Genome Database

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Gene: Saa4 (serum amyloid A4) Rattus norvegicus
Analyze
Symbol: Saa4
Name: serum amyloid A4
RGD ID: 1307371
Description: Orthologous to human SAA4 (serum amyloid A4, constitutive); PARTICIPATES IN lipid metabolic pathway; INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; acetamide; bisphenol A.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: LOC365245; MGC108857; serum amyloid A 4; serum amyloid A-4 protein; serum amyloid A4, constitutive
RGD Orthologs
Human
Mouse
Bonobo
Pig
Green Monkey
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81106,383,856 - 106,388,158 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1106,383,856 - 106,387,354 (-)EnsemblGRCr8
mRatBN7.2197,247,580 - 97,251,882 (-)NCBImRatBN7.2mRatBN7.2
UTH_Rnor_SHR_Utx1102,639,968 - 102,644,286 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01111,111,955 - 111,116,273 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01104,395,938 - 104,400,240 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.01102,776,079 - 102,780,381 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1102,776,082 - 102,849,430 (-)Ensemblrn6Rnor6.0
Rnor_5.01103,850,707 - 103,855,009 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4197,278,427 - 97,282,729 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera191,494,430 - 91,498,726 (-)NCBICelera
RGSC_v3.1197,356,540 - 97,360,840 (-)NCBI
Cytogenetic Map1q22NCBI
JBrowse:




Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
# Reference Title Reference Citation
1. Characterization of constitutive human serum amyloid A protein (SAA4) as an apolipoprotein. de Beer MC, etal., J Lipid Res. 1995 Mar;36(3):526-34.
2. 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.
3. Rat ISS GO annotations from GOA human gene data--August 2006 GOA data from the GO Consortium
4. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
5. GOA pipeline RGD automated data pipeline
6. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:12477932   PMID:23533145   PMID:25044109  


Genomics

Comparative Map Data
Saa4
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81106,383,856 - 106,388,158 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1106,383,856 - 106,387,354 (-)EnsemblGRCr8
mRatBN7.2197,247,580 - 97,251,882 (-)NCBImRatBN7.2mRatBN7.2
UTH_Rnor_SHR_Utx1102,639,968 - 102,644,286 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01111,111,955 - 111,116,273 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01104,395,938 - 104,400,240 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.01102,776,079 - 102,780,381 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1102,776,082 - 102,849,430 (-)Ensemblrn6Rnor6.0
Rnor_5.01103,850,707 - 103,855,009 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4197,278,427 - 97,282,729 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera191,494,430 - 91,498,726 (-)NCBICelera
RGSC_v3.1197,356,540 - 97,360,840 (-)NCBI
Cytogenetic Map1q22NCBI
SAA4
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381118,231,355 - 18,236,802 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1118,231,344 - 18,236,860 (-)Ensemblhg38GRCh38
GRCh371118,252,902 - 18,258,349 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361118,209,479 - 18,214,910 (-)NCBIBuild 36Build 36hg18NCBI36
Build 341118,209,478 - 18,214,910NCBI
Celera1118,385,194 - 18,390,662 (-)NCBICelera
Cytogenetic Map11p15.1NCBI
HuRef1117,935,586 - 17,941,082 (-)NCBIHuRef
CHM1_11118,252,385 - 18,257,866 (-)NCBICHM1_1
T2T-CHM13v2.01118,326,841 - 18,332,301 (-)NCBIT2T-CHM13v2.0
Saa4
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39746,377,416 - 46,382,027 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl746,377,422 - 46,382,027 (-)EnsemblGRCm39 EnsemblGRCm39
GRCm38746,727,992 - 46,732,603 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl746,727,998 - 46,732,603 (-)Ensemblmm10GRCm38
MGSCv37753,983,368 - 53,987,913 (-)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv36746,596,040 - 46,600,586 (-)NCBIMGSCv36mm8
Celera742,202,223 - 42,206,770 (-)NCBICelera
Cytogenetic Map7B3NCBI
cM Map730.53NCBI
SAA4
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2920,545,480 - 20,550,948 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11120,505,866 - 20,511,624 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01118,266,445 - 18,271,931 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11117,951,775 - 17,957,317 (-)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1117,951,775 - 17,957,317 (-)EnsemblpanPan2panpan1.1
SAA4
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1240,986,869 - 41,003,059 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2244,044,617 - 44,059,267 (+)NCBISscrofa10.2Sscrofa10.2susScr3
SAA4
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1146,703,086 - 46,709,083 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl146,702,959 - 46,712,572 (+)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_023666038144,086,097 - 144,092,216 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0

Variants

.
Variants in Saa4
34 total Variants

QTLs in Region (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1582234Gluco18Glucose level QTL 183.40.0003blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)187889942132889942Rat
1358359Sradr1Stress Responsive Adrenal Weight QTL 14.74adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)139728272132889942Rat
634314Niddm44Non-insulin dependent diabetes mellitus QTL 44blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)151941022208479811Rat
1331793Bp200Blood pressure QTL 2003.71601arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1102780511182384005Rat
1578654Bss10Bone structure and strength QTL 104femur morphology trait (VT:0000559)femoral neck cortical cross-sectional area (CMO:0001702)151940904168768703Rat
2300324Fetw1Fetal weight QTL 112.10.005fetal growth trait (VT:0004201)fetal body weight (CMO:0002080)192963855109494029Rat
1554320Bmd1Bone mineral density QTL 112.20.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)1101228864146228864Rat
1331800Scl25Serum cholesterol level QTL 253.013blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)187785026142582336Rat
7421628Bp361Blood pressure QTL 3610.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)183019780128019780Rat
631495Bp96Blood pressure QTL 964.52arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)166404680111404680Rat
70225Bp58Blood pressure QTL 583.3arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)134184556172281316Rat
2298545Neuinf8Neuroinflammation QTL 84.6nervous system integrity trait (VT:0010566)spinal cord beta-2 microglobulin mRNA level (CMO:0002125)166009857160501508Rat
10059597Bp377Blood pressure QTL 3773.420.025arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)134565911208798288Rat
631519Pia11Pristane induced arthritis QTL 115.3joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)193903998191260518Rat
1302788Scl19Serum cholesterol QTL 194.60.001blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)166400974132889942Rat
1549903Bp267Blood pressure QTL 267arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)184107164115183752Rat
2313083Bmd74Bone mineral density QTL 7440.0001tibia mineral mass (VT:1000283)total volumetric bone mineral density (CMO:0001728)191302413136302413Rat
2313402Anxrr24Anxiety related response QTL 24aggression-related behavior trait (VT:0015014)tameness/aggressiveness composite score (CMO:0002136)151511344153680016Rat
724567Tcas6Tongue tumor susceptibility QTL 66.85tongue integrity trait (VT:0010553)number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)1102359314153680016Rat
724521Uae1Urinary albumin excretion QTL 13.80.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)199645382182701046Rat
1358902Bw47Body weight QTL 471.67body mass (VT:0001259)body weight (CMO:0000012)199645382221502378Rat
1358192Ept13Estrogen-induced pituitary tumorigenesis QTL 133.4pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)186622262131622262Rat
2300164Bmd44Bone mineral density QTL 445.40.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)166077886111077886Rat
731168Bp154Blood pressure QTL 1543.4arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1103779152223964440Rat
631205Bp196Blood pressure QTL 19640.0001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)198879955208479939Rat
738022Anxrr13Anxiety related response QTL 134.60.00039locomotor behavior trait (VT:0001392)measurement of voluntary locomotion into, out of, or within a discrete space in an open field apparatus (CMO:0001514)192683681137683681Rat
152025249Scl82Serum cholesterol level QTL 824.77blood cholesterol amount (VT:0000180)152891222109116986Rat
10054135Gmadr2Adrenal mass QTL 21.970.0129adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)186993904131993904Rat
7411712Strs4Sensitivity to stroke QTL 48.7cerebrum integrity trait (VT:0010549)percentage of study population developing cerebrovascular lesions during a period of time (CMO:0000932)187558587132558587Rat
1331749Hrtrt11Heart rate QTL 112.973heart pumping trait (VT:2000009)heart rate (CMO:0000002)192683681137683681Rat
737977Bp160Blood pressure QTL 1600.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)197582336142582336Rat
2293142Bp314Blood pressure QTL 314arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1101594089146594089Rat
61433Cia2Collagen induced arthritis QTL 25joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1100345976145345976Rat
724529Cm16Cardiac mass QTL 162.7heart mass (VT:0007028)calculated heart weight (CMO:0000073)196717367160111531Rat

Markers in Region
RH141227  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2197,247,672 - 97,247,889 (+)MAPPERmRatBN7.2
Rnor_6.01102,776,172 - 102,776,388NCBIRnor6.0
Rnor_5.01103,850,800 - 103,851,016UniSTSRnor5.0
RGSC_v3.4197,278,520 - 97,278,736UniSTSRGSC3.4
Celera191,494,523 - 91,494,739UniSTS
RH 3.4 Map1922.3UniSTS
Cytogenetic Map1q22UniSTS


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
musculoskeletal system
nervous system
renal system
reproductive system
respiratory system
sensory system
visual system
9 11 51 123 91 90 59 29 59 6 234 105 2 101 53 67 31 3 3

Sequence


Ensembl Acc Id: ENSRNOT00000078692   ⟹   ENSRNOP00000071382
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1106,383,856 - 106,387,354 (-)Ensembl
mRatBN7.2 Ensembl197,247,598 - 97,321,019 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000082289   ⟹   ENSRNOP00000069924
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1106,417,902 - 106,452,859 (-)Ensembl
mRatBN7.2 Ensembl197,247,598 - 97,321,019 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000086856   ⟹   ENSRNOP00000075429
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1106,417,902 - 106,452,859 (-)Ensembl
mRatBN7.2 Ensembl197,281,632 - 97,321,019 (-)Ensembl
RefSeq Acc Id: NM_001009478   ⟹   NP_001009478
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81106,383,856 - 106,388,158 (-)NCBI
mRatBN7.2197,247,580 - 97,251,882 (-)NCBI
Rnor_6.01102,776,079 - 102,780,381 (-)NCBI
Rnor_5.01103,850,707 - 103,855,009 (-)NCBI
RGSC_v3.4197,278,427 - 97,282,729 (-)RGD
Celera191,494,430 - 91,498,726 (-)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_001009478 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAH88188 (Get FASTA)   NCBI Sequence Viewer  
  EDM07257 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000069924.3
  ENSRNOP00000071382
  ENSRNOP00000071382.2
RefSeq Acc Id: NP_001009478   ⟸   NM_001009478
- Peptide Label: precursor
- UniProtKB: Q5M878 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000071382   ⟸   ENSRNOT00000078692
Ensembl Acc Id: ENSRNOP00000069924   ⟸   ENSRNOT00000082289
Ensembl Acc Id: ENSRNOP00000075429   ⟸   ENSRNOT00000086856
Protein Domains
HPS5 TPR

Transcriptome

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

Promoters
RGD ID:13690064
Promoter ID:EPDNEW_R589
Type:initiation region
Name:Hps5_2
Description:HPS5, biogenesis of lysosomal organelles complex 2 subunit 2
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_R590  
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01102,780,401 - 102,780,461EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1307371 AgrOrtholog
BioCyc Gene G2FUF-59615 BioCyc
Ensembl Genes ENSRNOG00000055531 Ensembl, UniProtKB/TrEMBL
  ENSRNOG00000090606 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000078692 ENTREZGENE
  ENSRNOT00000078692.3 UniProtKB/TrEMBL
  ENSRNOT00000082289.3 UniProtKB/TrEMBL
Gene3D-CATH Serum amyloid A protein UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7371403 IMAGE-MGC_LOAD
InterPro HPS5 UniProtKB/TrEMBL
  Serum_amyloid_A UniProtKB/TrEMBL
  Synovial_Prolif_Regulator UniProtKB/TrEMBL
  TPR_HPS5 UniProtKB/TrEMBL
KEGG Report rno:365245 UniProtKB/TrEMBL
MGC_CLONE MGC:108857 IMAGE-MGC_LOAD
NCBI Gene 365245 ENTREZGENE
PANTHER HERMANSKY-PUDLAK SYNDROME 5 PROTEIN UniProtKB/TrEMBL
  RUBY-EYE2-LIKE PROTEIN UniProtKB/TrEMBL
  SERUM AMYLOID A UniProtKB/TrEMBL
  SERUM AMYLOID A PROTEIN UniProtKB/TrEMBL
Pfam SAA UniProtKB/TrEMBL
  TPR_HPS5 UniProtKB/TrEMBL
PhenoGen Saa4 PhenoGen
PIRSF BLOC-2_complex_Hps5 UniProtKB/TrEMBL
  Serum_amyloid_A UniProtKB/TrEMBL
PRINTS SERUMAMYLOID UniProtKB/TrEMBL
RatGTEx ENSRNOG00000055531 RatGTEx
  ENSRNOG00000090606 RatGTEx
SMART SAA UniProtKB/TrEMBL
UniProt A0A0G2JWL2_RAT UniProtKB/TrEMBL
  A6JBC7_RAT UniProtKB/TrEMBL
  Q5M878 ENTREZGENE, UniProtKB/TrEMBL
  Q7TMC3_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-07-18 Saa4  serum amyloid A4  Saa4  serum amyloid A4, constitutive  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-09-18 Saa4  serum amyloid A4, constitutive  Saa4  serum amyloid A 4  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-12-06 Saa4  serum amyloid A 4  Saa4_predicted  serum amyloid A 4 (predicted)  Symbol and Name updated 1559027 APPROVED
2005-01-12 Saa4_predicted  serum amyloid A 4 (predicted)      Symbol and Name status set to approved 70820 APPROVED