Saa4 (serum amyloid A4) - Rat Genome Database

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Gene: Saa4 (serum amyloid A4) Rattus norvegicus
Analyze
Symbol: Saa4 (Ensembl: Hps5)
Name: serum amyloid A4 (Ensembl:HPS5, biogenesis of lysosomal organelles complex 2 subunit 2)
RGD ID: 1307371
Description: Predicted to be involved in acute-phase response. Predicted to be located in cytosol and membrane. Predicted to be part of high-density lipoprotein particle. 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 Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81106,383,856 - 106,388,158 (-)NCBIGRCr8
mRatBN7.2197,247,580 - 97,251,882 (-)NCBImRatBN7.2mRatBN7.2
UTH_Rnor_SHR_Utx1102,639,968 - 102,644,286 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01111,111,955 - 111,116,273 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01104,395,938 - 104,400,240 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01102,776,079 - 102,780,381 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1102,776,082 - 102,849,430 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01103,850,707 - 103,855,009 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4197,278,427 - 97,282,729 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1197,356,540 - 97,360,840 (-)NCBI
Celera191,494,430 - 91,498,726 (-)NCBICelera
Cytogenetic Map1q22NCBI
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

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 (-)NCBIGRCr8
mRatBN7.2197,247,580 - 97,251,882 (-)NCBImRatBN7.2mRatBN7.2
UTH_Rnor_SHR_Utx1102,639,968 - 102,644,286 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01111,111,955 - 111,116,273 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01104,395,938 - 104,400,240 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01102,776,079 - 102,780,381 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1102,776,082 - 102,849,430 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01103,850,707 - 103,855,009 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4197,278,427 - 97,282,729 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1197,356,540 - 97,360,840 (-)NCBI
Celera191,494,430 - 91,498,726 (-)NCBICelera
Cytogenetic Map1q22NCBI
SAA4
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381118,231,355 - 18,236,802 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1118,231,355 - 18,236,802 (-)EnsemblGRCh38hg38GRCh38
GRCh371118,252,902 - 18,258,349 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361118,209,479 - 18,214,910 (-)NCBINCBI36Build 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 Ensembl
GRCm38746,727,992 - 46,732,603 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl746,727,998 - 46,732,603 (-)EnsemblGRCm38mm10GRCm38
MGSCv37753,983,368 - 53,987,913 (-)NCBIGRCm37MGSCv37mm9NCBIm37
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 (-)Ensemblpanpan1.1panPan2
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
LOC103239275
(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 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_023666038144,086,097 - 144,092,216 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0

Variants

.
Variants in Saa4
9 total Variants

QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
631688Hcas2Hepatocarcinoma susceptibility QTL 230.0001liver integrity trait (VT:0010547)liver tumorous lesion number (CMO:0001068)15925874115540829Rat
631495Bp96Blood pressure QTL 964.52arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)122340647102268831Rat
1358359Sradr1Stress Responsive Adrenal Weight QTL 14.74adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)130882023123479925Rat
70225Bp58Blood pressure QTL 583.3arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)132356093162846471Rat
10059597Bp377Blood pressure QTL 3773.420.025arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)132737458199368955Rat
2313051Bss57Bone structure and strength QTL 573.70.0001tibia strength trait (VT:1000284)bone polar moment of inertia (CMO:0001558)143284731118944897Rat
2313059Bss55Bone structure and strength QTL 553.20.0001tibia size trait (VT:0100001)tibia midshaft cross-sectional area (CMO:0001717)143284731118944897Rat
2313072Bss53Bone structure and strength QTL 534.30.0001tibia length (VT:0004357)tibia length (CMO:0000450)143284731118944897Rat
2313078Bss54Bone structure and strength QTL 543.50.0001tibia area (VT:1000281)tibia midshaft cross-sectional area (CMO:0001717)143284731118944897Rat
2313094Bss58Bone structure and strength QTL 583.70.0001tibia strength trait (VT:1000284)tibia total energy absorbed before break (CMO:0001736)143284731118944897Rat
2313098Bmd70Bone mineral density QTL 703.60.0001tibia mineral mass (VT:1000283)compact volumetric bone mineral density (CMO:0001730)143284731118944897Rat
2313099Bss56Bone structure and strength QTL 562.40.0001tibia size trait (VT:0100001)tibia midshaft endosteal cross-sectional area (CMO:0001716)143284731118944897Rat
2313402Anxrr24Anxiety related response QTL 24aggression-related behavior trait (VT:0015014)tameness/aggressiveness composite score (CMO:0002136)148963584144267916Rat
1578654Bss10Bone structure and strength QTL 104femur morphology trait (VT:0000559)femoral neck cortical cross-sectional area (CMO:0001702)149393172159356837Rat
634314Niddm44Non-insulin dependent diabetes mellitus QTL 44blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)149393289199050459Rat
61342Bp27Blood pressure QTL 273.40.0006arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)15673266898773277Rat
2300164Bmd44Bone mineral density QTL 445.40.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)156949932101949932Rat
2298545Neuinf8Neuroinflammation QTL 84.6nervous system integrity trait (VT:0010566)spinal cord beta-2 microglobulin mRNA level (CMO:0002125)157336763151090257Rat
1300121Hrtrt1Heart rate QTL 13.7heart pumping trait (VT:2000009)heart rate (CMO:0000002)165789093115540829Rat
7421628Bp361Blood pressure QTL 3610.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)166023617118608521Rat
1358192Ept13Estrogen-induced pituitary tumorigenesis QTL 133.4pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)177494165122494165Rat
10054135Gmadr2Adrenal mass QTL 21.970.0129adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)177857876122857876Rat
1549903Bp267Blood pressure QTL 267arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)177876254106047988Rat
61344Bp29Blood pressure QTL 297.5arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)178350581123350581Rat
7411712Strs4Sensitivity to stroke QTL 48.7cerebrum integrity trait (VT:0010549)percentage of study population developing cerebrovascular lesions during a period of time (CMO:0000932)178430536123430536Rat
1582234Gluco18Glucose level QTL 183.40.0003blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)178479925123479925Rat
4889494Scort2Serum corticosterone level QTL 24.2blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)180592172125592172Rat
1578780Cm52Cardiac mass QTL 523.30.0001heart mass (VT:0007028)heart wet weight (CMO:0000069)181591954219808434Rat
2313083Bmd74Bone mineral density QTL 7440.0001tibia mineral mass (VT:1000283)total volumetric bone mineral density (CMO:0001728)182174743118944897Rat
738022Anxrr13Anxiety related response QTL 134.60.00039locomotor behavior trait (VT:0001392)number of 20 x 20 cm floor squares crossed into, out of or within a discrete space in an experimental apparatus (CMO:0001514)183547917128547917Rat
2300324Fetw1Fetal weight QTL 112.10.005fetal growth trait (VT:0004201)fetal body weight (CMO:0002080)185424647100358001Rat
724529Cm16Cardiac mass QTL 162.7heart mass (VT:0007028)calculated heart weight (CMO:0000073)187580395150700247Rat
724521Uae1Urinary albumin excretion QTL 13.80.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)190508614173018436Rat
1358902Bw47Body weight QTL 471.67body mass (VT:0001259)body weight (CMO:0000012)190508614180359386Rat
1302788Scl19Serum cholesterol QTL 194.60.001blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)190532338123479925Rat
1300153Bp171Blood pressure QTL 1713.37arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)190664883143200202Rat
2293142Bp314Blood pressure QTL 314arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)192184926137184926Rat
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)192948896144267916Rat
1331800Scl25Serum cholesterol level QTL 253.013blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)194494440117601394Rat
1331793Bp200Blood pressure QTL 2003.71601arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)194494440172949803Rat
1331751Bp199Blood pressure QTL 1993.60022arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)194494440181830018Rat
1331749Hrtrt11Heart rate QTL 112.973heart pumping trait (VT:2000009)heart rate (CMO:0000002)194494440198211706Rat
70209Niddm23Non-insulin dependent diabetes mellitus QTL 232.82blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)194494440198324465Rat
731168Bp154Blood pressure QTL 1543.4arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)194642644214537671Rat

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
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 39 33 17 33 14 4 9 4
Low 1 43 18 8 2 8 8 11 60 31 32 7 8
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000078692   ⟹   ENSRNOP00000071382
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl197,247,598 - 97,321,019 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000082289   ⟹   ENSRNOP00000069924
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl197,247,598 - 97,321,019 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000086856   ⟹   ENSRNOP00000075429
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
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 ENSRNOP00000069924.2
  ENSRNOP00000071382.1
Reference Protein Sequences
RefSeq Acc Id: NP_001009478   ⟸   NM_001009478
- Peptide Label: precursor
- UniProtKB: Q5M878 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000071382   ⟸   ENSRNOT00000078692
RefSeq Acc Id: ENSRNOP00000069924   ⟸   ENSRNOT00000082289
RefSeq Acc Id: ENSRNOP00000075429   ⟸   ENSRNOT00000086856

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
Ensembl Transcript ENSRNOT00000078692.2 UniProtKB/TrEMBL
  ENSRNOT00000082289.2 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
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
Pfam SAA UniProtKB/TrEMBL
PhenoGen Saa4 PhenoGen
PIRSF BLOC-2_complex_Hps5 UniProtKB/TrEMBL
  Serum_amyloid_A UniProtKB/TrEMBL
PRINTS SERUMAMYLOID UniProtKB/TrEMBL
RatGTEx ENSRNOG00000055531 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