Siglec8 (sialic acid binding Ig-like lectin 8) - Rat Genome Database

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Gene: Siglec8 (sialic acid binding Ig-like lectin 8) Rattus norvegicus
Analyze
Symbol: Siglec8
Name: sialic acid binding Ig-like lectin 8
RGD ID: 1563073
Description: Orthologous to several human genes including SIGLEC8 (sialic acid binding Ig like lectin 8); INTERACTS WITH Cuprizon; thioacetamide; benzo[a]pyrene (ortholog).
Type: protein-coding
RefSeq Status: MODEL
Previously known as: LOC292846; RGD1563073; similar to SIGLEC-like 1
RGD Orthologs
Human
Bonobo
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2194,092,737 - 94,103,134 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl194,093,395 - 94,103,034 (-)EnsemblmRatBN7.2 Ensembl
Rnor_6.0199,576,946 - 99,587,441 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl199,578,372 - 99,587,205 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01100,645,666 - 100,656,065 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4194,062,030 - 94,071,181 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera188,361,882 - 88,372,377 (-)NCBICelera
Cytogenetic Map1q22NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. 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.
2. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
3. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:11171044   PMID:15048729   PMID:24227736  


Genomics

Comparative Map Data
Siglec8
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2194,092,737 - 94,103,134 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl194,093,395 - 94,103,034 (-)EnsemblmRatBN7.2 Ensembl
Rnor_6.0199,576,946 - 99,587,441 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl199,578,372 - 99,587,205 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01100,645,666 - 100,656,065 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4194,062,030 - 94,071,181 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera188,361,882 - 88,372,377 (-)NCBICelera
Cytogenetic Map1q22NCBI
SIGLEC8
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381951,450,997 - 51,458,454 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl1951,450,847 - 51,458,456 (-)EnsemblGRCh38hg38GRCh38
GRCh371951,954,251 - 51,961,708 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361956,646,063 - 56,653,520 (-)NCBINCBI36Build 36hg18NCBI36
Build 341956,646,074 - 56,653,501NCBI
Celera1949,005,289 - 49,012,746 (-)NCBICelera
Cytogenetic Map19q13.41NCBI
HuRef1948,286,202 - 48,293,659 (-)NCBIHuRef
CHM1_11951,956,163 - 51,963,620 (-)NCBICHM1_1
T2T-CHM13v2.01954,539,617 - 54,547,074 (-)NCBIT2T-CHM13v2.0
SIGLEC8
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan11959,416,971 - 59,424,449 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01948,393,285 - 48,400,767 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11957,278,143 - 57,285,598 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1957,278,143 - 57,285,598 (-)Ensemblpanpan1.1panPan2
Siglec8
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248323,462,397 - 3,465,758 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Siglec8
45 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:44
Count of miRNA genes:42
Interacting mature miRNAs:44
Transcripts:ENSRNOT00000048947
Prediction methods: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.


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
1578649Bmd8Bone mineral density QTL 84.9femur mineral mass (VT:0010011)trabecular volumetric bone mineral density (CMO:0001729)14939317294393172Rat
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


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 9 2 6
Low 3 21 48 32 10 32 7 8 25 29 23 5 7
Below cutoff 14 9 9 9 1 3 49 6 15 1

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000048947   ⟹   ENSRNOP00000040647
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl194,093,395 - 94,103,034 (-)Ensembl
Rnor_6.0 Ensembl199,578,372 - 99,587,205 (-)Ensembl
RefSeq Acc Id: XR_350321
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2194,092,737 - 94,103,116 (-)NCBI
Rnor_6.0199,576,946 - 99,587,437 (-)NCBI
Sequence:
RefSeq Acc Id: XR_590162
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2194,092,737 - 94,103,134 (-)NCBI
Rnor_6.0199,576,946 - 99,587,441 (-)NCBI
Sequence:
Protein Sequences
GenBank Protein EDM07543 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: ENSRNOP00000040647   ⟸   ENSRNOT00000048947
Protein Domains
Ig-like

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-F1M8J5-F1-model_v2 AlphaFold F1M8J5 1-457 view protein structure

Transcriptome

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


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1563073 AgrOrtholog
BioCyc Gene G2FUF-59830 BioCyc
Ensembl Genes ENSRNOG00000022640 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000040647.4 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000048947 ENTREZGENE
  ENSRNOT00000048947.5 UniProtKB/TrEMBL
Gene3D-CATH 2.60.40.10 UniProtKB/TrEMBL
InterPro Ig-like_dom UniProtKB/TrEMBL
  Ig-like_dom_sf UniProtKB/TrEMBL
  Ig-like_fold UniProtKB/TrEMBL
  Ig/MHC_CS UniProtKB/TrEMBL
  Ig_sub UniProtKB/TrEMBL
  Ig_sub2 UniProtKB/TrEMBL
  Ig_V-set UniProtKB/TrEMBL
NCBI Gene 292846 ENTREZGENE
PANTHER SIALIC ACID BINDING IMMUNOGLOBULIN-LIKE LECTIN UniProtKB/TrEMBL
  SIALIC ACID-BINDING IG-LIKE LECTIN 9 UniProtKB/TrEMBL
Pfam Ig_3 UniProtKB/TrEMBL
  V-set UniProtKB/TrEMBL
PhenoGen Siglec8 PhenoGen
PROSITE IG_LIKE UniProtKB/TrEMBL
  IG_MHC UniProtKB/TrEMBL
SMART IGc2 UniProtKB/TrEMBL
  SM00409 UniProtKB/TrEMBL
Superfamily-SCOP SSF48726 UniProtKB/TrEMBL
UniProt F1M8J5_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2012-10-12 Siglec8  sialic acid binding Ig-like lectin 8  RGD1563073  similar to SIGLEC-like 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 RGD1563073  similar to SIGLEC-like 1   RGD1563073_predicted  similar to SIGLEC-like 1 (predicted)  'predicted' is removed 2292626 APPROVED
2006-03-07 RGD1563073_predicted  similar to SIGLEC-like 1 (predicted)  LOC292846  similar to SIGLEC-like 1  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC292846  similar to SIGLEC-like 1      Symbol and Name status set to provisional 70820 PROVISIONAL