Siglecl1 (SIGLEC family like 1) - Rat Genome Database

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Gene: Siglecl1 (SIGLEC family like 1) Rattus norvegicus
Analyze
Symbol: Siglecl1
Name: SIGLEC family like 1
RGD ID: 2324488
Description: Predicted to be located in membrane. Orthologous to human SIGLECL1 (SIGLEC family like 1); INTERACTS WITH benzo[a]pyrene (ortholog); lipopolysaccharide (ortholog); S-(1,2-dichlorovinyl)-L-cysteine (ortholog).
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: hypothetical protein LOC690483; LOC100362567; LOC690483; sialic acid binding Ig-like lectin 5-like; sialic acid-binding Ig-like lectin 10; SIGLEC family-like protein 1
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81103,053,539 - 103,062,054 (-)NCBIGRCr8
mRatBN7.2193,916,971 - 93,924,742 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl193,916,970 - 93,924,758 (-)EnsemblmRatBN7.2 Ensembl
mRatBN7.2 Ensembl193,900,773 - 93,913,028 (-)EnsemblmRatBN7.2 Ensembl
Rnor_6.0198,424,994 - 98,436,634 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl198,425,903 - 98,438,776 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0 Ensembl198,414,226 - 98,421,973 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0199,491,038 - 99,498,849 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4193,884,846 - 93,902,421 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera188,179,043 - 88,190,111 (-)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. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:12477932   PMID:32007531  


Genomics

Comparative Map Data
Siglecl1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81103,053,539 - 103,062,054 (-)NCBIGRCr8
mRatBN7.2193,916,971 - 93,924,742 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl193,916,970 - 93,924,758 (-)EnsemblmRatBN7.2 Ensembl
mRatBN7.2 Ensembl193,900,773 - 93,913,028 (-)EnsemblmRatBN7.2 Ensembl
Rnor_6.0198,424,994 - 98,436,634 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl198,425,903 - 98,438,776 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0 Ensembl198,414,226 - 98,421,973 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0199,491,038 - 99,498,849 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4193,884,846 - 93,902,421 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera188,179,043 - 88,190,111 (-)NCBICelera
Cytogenetic Map1q22NCBI
SIGLECL1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381951,246,332 - 51,269,330 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1951,246,348 - 51,269,330 (+)EnsemblGRCh38hg38GRCh38
GRCh371951,749,587 - 51,772,584 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361956,452,776 - 56,464,394 (+)NCBINCBI36Build 36hg18NCBI36
Celera1948,813,054 - 48,824,675 (+)NCBICelera
Cytogenetic Map19q13.41NCBI
HuRef1948,087,388 - 48,105,641 (+)NCBIHuRef
CHM1_11951,756,401 - 51,774,655 (+)NCBICHM1_1
T2T-CHM13v2.01954,334,953 - 54,357,956 (+)NCBIT2T-CHM13v2.0
Siglecl1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39743,160,589 - 43,172,609 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl743,160,589 - 43,168,394 (-)EnsemblGRCm39 Ensembl
GRCm38743,511,165 - 43,519,079 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl743,511,165 - 43,518,970 (-)EnsemblGRCm38mm10GRCm38
MGSCv37750,766,538 - 50,774,340 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36750,766,538 - 50,774,340 (-)NCBIMGSCv36mm8
Celera738,979,953 - 38,987,875 (-)NCBICelera
Cytogenetic Map7B3NCBI
Siglecl1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0NW_0049555581,101,532 - 1,116,578 (-)NCBIChiLan1.0ChiLan1.0
SIGLECL1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v22057,303,190 - 57,307,712 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11959,224,672 - 59,229,193 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01948,200,978 - 48,206,643 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11957,088,147 - 57,092,876 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1957,088,147 - 57,092,665 (+)Ensemblpanpan1.1panPan2
SIGLECL1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11105,683,766 - 105,698,305 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1105,674,317 - 105,674,871 (-)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1105,684,260 - 105,698,903 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1105,256,386 - 105,270,971 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.01106,193,044 - 106,207,594 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl1106,193,843 - 106,198,116 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.11105,864,876 - 105,879,396 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01105,505,875 - 105,520,422 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01106,301,067 - 106,315,665 (-)NCBIUU_Cfam_GSD_1.0
Siglecl1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440934922,992,481 - 23,009,582 (+)NCBIHiC_Itri_2
SpeTri2.0NW_00493698164,077 - 68,167 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SIGLECL1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1644,179,076 - 44,194,110 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl644,188,702 - 44,193,214 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366607324,219,877 - 24,241,062 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Siglecl1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248323,570,765 - 3,580,342 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Siglecl1
30 total Variants

QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2313402Anxrr24Anxiety related response QTL 24aggression-related behavior trait (VT:0015014)tameness/aggressiveness composite score (CMO:0002136)148963584144267916Rat
631688Hcas2Hepatocarcinoma susceptibility QTL 230.0001liver integrity trait (VT:0010547)liver tumorous lesion number (CMO:0001068)15925874115540829Rat
4889494Scort2Serum corticosterone level QTL 24.2blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)180592172125592172Rat
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
631495Bp96Blood pressure QTL 964.52arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)122340647102268831Rat
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
7421628Bp361Blood pressure QTL 3610.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)166023617118608521Rat
1300121Hrtrt1Heart rate QTL 13.7heart pumping trait (VT:2000009)heart rate (CMO:0000002)165789093115540829Rat
1358359Sradr1Stress Responsive Adrenal Weight QTL 14.74adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)130882023123479925Rat
10059597Bp377Blood pressure QTL 3773.420.025arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)132737458199368955Rat
1300153Bp171Blood pressure QTL 1713.37arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)190664883143200202Rat
1302788Scl19Serum cholesterol QTL 194.60.001blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)190532338123479925Rat
1549903Bp267Blood pressure QTL 267arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)177876254106047988Rat
1358192Ept13Estrogen-induced pituitary tumorigenesis QTL 133.4pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)177494165122494165Rat
1582234Gluco18Glucose level QTL 183.40.0003blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)178479925123479925Rat
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
61342Bp27Blood pressure QTL 273.40.0006arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)15673266898773277Rat
61344Bp29Blood pressure QTL 297.5arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)178350581123350581Rat
2293142Bp314Blood pressure QTL 314arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)192184926137184926Rat
70225Bp58Blood pressure QTL 583.3arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)132356093162846471Rat
724521Uae1Urinary albumin excretion QTL 13.80.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)190508614173018436Rat
2298545Neuinf8Neuroinflammation QTL 84.6nervous system integrity trait (VT:0010566)spinal cord beta-2 microglobulin mRNA level (CMO:0002125)157336763151090257Rat
2313059Bss55Bone structure and strength QTL 553.20.0001tibia size trait (VT:0100001)tibia midshaft cross-sectional area (CMO:0001717)143284731118944897Rat
2313051Bss57Bone structure and strength QTL 573.70.0001tibia strength trait (VT:1000284)bone polar moment of inertia (CMO:0001558)143284731118944897Rat
2313094Bss58Bone structure and strength QTL 583.70.0001tibia strength trait (VT:1000284)tibia total energy absorbed before break (CMO:0001736)143284731118944897Rat
10054135Gmadr2Adrenal mass QTL 21.970.0129adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)177857876122857876Rat
2300324Fetw1Fetal weight QTL 112.10.005fetal growth trait (VT:0004201)fetal body weight (CMO:0002080)185424647100358001Rat
2313099Bss56Bone structure and strength QTL 562.40.0001tibia size trait (VT:0100001)tibia midshaft endosteal cross-sectional area (CMO:0001716)143284731118944897Rat
2313078Bss54Bone structure and strength QTL 543.50.0001tibia area (VT:1000281)tibia midshaft cross-sectional area (CMO:0001717)143284731118944897Rat
1358902Bw47Body weight QTL 471.67body mass (VT:0001259)body weight (CMO:0000012)190508614180359386Rat
2313098Bmd70Bone mineral density QTL 703.60.0001tibia mineral mass (VT:1000283)compact volumetric bone mineral density (CMO:0001730)143284731118944897Rat
634314Niddm44Non-insulin dependent diabetes mellitus QTL 44blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)149393289199050459Rat
2313072Bss53Bone structure and strength QTL 534.30.0001tibia length (VT:0004357)tibia length (CMO:0000450)143284731118944897Rat
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
724529Cm16Cardiac mass QTL 162.7heart mass (VT:0007028)calculated heart weight (CMO:0000073)187580395150700247Rat
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
2300164Bmd44Bone mineral density QTL 445.40.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)156949932101949932Rat

Markers in Region
RH134832  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2193,935,487 - 93,935,691 (-)MAPPERmRatBN7.2
Rnor_6.0198,403,266 - 98,403,469NCBIRnor6.0
Rnor_5.0199,480,139 - 99,480,342UniSTSRnor5.0
RGSC_v3.4193,904,103 - 93,904,306UniSTSRGSC3.4
Celera188,211,594 - 88,211,797UniSTS
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

endocrine system hemolymphoid system integumental system musculoskeletal system renal system reproductive system respiratory system appendage
High
Medium 7
Low
Below cutoff 1 6 1 1 12 2 4 1

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000024170   ⟹   ENSRNOP00000024170
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl193,900,773 - 93,913,028 (-)Ensembl
Rnor_6.0 Ensembl198,425,903 - 98,438,776 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000090785   ⟹   ENSRNOP00000072900
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl193,916,970 - 93,924,758 (-)Ensembl
Rnor_6.0 Ensembl198,414,226 - 98,421,973 (+)Ensembl
RefSeq Acc Id: NM_001421472   ⟹   NP_001408401
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81103,053,544 - 103,061,309 (-)NCBI
mRatBN7.2193,916,971 - 93,924,742 (-)NCBI
RefSeq Acc Id: XM_063274777   ⟹   XP_063130847
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81103,053,539 - 103,062,054 (-)NCBI
RefSeq Acc Id: XM_063274781   ⟹   XP_063130851
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81103,053,539 - 103,061,520 (-)NCBI
Protein Sequences
Protein RefSeqs NP_001408401 (Get FASTA)   NCBI Sequence Viewer  
  XP_063130847 (Get FASTA)   NCBI Sequence Viewer  
  XP_063130851 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDM07551 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000024170.5
  ENSRNOP00000072900
  ENSRNOP00000072900.1
Reference Protein Sequences
RefSeq Acc Id: ENSRNOP00000072900   ⟸   ENSRNOT00000090785
RefSeq Acc Id: ENSRNOP00000024170   ⟸   ENSRNOT00000024170
RefSeq Acc Id: NP_001408401   ⟸   NM_001421472
- UniProtKB: A0A0G2K443 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_063130847   ⟸   XM_063274777
- Peptide Label: isoform X1
RefSeq Acc Id: XP_063130851   ⟸   XM_063274781
- Peptide Label: isoform X1
Protein Domains
Ig-like

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-A0A0G2K443-F1-model_v2 AlphaFold A0A0G2K443 1-226 view protein structure
AF-D3Z8D1-F1-model_v2 AlphaFold D3Z8D1 1-369 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:2324488 AgrOrtholog
Ensembl Genes ENSRNOG00000032990 Ensembl, UniProtKB/TrEMBL
  ENSRNOG00000059992 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000024170.6 UniProtKB/TrEMBL
  ENSRNOT00000090785 ENTREZGENE
  ENSRNOT00000090785.2 UniProtKB/TrEMBL
Gene3D-CATH 2.60.40.10 UniProtKB/TrEMBL
InterPro Ig-like UniProtKB/TrEMBL
  Ig-like_dom_sf UniProtKB/TrEMBL
  Ig-like_fold UniProtKB/TrEMBL
KEGG Report rno:690483 UniProtKB/TrEMBL
NCBI Gene Siglecl1 ENTREZGENE
PANTHER RIKEN CDNA 4931406B18 GENE UniProtKB/TrEMBL
  SIALIC ACID BINDING IMMUNOGLOBULIN-LIKE LECTIN UniProtKB/TrEMBL
PhenoGen Siglecl1 PhenoGen
PROSITE IG_LIKE UniProtKB/TrEMBL
RatGTEx ENSRNOG00000032990 RatGTEx
  ENSRNOG00000059992 RatGTEx
Superfamily-SCOP SSF48726 UniProtKB/TrEMBL
UniProt A0A0G2K443 ENTREZGENE, UniProtKB/TrEMBL
  A6JAI3_RAT UniProtKB/TrEMBL
  D3Z8D1_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2021-03-09 Siglecl1  SIGLEC family like 1  LOC690483  hypothetical protein LOC690483  Data merged from RGD:1596028 737654 PROVISIONAL
2013-07-18 Siglecl1  SIGLEC family like 1  LOC100362567  sialic acid binding Ig-like lectin 5-like  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2010-05-06 LOC100362567  sialic acid binding Ig-like lectin 5-like      Symbol and Name status set to provisional 70820 PROVISIONAL
2006-11-20 LOC690483  hypothetical protein LOC690483      Symbol and Name status set to provisional 70820 PROVISIONAL