Sdc3 (syndecan 3) - Rat Genome Database

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Gene: Sdc3 (syndecan 3) Chinchilla lanigera
Analyze
Symbol: Sdc3
Name: syndecan 3
RGD ID: 8944439
Description: ENCODES a protein that exhibits identical protein binding (ortholog); INVOLVED IN cell adhesion (ortholog); regulation of cell migration (ortholog); PARTICIPATES IN melanocortin system pathway; syndecan signaling pathway; ASSOCIATED WITH genetic disease (ortholog); obesity (ortholog); FOUND IN axon (ortholog); membrane (ortholog); microspike (ortholog)
Type: protein-coding
RefSeq Status: MODEL
Previously known as: syndecan-3
RGD Orthologs
Human
Mouse
Rat
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: ChiLan1.0 - Chinchilla ChiLan1.0 Assembly
Position:
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554529,442,759 - 9,452,027 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554529,442,860 - 9,479,776 (-)NCBIChiLan1.0ChiLan1.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View
genetic disease  (ISO)
obesity  (ISO)

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. Transitive Annotation Pipeline Automated assignment of GO, PW and RDO ISO annotations across species
2. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
Additional References at PubMed
PMID:30032202  


Genomics

Comparative Map Data
Sdc3
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554529,442,759 - 9,452,027 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554529,442,860 - 9,479,776 (-)NCBIChiLan1.0ChiLan1.0
SDC3
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38130,869,466 - 30,909,735 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl130,869,466 - 30,908,758 (-)EnsemblGRCh38hg38GRCh38
GRCh37131,342,313 - 31,381,605 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36131,118,567 - 31,154,067 (-)NCBINCBI36Build 36hg18NCBI36
Build 34131,015,074 - 31,050,573NCBI
Celera129,598,020 - 29,607,292 (-)NCBICelera
Cytogenetic Map1p35.2NCBI
HuRef129,448,414 - 29,487,313 (-)NCBIHuRef
CHM1_1131,458,707 - 31,467,979 (-)NCBICHM1_1
T2T-CHM13v2.0130,721,742 - 30,761,962 (-)NCBIT2T-CHM13v2.0
Sdc3
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm394130,519,855 - 130,553,629 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl4130,519,848 - 130,553,630 (+)EnsemblGRCm39 Ensembl
GRCm384130,792,537 - 130,826,318 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl4130,792,537 - 130,826,319 (+)EnsemblGRCm38mm10GRCm38
MGSCv374130,348,452 - 130,382,233 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv364130,064,654 - 130,098,393 (+)NCBIMGSCv36mm8
Celera4128,959,630 - 128,992,669 (+)NCBICelera
Cytogenetic Map4D2.2NCBI
cM Map463.63NCBI
Sdc3
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr85148,249,792 - 148,282,524 (+)NCBIGRCr8
mRatBN7.25142,965,659 - 142,998,390 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl5142,965,591 - 142,996,480 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx5145,664,910 - 145,697,641 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.05147,434,735 - 147,467,464 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.05147,431,294 - 147,464,044 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.05148,923,098 - 148,956,404 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl5148,923,098 - 148,956,404 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.05152,628,005 - 152,660,586 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.45149,486,028 - 149,518,849 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.15149,497,976 - 149,528,956 (-)NCBI
Celera5141,427,897 - 141,460,387 (+)NCBICelera
Cytogenetic Map5q36NCBI
SDC3
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21195,930,956 - 195,970,722 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11195,048,132 - 195,087,879 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0130,143,050 - 30,182,795 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1131,169,002 - 31,181,000 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl131,169,002 - 31,178,265 (-)Ensemblpanpan1.1panPan2
SDC3
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1270,081,287 - 70,090,290 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl270,056,458 - 70,088,426 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha266,631,617 - 66,667,833 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0270,616,352 - 70,652,558 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl270,616,352 - 70,652,573 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1267,451,512 - 67,487,703 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0268,450,471 - 68,486,798 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0269,445,397 - 69,485,652 (+)NCBIUU_Cfam_GSD_1.0
Sdc3
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440505848,375,754 - 48,389,777 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_00493647414,204,118 - 14,233,635 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_00493647414,203,322 - 14,209,187 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SDC3
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl687,495,045 - 87,507,235 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1687,495,041 - 87,535,689 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2681,263,544 - 81,287,288 (+)NCBISscrofa10.2Sscrofa10.2susScr3
LOC103225235
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.120101,931,276 - 101,970,626 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl20101,961,371 - 101,970,950 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366603314,685,587 - 14,688,871 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Sdc3
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462476414,316,799 - 14,353,735 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462476414,316,727 - 14,353,735 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2


Expression


Sequence


Reference Sequences
RefSeq Acc Id: ENSCLAT00000016129   ⟹   ENSCLAP00000015965
Type: CODING
Position:
Chinchilla AssemblyChrPosition (strand)Source
ChiLan1.0 EnsemblNW_0049554529,442,759 - 9,452,027 (-)Ensembl
RefSeq Acc Id: XM_005395001   ⟹   XP_005395058
Type: CODING
Position:
Chinchilla AssemblyChrPosition (strand)Source
ChiLan1.0NW_0049554529,442,860 - 9,454,362 (-)NCBI
Sequence:
RefSeq Acc Id: XM_005395002   ⟹   XP_005395059
Type: CODING
Position:
Chinchilla AssemblyChrPosition (strand)Source
ChiLan1.0NW_0049554529,442,860 - 9,454,549 (-)NCBI
Sequence:
RefSeq Acc Id: XM_013519686   ⟹   XP_013375140
Type: CODING
Position:
Chinchilla AssemblyChrPosition (strand)Source
ChiLan1.0NW_0049554529,442,860 - 9,479,776 (-)NCBI
Sequence:
Protein Sequences
Protein RefSeqs XP_005395058 (Get FASTA)   NCBI Sequence Viewer  
  XP_005395059 (Get FASTA)   NCBI Sequence Viewer  
  XP_013375140 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSCLAP00000015965
  ENSCLAP00000015965.1
Reference Protein Sequences
RefSeq Acc Id: XP_005395059   ⟸   XM_005395002
- Peptide Label: isoform X3
- UniProtKB: A0A8C2VQC8 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_005395058   ⟸   XM_005395001
- Peptide Label: isoform X2
- UniProtKB: A0A8C2VQC8 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_013375140   ⟸   XM_013519686
- Peptide Label: isoform X1
- UniProtKB: A0A8C2VQC8 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSCLAP00000015965   ⟸   ENSCLAT00000016129
Protein Domains
Neurexin/syndecan/glycophorin C


Additional Information

Database Acc Id Source(s)
Ensembl Genes ENSCLAG00000010987 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSCLAT00000016129 ENTREZGENE
  ENSCLAT00000016129.1 UniProtKB/TrEMBL
InterPro Neurexin-like UniProtKB/TrEMBL
  Syndecan UniProtKB/TrEMBL
  Syndecan/Neurexin_dom UniProtKB/TrEMBL
  Syndecan_CS UniProtKB/TrEMBL
NCBI Gene Sdc3 ENTREZGENE
PANTHER PTHR10915 UniProtKB/TrEMBL
  PTHR10915:SF7 UniProtKB/TrEMBL
Pfam Syndecan UniProtKB/TrEMBL
PROSITE SYNDECAN UniProtKB/TrEMBL
SMART 4.1m UniProtKB/TrEMBL
UniProt A0A8C2VQC8 ENTREZGENE, UniProtKB/TrEMBL