SDC4 (syndecan 4) - Rat Genome Database

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Gene: SDC4 (syndecan 4) Sus scrofa
Analyze
Symbol: SDC4
Name: syndecan 4
RGD ID: 14218270
Description: ENCODES a protein that exhibits fibronectin binding (ortholog); identical protein binding (ortholog); protein kinase C binding (ortholog); INVOLVED IN inner ear receptor cell stereocilium organization (ortholog); negative regulation of T cell proliferation (ortholog); neural tube closure (ortholog); PARTICIPATES IN syndecan signaling pathway; ASSOCIATED WITH bacterial infectious disease (ortholog); COVID-19 (ortholog); lung non-small cell carcinoma (ortholog); FOUND IN cell surface (ortholog); costamere (ortholog); focal adhesion (ortholog)
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: SYND4; syndecan-4
RGD Orthologs
Human
Mouse
Rat
Chinchilla
Bonobo
Dog
Squirrel
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: Sscrofa11.1 - Pig Sscrofa11.1 Assembly
Position:
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.11747,650,387 - 47,670,499 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21753,254,792 - 53,270,726 (-)NCBISscrofa10.2Sscrofa10.2susScr3
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Molecular Pathway Annotations     Click to see Annotation Detail View
References
Additional References at PubMed
PMID:27208778  


Genomics

Comparative Map Data
SDC4
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.11747,650,387 - 47,670,499 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21753,254,792 - 53,270,726 (-)NCBISscrofa10.2Sscrofa10.2susScr3
SDC4
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl2045,325,288 - 45,348,424 (-)EnsemblGRCh38hg38GRCh38
GRCh382045,325,288 - 45,348,424 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh372043,953,928 - 43,977,064 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 362043,387,342 - 43,410,478 (-)NCBINCBI36hg18NCBI36
Build 342043,387,343 - 43,410,478NCBI
Celera2040,662,456 - 40,685,588 (-)NCBI
Cytogenetic Map20q13.12NCBI
HuRef2040,695,444 - 40,718,573 (-)NCBIHuRef
CHM1_12043,856,488 - 43,879,617 (-)NCBICHM1_1
Sdc4
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm392164,266,167 - 164,285,512 (-)NCBIGRCm39mm39
GRCm39 Ensembl2164,266,167 - 164,285,807 (-)Ensembl
GRCm382164,424,247 - 164,443,188 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl2164,424,247 - 164,443,887 (-)EnsemblGRCm38mm10GRCm38
MGSCv372164,249,747 - 164,268,688 (-)NCBIGRCm37mm9NCBIm37
MGSCv362164,115,452 - 164,134,393 (-)NCBImm8
Celera2170,361,365 - 170,380,306 (-)NCBICelera
Cytogenetic Map2H3NCBI
cM Map285.16NCBI
Sdc4
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.23153,154,888 - 153,173,576 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl3153,154,896 - 153,173,580 (-)Ensembl
Rnor_6.03160,872,503 - 160,891,190 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl3160,872,503 - 160,891,190 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.03167,052,789 - 167,071,476 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.43155,446,138 - 155,464,825 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.13155,352,182 - 155,370,861 (-)NCBI
Celera3151,766,226 - 151,784,912 (-)NCBICelera
Cytogenetic Map3q42NCBI
Sdc4
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495544511,990,792 - 12,011,553 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495544511,990,916 - 12,009,178 (+)NCBIChiLan1.0ChiLan1.0
SDC4
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.12042,746,597 - 42,769,736 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2042,746,281 - 42,769,737 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v02041,656,406 - 41,679,549 (-)NCBIMhudiblu_PPA_v0panPan3
SDC4
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12432,628,704 - 32,648,809 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2432,630,437 - 32,649,114 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2432,273,638 - 32,293,743 (-)NCBI
ROS_Cfam_1.02433,339,093 - 33,359,207 (-)NCBI
UMICH_Zoey_3.12432,600,350 - 32,620,457 (-)NCBI
UNSW_CanFamBas_1.02432,715,919 - 32,736,026 (-)NCBI
UU_Cfam_GSD_1.02433,259,679 - 33,280,258 (-)NCBI
Sdc4
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024408640192,074,895 - 192,108,750 (+)NCBI
SpeTri2.0NW_0049365147,528,538 - 7,562,391 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SDC4
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1218,490,474 - 18,513,329 (+)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl218,490,485 - 18,513,332 (+)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366605067,132,278 - 67,155,156 (+)NCBIVero_WHO_p1.0
Sdc4
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247909,146,371 - 9,166,729 (+)NCBIHetGla_female_1.0hetGla2


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 hemolymphoid system musculoskeletal system nervous system renal system reproductive system respiratory system
High
Medium 10 2 1 5 6 2 3 1
Low 2 2 2 17 2
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: NM_214284   ⟹   NP_999449
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.11747,650,387 - 47,670,486 (-)NCBI
Sequence:
RefSeq Acc Id: XM_021077291   ⟹   XP_020932950
RefSeq Status:
Type: CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.11747,651,351 - 47,670,499 (-)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_999449 (Get FASTA)   NCBI Sequence Viewer  
  XP_020932950 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAN59952 (Get FASTA)   NCBI Sequence Viewer  
  Q8HZJ6 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_999449   ⟸   NM_214284
- Peptide Label: precursor
- UniProtKB: Q8HZJ6 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_020932950   ⟸   XM_021077291
- Peptide Label: isoform X1
- Sequence:
Protein Domains
4.1m


Additional Information

Database Acc Id Source(s)
Ensembl Genes ENSSSCG00040017528 UniProtKB/Swiss-Prot
  ENSSSCG00070012642 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Protein ENSSSCP00040010013 UniProtKB/Swiss-Prot
  ENSSSCP00070020431 UniProtKB/Swiss-Prot
  ENSSSCP00070020434 UniProtKB/TrEMBL
Ensembl Transcript ENSSSCT00040023680 UniProtKB/Swiss-Prot
  ENSSSCT00070024682 UniProtKB/Swiss-Prot
  ENSSSCT00070024685 UniProtKB/TrEMBL
InterPro Neurexin-like UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Syndecan UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Syndecan/Neurexin_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Syndecan_CS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report ssc:397528 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
NCBI Gene SDC4 ENTREZGENE
PANTHER PTHR10915 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam Syndecan UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE SYNDECAN UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART 4.1m UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A480JRC1_PIG UniProtKB/TrEMBL
  A0A4X1TY81_PIG UniProtKB/TrEMBL
  Q8HZJ6 ENTREZGENE, UniProtKB/Swiss-Prot
VGNC ID VGNC:95487 ENTREZGENE