Sdc2 (syndecan 2) - Rat Genome Database

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Gene: Sdc2 (syndecan 2) Ictidomys tridecemlineatus
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Symbol: Sdc2
Name: syndecan 2
RGD ID: 12467842
Description: ENCODES a protein that exhibits PDZ domain binding (ortholog); INVOLVED IN dendrite morphogenesis (ortholog); regulation of synapse assembly (ortholog); regulation of synapse maturation (ortholog); PARTICIPATES IN fibroblast growth factor signaling pathway; syndecan signaling pathway; ASSOCIATED WITH cleft lip (ortholog); cleft palate (ortholog); type 2 diabetes mellitus (ortholog); FOUND IN glutamatergic synapse (ortholog); neuronal cell body (ortholog); postsynaptic membrane (ortholog)
Type: protein-coding
RefSeq Status: MODEL
Previously known as: syndecan-2
RGD Orthologs
Human
Mouse
Rat
Chinchilla
Bonobo
Dog
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: SpeTri2.0 - Squirrel SpeTri2.0 Assembly
Position:
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440530338,541,717 - 38,648,722 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_00493647045,967,303 - 46,074,812 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_00493647045,967,816 - 46,074,820 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
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
Additional References at PubMed
PMID:30032202  


Genomics

Comparative Map Data
Sdc2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440530338,541,717 - 38,648,722 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_00493647045,967,303 - 46,074,812 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_00493647045,967,816 - 46,074,820 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SDC2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38896,493,813 - 96,611,790 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl896,493,813 - 96,611,790 (+)EnsemblGRCh38hg38GRCh38
GRCh37897,506,041 - 97,624,018 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36897,575,058 - 97,693,213 (+)NCBINCBI36Build 36hg18NCBI36
Build 34897,575,057 - 97,693,213NCBI
Celera893,691,860 - 93,810,255 (+)NCBICelera
Cytogenetic Map8q22.1NCBI
HuRef892,711,380 - 92,829,628 (+)NCBIHuRef
CHM1_1897,546,134 - 97,664,535 (+)NCBICHM1_1
T2T-CHM13v2.0897,619,532 - 97,737,516 (+)NCBIT2T-CHM13v2.0
Sdc2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391532,920,869 - 33,034,867 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1532,920,869 - 33,035,081 (+)EnsemblGRCm39 Ensembl
GRCm381532,920,723 - 33,034,721 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1532,920,723 - 33,034,935 (+)EnsemblGRCm38mm10GRCm38
MGSCv371532,850,478 - 32,964,476 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361532,865,312 - 32,979,310 (+)NCBIMGSCv36mm8
Celera1533,584,115 - 33,695,490 (+)NCBICelera
Cytogenetic Map15B3.1NCBI
cM Map1513.74NCBI
Sdc2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8766,012,405 - 66,125,101 (+)NCBIGRCr8
mRatBN7.2764,127,185 - 64,239,885 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl764,127,110 - 64,241,081 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx766,016,363 - 66,129,168 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0768,218,571 - 68,331,380 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0768,008,023 - 68,120,333 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0771,572,731 - 71,686,139 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl771,572,941 - 71,686,044 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0771,743,895 - 71,857,365 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4768,290,558 - 68,405,183 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1768,311,497 - 68,426,917 (+)NCBI
Celera761,250,356 - 61,362,471 (+)NCBICelera
Cytogenetic Map7q22NCBI
Sdc2
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495541712,462,354 - 12,564,633 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495541712,462,354 - 12,563,374 (+)NCBIChiLan1.0ChiLan1.0
SDC2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v27113,822,721 - 113,937,524 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1889,361,614 - 89,478,168 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0893,118,379 - 93,230,803 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1895,314,910 - 95,428,519 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl895,314,910 - 95,428,519 (+)Ensemblpanpan1.1panPan2
SDC2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12940,939,498 - 41,026,694 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2940,939,257 - 41,024,357 (+)EnsemblCanFam3.1canFam3CanFam3.1
ROS_Cfam_1.02941,126,548 - 41,219,188 (+)NCBIROS_Cfam_1.0
UMICH_Zoey_3.12941,169,044 - 41,261,257 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02941,141,750 - 41,229,172 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02941,600,748 - 41,693,152 (+)NCBIUU_Cfam_GSD_1.0
SDC2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl440,001,395 - 40,129,697 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1440,003,618 - 40,129,483 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2443,121,719 - 43,248,283 (-)NCBISscrofa10.2Sscrofa10.2susScr3
SDC2
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1891,451,808 - 91,570,778 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl891,552,647 - 91,568,828 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366603949,216,156 - 49,335,471 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Sdc2
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247633,809,569 - 3,919,346 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046247633,809,850 - 3,920,364 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2


Expression

RNA-SEQ Expression


Sequence

Nucleotide Sequences
RefSeq Transcripts XM_005316321 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide JAESOR010000362 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Ensembl Acc Id: ENSSTOT00000008042   ⟹   ENSSTOP00000007199
Type: CODING
Position:
Squirrel AssemblyChrPosition (strand)Source
SpeTri2.0 EnsemblNW_00493647045,967,303 - 46,074,812 (-)Ensembl
RefSeq Acc Id: XM_005316321   ⟹   XP_005316378
Type: CODING
Position:
Squirrel AssemblyChrPosition (strand)Source
HiC_Itri_2NW_02440530338,541,717 - 38,648,722 (-)NCBI
SpeTri2.0NW_00493647045,967,816 - 46,074,820 (-)NCBI
Sequence:
Protein Sequences
Protein RefSeqs XP_005316378 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSSTOP00000007199.3
GenBank Protein KAG3273863 (Get FASTA)   NCBI Sequence Viewer  
RefSeq Acc Id: XP_005316378   ⟸   XM_005316321
- UniProtKB: I3MAX0 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSSTOP00000007199   ⟸   ENSSTOT00000008042
Protein Domains
Neurexin/syndecan/glycophorin C


Additional Information

Database Acc Id Source(s)
Ensembl Genes ENSSTOG00000008050 Ensembl, UniProtKB/TrEMBL
Ensembl Transcript ENSSTOT00000008042.3 UniProtKB/TrEMBL
InterPro Neurexin-like UniProtKB/TrEMBL
  Syndecan UniProtKB/TrEMBL
  Syndecan/Neurexin_dom UniProtKB/TrEMBL
  Syndecan_CS UniProtKB/TrEMBL
NCBI Gene Sdc2 ENTREZGENE
PANTHER PTHR10915 UniProtKB/TrEMBL
  PTHR10915:SF6 UniProtKB/TrEMBL
Pfam Syndecan UniProtKB/TrEMBL
PROSITE PROKAR_LIPOPROTEIN UniProtKB/TrEMBL
  SYNDECAN UniProtKB/TrEMBL
SMART 4.1m UniProtKB/TrEMBL
UniProt I3MAX0 ENTREZGENE, UniProtKB/TrEMBL