LOC482977 (syndecan binding protein) - Rat Genome Database

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Gene: LOC482977 (syndecan binding protein) Canis lupus familiaris
Analyze
Symbol: LOC482977
Name: syndecan binding protein
RGD ID: 12067089
Description: ENCODES a protein that exhibits cell adhesion molecule binding (ortholog); ephrin receptor binding (ortholog); frizzled binding (ortholog); INVOLVED IN negative regulation of proteasomal ubiquitin-dependent protein catabolic process (ortholog); negative regulation of receptor internalization (ortholog); negative regulation of transcription by RNA polymerase II (ortholog); PARTICIPATES IN interleukin-5 signaling pathway; syndecan signaling pathway; ASSOCIATED WITH osteoarthritis (ortholog); FOUND IN cytoplasm (ortholog); cytosol (ortholog); extracellular exosome (ortholog)
Type: protein-coding
RefSeq Status: MODEL
Also known as: SDCBP; syntenin-1
RGD Orthologs
Human
Mouse
Rat
Chinchilla
Bonobo
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: CanFam3.1 - Dog CanFam3.1 Assembly
Position:
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1299,331,876 - 9,370,489 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha299,644,617 - 9,683,238 (+)NCBI
ROS_Cfam_1.0299,417,267 - 9,455,907 (+)NCBI
UMICH_Zoey_3.1299,415,389 - 9,453,988 (+)NCBI
UNSW_CanFamBas_1.0299,541,083 - 9,579,672 (+)NCBI
UU_Cfam_GSD_1.0299,820,349 - 9,859,247 (+)NCBI
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

Cellular Component

Molecular Pathway Annotations     Click to see Annotation Detail View
References

Genomics

Comparative Map Data
LOC482977
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1299,331,876 - 9,370,489 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha299,644,617 - 9,683,238 (+)NCBI
ROS_Cfam_1.0299,417,267 - 9,455,907 (+)NCBI
UMICH_Zoey_3.1299,415,389 - 9,453,988 (+)NCBI
UNSW_CanFamBas_1.0299,541,083 - 9,579,672 (+)NCBI
UU_Cfam_GSD_1.0299,820,349 - 9,859,247 (+)NCBI
SDCBP
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl858,552,924 - 58,582,859 (+)EnsemblGRCh38hg38GRCh38
GRCh38858,553,261 - 58,582,860 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh37859,465,820 - 59,495,417 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36859,628,282 - 59,657,973 (+)NCBINCBI36hg18NCBI36
Build 34859,628,281 - 59,657,972NCBI
Celera855,458,752 - 55,488,443 (+)NCBI
Cytogenetic Map8q12.1NCBI
HuRef854,952,903 - 54,982,593 (+)NCBIHuRef
CHM1_1859,517,611 - 59,547,302 (+)NCBICHM1_1
Sdcbp
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm3946,365,654 - 6,396,122 (+)NCBIGRCm39mm39
GRCm39 Ensembl46,365,650 - 6,408,423 (+)Ensembl
GRCm3846,365,680 - 6,396,122 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl46,365,650 - 6,408,423 (+)EnsemblGRCm38mm10GRCm38
MGSCv3746,292,827 - 6,323,269 (+)NCBIGRCm37mm9NCBIm37
MGSCv3646,292,868 - 6,322,797 (+)NCBImm8
Celera46,283,969 - 6,314,409 (+)NCBICelera
Cytogenetic Map4A1NCBI
Sdcbp
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2519,473,499 - 19,517,188 (+)NCBI
Rnor_6.0 Ensembl519,471,664 - 19,498,485 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0519,471,664 - 19,498,499 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0524,256,110 - 24,283,037 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4519,822,440 - 19,849,223 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1519,822,439 - 19,849,220 (+)NCBI
Celera518,790,757 - 18,817,395 (+)NCBICelera
Cytogenetic Map5q12NCBI
Sdcbp
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495545417,089,232 - 17,113,484 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495545417,093,930 - 17,113,491 (+)NCBIChiLan1.0ChiLan1.0
SDCBP
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1856,643,962 - 56,673,834 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl856,643,962 - 56,673,833 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0854,992,627 - 55,022,560 (+)NCBIMhudiblu_PPA_v0panPan3
LOC101960082
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440530360,438,300 - 60,453,495 (+)NCBI
SpeTri2.0NW_00493649614,331,971 - 14,347,123 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SDCBP
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl474,295,922 - 74,341,085 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1474,295,941 - 74,357,720 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2481,090,105 - 81,122,727 (-)NCBISscrofa10.2Sscrofa10.2susScr3
LOC103236850
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1854,536,286 - 54,565,884 (+)NCBI
Sdcbp
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462474433,524,045 - 33,558,963 (-)NCBI


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 reproductive system respiratory system adipose tissue
High
Medium 5 5 22 6 6 6 6 6 12 8 10 6
Low
Below cutoff

Sequence

Nucleotide Sequences
RefSeq Transcripts XM_005638003 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_014109249 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_022412320 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_022412321 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_022412322 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_038441224 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_038441225 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_038441226 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_038441227 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_038441228 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_038515801 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_038515802 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_038515803 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_038515804 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_038515805 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_038579369 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_038579370 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_038579371 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_038579372 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_038579373 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_038643612 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_038643613 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_038643615 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_038643616 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_038643617 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_852382 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AAEX04000029 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JAAHUQ010000305 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JAAQRD010000073 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JAAUVH010000364 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  REHQ01000029 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: XM_005638003   ⟹   XP_005638060
RefSeq Status:
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.1299,331,919 - 9,370,489 (+)NCBI
Dog10K_Boxer_Tasha299,644,685 - 9,683,238 (+)NCBI
Sequence:
RefSeq Acc Id: XM_014109249   ⟹   XP_013964724
RefSeq Status:
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.1299,331,876 - 9,370,489 (+)NCBI
Dog10K_Boxer_Tasha299,644,617 - 9,683,238 (+)NCBI
Sequence:
RefSeq Acc Id: XM_022412320   ⟹   XP_022268028
RefSeq Status:
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.1299,332,737 - 9,370,489 (+)NCBI
Dog10K_Boxer_Tasha299,645,470 - 9,683,238 (+)NCBI
Sequence:
RefSeq Acc Id: XM_022412321   ⟹   XP_022268029
RefSeq Status:
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.1299,332,753 - 9,370,489 (+)NCBI
Dog10K_Boxer_Tasha299,645,519 - 9,683,238 (+)NCBI
Sequence:
RefSeq Acc Id: XM_022412322   ⟹   XP_022268030
RefSeq Status:
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.1299,331,919 - 9,370,489 (+)NCBI
Sequence:
RefSeq Acc Id: XM_038441224   ⟹   XP_038297152
RefSeq Status:
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
ROS_Cfam_1.0299,417,267 - 9,455,907 (+)NCBI
RefSeq Acc Id: XM_038441225   ⟹   XP_038297153
RefSeq Status:
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
ROS_Cfam_1.0299,418,122 - 9,455,907 (+)NCBI
RefSeq Acc Id: XM_038441226   ⟹   XP_038297154
RefSeq Status:
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
ROS_Cfam_1.0299,417,335 - 9,455,907 (+)NCBI
RefSeq Acc Id: XM_038441227   ⟹   XP_038297155
RefSeq Status:
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
ROS_Cfam_1.0299,418,171 - 9,455,907 (+)NCBI
RefSeq Acc Id: XM_038441228   ⟹   XP_038297156
RefSeq Status:
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
ROS_Cfam_1.0299,417,267 - 9,455,907 (+)NCBI
RefSeq Acc Id: XM_038515801   ⟹   XP_038371729
RefSeq Status:
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UMICH_Zoey_3.1299,415,389 - 9,453,988 (+)NCBI
RefSeq Acc Id: XM_038515802   ⟹   XP_038371730
RefSeq Status:
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UMICH_Zoey_3.1299,416,236 - 9,453,988 (+)NCBI
RefSeq Acc Id: XM_038515803   ⟹   XP_038371731
RefSeq Status:
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UMICH_Zoey_3.1299,415,457 - 9,453,988 (+)NCBI
RefSeq Acc Id: XM_038515804   ⟹   XP_038371732
RefSeq Status:
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UMICH_Zoey_3.1299,416,285 - 9,453,988 (+)NCBI
RefSeq Acc Id: XM_038515805   ⟹   XP_038371733
RefSeq Status:
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UMICH_Zoey_3.1299,415,389 - 9,453,988 (+)NCBI
RefSeq Acc Id: XM_038579369   ⟹   XP_038435297
RefSeq Status:
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UU_Cfam_GSD_1.0299,820,349 - 9,859,247 (+)NCBI
RefSeq Acc Id: XM_038579370   ⟹   XP_038435298
RefSeq Status:
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UU_Cfam_GSD_1.0299,821,208 - 9,859,247 (+)NCBI
RefSeq Acc Id: XM_038579371   ⟹   XP_038435299
RefSeq Status:
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UU_Cfam_GSD_1.0299,820,415 - 9,859,247 (+)NCBI
RefSeq Acc Id: XM_038579372   ⟹   XP_038435300
RefSeq Status:
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UU_Cfam_GSD_1.0299,821,264 - 9,859,247 (+)NCBI
RefSeq Acc Id: XM_038579373   ⟹   XP_038435301
RefSeq Status:
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UU_Cfam_GSD_1.0299,820,349 - 9,859,247 (+)NCBI
RefSeq Acc Id: XM_038643612   ⟹   XP_038499540
RefSeq Status:
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UNSW_CanFamBas_1.0299,541,083 - 9,579,672 (+)NCBI
RefSeq Acc Id: XM_038643613   ⟹   XP_038499541
RefSeq Status:
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UNSW_CanFamBas_1.0299,541,937 - 9,579,672 (+)NCBI
RefSeq Acc Id: XM_038643615   ⟹   XP_038499543
RefSeq Status:
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UNSW_CanFamBas_1.0299,541,151 - 9,579,672 (+)NCBI
RefSeq Acc Id: XM_038643616   ⟹   XP_038499544
RefSeq Status:
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UNSW_CanFamBas_1.0299,541,986 - 9,579,672 (+)NCBI
RefSeq Acc Id: XM_038643617   ⟹   XP_038499545
RefSeq Status:
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UNSW_CanFamBas_1.0299,541,083 - 9,579,672 (+)NCBI
RefSeq Acc Id: XM_852382   ⟹   XP_857475
RefSeq Status:
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.1299,331,876 - 9,370,489 (+)NCBI
Dog10K_Boxer_Tasha299,644,617 - 9,683,238 (+)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: XP_005638060   ⟸   XM_005638003
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_857475   ⟸   XM_852382
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_013964724   ⟸   XM_014109249
- Peptide Label: isoform X2
- UniProtKB: F1PKR0 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_022268030   ⟸   XM_022412322
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_022268028   ⟸   XM_022412320
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_022268029   ⟸   XM_022412321
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_038371729   ⟸   XM_038515801
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038371733   ⟸   XM_038515805
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038371731   ⟸   XM_038515803
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038371730   ⟸   XM_038515802
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038371732   ⟸   XM_038515804
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038499540   ⟸   XM_038643612
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038499545   ⟸   XM_038643617
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038499543   ⟸   XM_038643615
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038499541   ⟸   XM_038643613
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038499544   ⟸   XM_038643616
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038297152   ⟸   XM_038441224
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038297156   ⟸   XM_038441228
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038297154   ⟸   XM_038441226
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038297153   ⟸   XM_038441225
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038297155   ⟸   XM_038441227
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038435297   ⟸   XM_038579369
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038435301   ⟸   XM_038579373
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038435299   ⟸   XM_038579371
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038435298   ⟸   XM_038579370
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038435300   ⟸   XM_038579372
- Peptide Label: isoform X1
Protein Domains
PDZ


Additional Information

Database Acc Id Source(s)
Ensembl Genes ENSCAFG00000007112 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSCAFP00000010554 ENTREZGENE, UniProtKB/TrEMBL
  ENSCAFP00000055244 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSCAFT00000011393 UniProtKB/TrEMBL
  ENSCAFT00000078722 UniProtKB/TrEMBL
Gene3D-CATH 2.30.42.10 UniProtKB/TrEMBL
InterPro PDZ UniProtKB/TrEMBL
  PDZ_6 UniProtKB/TrEMBL
  PDZ_sf UniProtKB/TrEMBL
  SDCBP UniProtKB/TrEMBL
KEGG Report cfa:482977 UniProtKB/TrEMBL
NCBI Gene SDCBP ENTREZGENE
PANTHER PTHR12345:SF10 UniProtKB/TrEMBL
Pfam PDZ UniProtKB/TrEMBL
  PDZ_6 UniProtKB/TrEMBL
PROSITE PDZ UniProtKB/TrEMBL
SMART PDZ UniProtKB/TrEMBL
Superfamily-SCOP SSF50156 UniProtKB/TrEMBL
UniProt A0A5F4CLT9_CANLF UniProtKB/TrEMBL
  F1PKR0 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2021-01-12 LOC482977  syndecan binding protein  SDCBP  syndecan binding protein  Symbol and/or name change 5135510 APPROVED