SNED1 (sushi, nidogen and EGF like domains 1) - Rat Genome Database

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Gene: SNED1 (sushi, nidogen and EGF like domains 1) Chlorocebus sabaeus
Analyze
Symbol: SNED1
Name: sushi, nidogen and EGF like domains 1
RGD ID: 18402531
Description: ENCODES a protein that exhibits calcium ion binding (inferred); Notch binding (inferred); INVOLVED IN cell-matrix adhesion (inferred); Notch signaling pathway (inferred); ASSOCIATED WITH Bethlem Myopathy 1A (ortholog); chromosome 2q37 deletion syndrome (ortholog); D-2-hydroxyglutaric aciduria 1 (ortholog); FOUND IN extracellular matrix (inferred)
Type: protein-coding
RefSeq Status: MODEL
Previously known as: sushi, nidogen and EGF-like domain-containing protein 1
RGD Orthologs
Human
Mouse
Rat
Chinchilla
Bonobo
Dog
Squirrel
Pig
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: ChlSab1.1 - Green Monkey 1.1 Assembly
Position:
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.110127,058,188 - 127,142,945 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl10127,058,358 - 127,138,704 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366604072,239,399 - 72,327,431 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Function

References
Additional References at PubMed
PMID:22301074  


Genomics

Comparative Map Data
SNED1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.110127,058,188 - 127,142,945 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl10127,058,358 - 127,138,704 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366604072,239,399 - 72,327,431 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
SNED1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh382240,997,650 - 241,095,568 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl2240,998,618 - 241,095,568 (+)EnsemblGRCh38hg38GRCh38
GRCh372241,938,035 - 242,034,983 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 362241,586,928 - 241,682,316 (+)NCBINCBI36Build 36hg18NCBI36
Celera2235,639,389 - 235,703,345 (+)NCBICelera
Cytogenetic Map2q37.3NCBI
HuRef2233,693,935 - 233,789,651 (+)NCBIHuRef
CHM1_12241,941,955 - 242,039,698 (+)NCBICHM1_1
T2T-CHM13v2.02241,496,555 - 241,594,674 (+)NCBIT2T-CHM13v2.0
Sned1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39193,163,563 - 93,228,787 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl193,163,563 - 93,228,787 (+)EnsemblGRCm39 Ensembl
GRCm38193,235,796 - 93,301,065 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl193,235,841 - 93,301,065 (+)EnsemblGRCm38mm10GRCm38
MGSCv37195,132,474 - 95,193,025 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36195,066,247 - 95,131,471 (+)NCBIMGSCv36mm8
Celera196,180,585 - 96,241,119 (+)NCBICelera
Cytogenetic Map1DNCBI
cM Map147.21NCBI
Sned1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr89101,221,497 - 101,281,401 (+)NCBIGRCr8
mRatBN7.2993,774,087 - 93,834,003 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl993,774,119 - 93,830,694 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx9102,209,684 - 102,266,255 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.09107,345,440 - 107,402,056 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.09105,701,582 - 105,758,198 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.09100,380,487 - 100,439,125 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl9100,380,515 - 100,437,056 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.09100,037,552 - 100,095,480 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4992,509,499 - 92,568,597 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera991,309,255 - 91,365,649 (+)NCBICelera
Cytogenetic Map9q36NCBI
Sned1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_004955542589,746 - 627,519 (-)EnsemblChiLan1.0
ChiLan1.0NW_004955542587,159 - 628,159 (-)NCBIChiLan1.0ChiLan1.0
SNED1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v213143,683,163 - 143,785,268 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan12B143,698,173 - 143,797,822 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v02B128,253,888 - 128,351,819 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.12B247,067,282 - 247,149,093 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2B247,085,509 - 247,144,421 (+)Ensemblpanpan1.1panPan2
SNED1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12551,057,358 - 51,139,808 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2551,057,376 - 51,135,412 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2551,270,707 - 51,351,866 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.02551,252,472 - 51,333,679 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2551,252,316 - 51,330,535 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12551,100,189 - 51,181,355 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02550,839,827 - 50,920,931 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02551,115,989 - 51,197,175 (+)NCBIUU_Cfam_GSD_1.0
Sned1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405303192,442,944 - 192,509,852 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_004936745714,368 - 776,355 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_004936745709,446 - 761,932 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SNED1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl15139,821,062 - 139,881,095 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.115139,821,021 - 139,881,099 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.215154,937,025 - 154,997,243 (+)NCBISscrofa10.2Sscrofa10.2susScr3
Sned1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248475,147,008 - 5,202,666 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046248475,146,973 - 5,207,481 (+)NCBIHetGla_female_1.0HetGla 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

endocrine system hemolymphoid system nervous system
High
Medium 34 27
Low 2 14 33
Below cutoff 6

Sequence

Nucleotide Sequences
RefSeq Transcripts XM_007966955 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_007966956 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_007966957 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_007966958 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_007966960 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_007966961 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_007966962 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_007966963 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_007966964 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_007966965 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_007966966 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_038000606 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_038000608 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_005241188 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_005241189 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_005241190 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide JACDXN010000008 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSCSAT00000003884   ⟹   ENSCSAP00000002156
Type: CODING
Position:
Green Monkey AssemblyChrPosition (strand)Source
ChlSab1.1 Ensembl10127,058,358 - 127,138,704 (+)Ensembl
RefSeq Acc Id: XM_007966961   ⟹   XP_007965152
Type: CODING
Position:
Green Monkey AssemblyChrPosition (strand)Source
ChlSab1.110127,058,199 - 127,142,945 (+)NCBI
Vero_WHO_p1.0NW_02366604072,239,399 - 72,327,107 (-)NCBI
Sequence:
RefSeq Acc Id: XM_038000606   ⟹   XP_037856534
Type: CODING
Position:
Green Monkey AssemblyChrPosition (strand)Source
Vero_WHO_p1.0NW_02366604072,243,319 - 72,327,107 (-)NCBI
RefSeq Acc Id: XM_038000608   ⟹   XP_037856536
Type: CODING
Position:
Green Monkey AssemblyChrPosition (strand)Source
Vero_WHO_p1.0NW_02366604072,243,319 - 72,327,107 (-)NCBI
RefSeq Acc Id: XR_005241188
Type: NON-CODING
Position:
Green Monkey AssemblyChrPosition (strand)Source
Vero_WHO_p1.0NW_02366604072,244,325 - 72,327,431 (-)NCBI
RefSeq Acc Id: XR_005241189
Type: NON-CODING
Position:
Green Monkey AssemblyChrPosition (strand)Source
Vero_WHO_p1.0NW_02366604072,244,325 - 72,327,431 (-)NCBI
RefSeq Acc Id: XR_005241190
Type: NON-CODING
Position:
Green Monkey AssemblyChrPosition (strand)Source
Vero_WHO_p1.0NW_02366604072,248,969 - 72,327,431 (-)NCBI
Protein Sequences
Protein RefSeqs XP_007965152 (Get FASTA)   NCBI Sequence Viewer  
  XP_037856534 (Get FASTA)   NCBI Sequence Viewer  
  XP_037856536 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSCSAP00000002156.1
Reference Protein Sequences
RefSeq Acc Id: XP_007965152   ⟸   XM_007966961
- UniProtKB: A0A0D9R0L7 (UniProtKB/TrEMBL)
RefSeq Acc Id: ENSCSAP00000002156   ⟸   ENSCSAT00000003884
RefSeq Acc Id: XP_037856536   ⟸   XM_038000608
- UniProtKB: A0A0D9R0L7 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_037856534   ⟸   XM_038000606
- UniProtKB: A0A0D9R0L7 (UniProtKB/TrEMBL)


Additional Information

Database Acc Id Source(s)
Ensembl Genes ENSCSAG00000005891 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSCSAT00000003884.1 UniProtKB/TrEMBL
Gene3D-CATH 2.60.40.10 UniProtKB/TrEMBL
  Laminin UniProtKB/TrEMBL
InterPro EGF-like_Ca-bd_dom UniProtKB/TrEMBL
  EGF-like_CS UniProtKB/TrEMBL
  EGF-like_dom UniProtKB/TrEMBL
  EGF-type_Asp/Asn_hydroxyl_site UniProtKB/TrEMBL
  EGF_Ca-bd_CS UniProtKB/TrEMBL
  FN3_dom UniProtKB/TrEMBL
  FN3_sf UniProtKB/TrEMBL
  Growth_fac_rcpt_cys_sf UniProtKB/TrEMBL
  Ig-like_fold UniProtKB/TrEMBL
  NIDO_dom UniProtKB/TrEMBL
  Sushi/SCR/CCP_sf UniProtKB/TrEMBL
  Sushi_SCR_CCP_dom UniProtKB/TrEMBL
NCBI Gene SNED1 ENTREZGENE
PANTHER CYTOCHROME C OXIDASE POLYPEPTIDE VIC-2 UniProtKB/TrEMBL
  NEUROGENIC LOCUS NOTCH HOMOLOG PROTEIN 1-RELATED UniProtKB/TrEMBL
Pfam EGF UniProtKB/TrEMBL
  fn3 UniProtKB/TrEMBL
  hEGF UniProtKB/TrEMBL
  NIDO UniProtKB/TrEMBL
PRINTS EGFBLOOD UniProtKB/TrEMBL
PROSITE ASX_HYDROXYL UniProtKB/TrEMBL
  EGF_1 UniProtKB/TrEMBL
  EGF_2 UniProtKB/TrEMBL
  EGF_3 UniProtKB/TrEMBL
  EGF_CA UniProtKB/TrEMBL
  FN3 UniProtKB/TrEMBL
  NIDO UniProtKB/TrEMBL
  SUSHI UniProtKB/TrEMBL
SMART CCP UniProtKB/TrEMBL
  EGF UniProtKB/TrEMBL
  EGF_CA UniProtKB/TrEMBL
  FN3 UniProtKB/TrEMBL
  NIDO UniProtKB/TrEMBL
Superfamily-SCOP EGF/Laminin UniProtKB/TrEMBL
  SSF49265 UniProtKB/TrEMBL
  SSF57184 UniProtKB/TrEMBL
  SSF57535 UniProtKB/TrEMBL
UniProt A0A0D9R0L7 ENTREZGENE, UniProtKB/TrEMBL