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

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Gene: SNED1 (sushi, nidogen and EGF like domains 1) Pan paniscus
Analyze
Symbol: SNED1
Name: sushi, nidogen and EGF like domains 1
RGD ID: 11707592
Description: ENCODES a protein that exhibits calcium ion binding (inferred); Notch binding (inferred); INVOLVED IN cell-matrix adhesion (inferred); negative regulation of Notch signaling pathway (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); plasma membrane (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
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: Mhudiblu_PPA_v0 - Bonobo Mhudiblu_PPA_v0 Assembly
Position:
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
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   PMID:30032202  


Genomics

Comparative Map Data
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
(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
(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
(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
(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


Sequence

Nucleotide Sequences
RefSeq Transcripts XM_034955554 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_034955555 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_055109304 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_063595630 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_063595631 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_063595632 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_063595633 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_063595634 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_063595635 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_063595636 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_063595637 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_063595638 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_063595639 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_063595640 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_063595641 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_063595642 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_063595643 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_004670376 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_004670377 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_004670378 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_010109558 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_010109559 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_010109560 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_010109561 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide JARIFH020000013 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSPPAT00000051534   ⟹   ENSPPAP00000028686
Type: CODING
Position:
Bonobo AssemblyChrPosition (strand)Source
PanPan1.1 Ensembl2B247,085,509 - 247,144,421 (+)Ensembl
RefSeq Acc Id: XM_034955554   ⟹   XP_034811445
Type: CODING
Position:
Bonobo AssemblyChrPosition (strand)Source
NHGRI_mPanPan1-v213143,684,201 - 143,785,268 (+)NCBI
NHGRI_mPanPan12B143,699,367 - 143,797,822 (+)NCBI
Mhudiblu_PPA_v02B128,253,903 - 128,351,819 (+)NCBI
RefSeq Acc Id: XM_034955555   ⟹   XP_034811446
Type: CODING
Position:
Bonobo AssemblyChrPosition (strand)Source
NHGRI_mPanPan1-v213143,684,203 - 143,785,268 (+)NCBI
NHGRI_mPanPan12B143,699,367 - 143,797,822 (+)NCBI
Mhudiblu_PPA_v02B128,253,888 - 128,351,819 (+)NCBI
RefSeq Acc Id: XM_055109304   ⟹   XP_054965279
Type: CODING
Position:
Bonobo AssemblyChrPosition (strand)Source
NHGRI_mPanPan1-v213143,684,198 - 143,780,461 (+)NCBI
NHGRI_mPanPan12B143,699,366 - 143,793,211 (+)NCBI
RefSeq Acc Id: XM_063595630   ⟹   XP_063451700
Type: CODING
Position:
Bonobo AssemblyChrPosition (strand)Source
NHGRI_mPanPan1-v213143,684,196 - 143,780,461 (+)NCBI
RefSeq Acc Id: XM_063595631   ⟹   XP_063451701
Type: CODING
Position:
Bonobo AssemblyChrPosition (strand)Source
NHGRI_mPanPan1-v213143,684,199 - 143,785,268 (+)NCBI
RefSeq Acc Id: XM_063595632   ⟹   XP_063451702
Type: CODING
Position:
Bonobo AssemblyChrPosition (strand)Source
NHGRI_mPanPan1-v213143,684,196 - 143,780,461 (+)NCBI
RefSeq Acc Id: XM_063595633   ⟹   XP_063451703
Type: CODING
Position:
Bonobo AssemblyChrPosition (strand)Source
NHGRI_mPanPan1-v213143,684,200 - 143,785,268 (+)NCBI
RefSeq Acc Id: XM_063595634   ⟹   XP_063451704
Type: CODING
Position:
Bonobo AssemblyChrPosition (strand)Source
NHGRI_mPanPan1-v213143,684,196 - 143,780,461 (+)NCBI
RefSeq Acc Id: XM_063595635   ⟹   XP_063451705
Type: CODING
Position:
Bonobo AssemblyChrPosition (strand)Source
NHGRI_mPanPan1-v213143,684,196 - 143,780,461 (+)NCBI
RefSeq Acc Id: XM_063595636   ⟹   XP_063451706
Type: CODING
Position:
Bonobo AssemblyChrPosition (strand)Source
NHGRI_mPanPan1-v213143,684,196 - 143,780,461 (+)NCBI
RefSeq Acc Id: XM_063595637   ⟹   XP_063451707
Type: CODING
Position:
Bonobo AssemblyChrPosition (strand)Source
NHGRI_mPanPan1-v213143,684,201 - 143,785,268 (+)NCBI
RefSeq Acc Id: XM_063595638   ⟹   XP_063451708
Type: CODING
Position:
Bonobo AssemblyChrPosition (strand)Source
NHGRI_mPanPan1-v213143,684,197 - 143,780,461 (+)NCBI
RefSeq Acc Id: XM_063595639   ⟹   XP_063451709
Type: CODING
Position:
Bonobo AssemblyChrPosition (strand)Source
NHGRI_mPanPan1-v213143,684,196 - 143,780,461 (+)NCBI
RefSeq Acc Id: XM_063595640   ⟹   XP_063451710
Type: CODING
Position:
Bonobo AssemblyChrPosition (strand)Source
NHGRI_mPanPan1-v213143,684,203 - 143,785,268 (+)NCBI
RefSeq Acc Id: XM_063595641   ⟹   XP_063451711
Type: CODING
Position:
Bonobo AssemblyChrPosition (strand)Source
NHGRI_mPanPan1-v213143,684,196 - 143,769,752 (+)NCBI
RefSeq Acc Id: XM_063595642   ⟹   XP_063451712
Type: CODING
Position:
Bonobo AssemblyChrPosition (strand)Source
NHGRI_mPanPan1-v213143,684,198 - 143,769,752 (+)NCBI
RefSeq Acc Id: XM_063595643   ⟹   XP_063451713
Type: CODING
Position:
Bonobo AssemblyChrPosition (strand)Source
NHGRI_mPanPan1-v213143,683,163 - 143,780,461 (+)NCBI
RefSeq Acc Id: XR_004670377
Type: NON-CODING
Position:
Bonobo AssemblyChrPosition (strand)Source
NHGRI_mPanPan1-v213143,684,198 - 143,777,207 (+)NCBI
NHGRI_mPanPan12B143,699,366 - 143,792,172 (+)NCBI
Mhudiblu_PPA_v02B128,253,888 - 128,340,598 (+)NCBI
RefSeq Acc Id: XR_004670378
Type: NON-CODING
Position:
Bonobo AssemblyChrPosition (strand)Source
NHGRI_mPanPan1-v213143,684,190 - 143,761,498 (+)NCBI
NHGRI_mPanPan12B143,699,363 - 143,776,462 (+)NCBI
Mhudiblu_PPA_v02B128,253,888 - 128,330,513 (+)NCBI
RefSeq Acc Id: XR_010109558
Type: NON-CODING
Position:
Bonobo AssemblyChrPosition (strand)Source
NHGRI_mPanPan1-v213143,684,196 - 143,772,036 (+)NCBI
RefSeq Acc Id: XR_010109559
Type: NON-CODING
Position:
Bonobo AssemblyChrPosition (strand)Source
NHGRI_mPanPan1-v213143,684,196 - 143,777,207 (+)NCBI
RefSeq Acc Id: XR_010109560
Type: NON-CODING
Position:
Bonobo AssemblyChrPosition (strand)Source
NHGRI_mPanPan1-v213143,684,196 - 143,772,036 (+)NCBI
RefSeq Acc Id: XR_010109561
Type: NON-CODING
Position:
Bonobo AssemblyChrPosition (strand)Source
NHGRI_mPanPan1-v213143,684,198 - 143,772,036 (+)NCBI
Reference Protein Sequences
RefSeq Acc Id: XP_034811446   ⟸   XM_034955555
- Peptide Label: isoform X9
- UniProtKB: A0A2R9BPX2 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_034811445   ⟸   XM_034955554
- Peptide Label: isoform X6
- UniProtKB: A0A2R9BPX2 (UniProtKB/TrEMBL)
RefSeq Acc Id: ENSPPAP00000028686   ⟸   ENSPPAT00000051534
RefSeq Acc Id: XP_054965279   ⟸   XM_055109304
- Peptide Label: isoform X5
RefSeq Acc Id: XP_063451713   ⟸   XM_063595643
- Peptide Label: isoform X17
RefSeq Acc Id: XP_063451700   ⟸   XM_063595630
- Peptide Label: isoform X1
RefSeq Acc Id: XP_063451704   ⟸   XM_063595634
- Peptide Label: isoform X7
RefSeq Acc Id: XP_063451705   ⟸   XM_063595635
- Peptide Label: isoform X8
RefSeq Acc Id: XP_063451709   ⟸   XM_063595639
- Peptide Label: isoform X13
RefSeq Acc Id: XP_063451702   ⟸   XM_063595632
- Peptide Label: isoform X3
RefSeq Acc Id: XP_063451706   ⟸   XM_063595636
- Peptide Label: isoform X10
RefSeq Acc Id: XP_063451711   ⟸   XM_063595641
- Peptide Label: isoform X15
RefSeq Acc Id: XP_063451708   ⟸   XM_063595638
- Peptide Label: isoform X12
RefSeq Acc Id: XP_063451712   ⟸   XM_063595642
- Peptide Label: isoform X16
RefSeq Acc Id: XP_063451701   ⟸   XM_063595631
- Peptide Label: isoform X2
RefSeq Acc Id: XP_063451703   ⟸   XM_063595633
- Peptide Label: isoform X4
RefSeq Acc Id: XP_063451707   ⟸   XM_063595637
- Peptide Label: isoform X11
RefSeq Acc Id: XP_063451710   ⟸   XM_063595640
- Peptide Label: isoform X14
Protein Domains
EGF-like   Fibronectin type-III   NIDO   Sushi


Additional Information

Database Acc Id Source(s)
Ensembl Genes ENSPPAG00000037340 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSPPAT00000051534.1 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 NEUROGENIC LOCUS PROTEIN DELTA UniProtKB/TrEMBL
  NOTCH LIGAND FAMILY MEMBER 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 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 A0A2R9BPX2 ENTREZGENE, UniProtKB/TrEMBL