NID1 (nidogen 1) - Rat Genome Database

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Gene: NID1 (nidogen 1) Sus scrofa
Analyze
Symbol: NID1
Name: nidogen 1
RGD ID: 13883208
Description: ENCODES a protein that exhibits calcium ion binding (inferred); collagen binding (inferred); extracellular matrix binding (inferred); INVOLVED IN cell-matrix adhesion (ortholog); extracellular matrix organization (ortholog); glomerular basement membrane development (ortholog); ASSOCIATED WITH common variable immunodeficiency 14 (ortholog); Experimental Liver Cirrhosis (ortholog); gastrointestinal stromal tumor (ortholog); FOUND IN basement membrane (inferred); cell periphery (inferred); extracellular matrix (inferred)
Type: protein-coding
RefSeq Status: MODEL
Previously known as: nidogen-1
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
Sscrofa11.1 Ensembl1455,239,577 - 55,390,782 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11455,239,327 - 55,346,948 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21459,435,378 - 59,454,804 (+)NCBISscrofa10.2Sscrofa10.2susScr3
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

References
Additional References at PubMed
PMID:14681463   PMID:17145712   PMID:22301074  


Genomics

Comparative Map Data
NID1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1455,239,577 - 55,390,782 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11455,239,327 - 55,346,948 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21459,435,378 - 59,454,804 (+)NCBISscrofa10.2Sscrofa10.2susScr3
NID1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381235,975,830 - 236,065,090 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1235,975,830 - 236,065,109 (-)EnsemblGRCh38hg38GRCh38
GRCh371236,139,130 - 236,228,390 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361234,205,753 - 234,295,104 (-)NCBINCBI36Build 36hg18NCBI36
Build 341232,466,151 - 232,554,503NCBI
Celera1209,382,414 - 209,471,741 (-)NCBICelera
Cytogenetic Map1q42.3NCBI
HuRef1206,590,270 - 206,679,579 (-)NCBIHuRef
CHM1_11237,411,406 - 237,500,740 (-)NCBICHM1_1
T2T-CHM13v2.01235,372,074 - 235,461,403 (-)NCBIT2T-CHM13v2.0
Nid1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391313,612,252 - 13,686,849 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1313,612,136 - 13,686,854 (+)EnsemblGRCm39 Ensembl
GRCm381313,437,602 - 13,512,275 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1313,437,551 - 13,512,269 (+)EnsemblGRCm38mm10GRCm38
MGSCv371313,529,869 - 13,604,542 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361312,880,801 - 12,929,308 (+)NCBIMGSCv36mm8
MGSCv361313,229,817 - 13,304,390 (+)NCBIMGSCv36mm8
Celera1313,574,663 - 13,580,605 (+)NCBICelera
Cytogenetic Map13A1NCBI
cM Map135.26NCBI
Nid1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81793,069,013 - 93,142,416 (+)NCBIGRCr8
mRatBN7.21786,085,133 - 86,158,272 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1786,085,077 - 86,158,267 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1790,329,167 - 90,402,263 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01794,165,066 - 94,238,159 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01788,181,572 - 88,254,677 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01790,553,161 - 90,627,133 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1790,553,394 - 90,627,101 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01792,213,995 - 92,287,999 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41766,857,529 - 66,930,273 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11766,907,493 - 66,916,781 (-)NCBI
Celera1785,451,906 - 85,525,217 (-)NCBICelera
Cytogenetic Map17q12.3NCBI
Nid1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554924,014,912 - 4,096,829 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554924,014,912 - 4,096,659 (+)NCBIChiLan1.0ChiLan1.0
NID1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2113,114,692 - 13,203,241 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1113,326,559 - 13,415,078 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01211,543,294 - 211,631,769 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11216,544,821 - 216,632,935 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1216,544,829 - 216,632,935 (-)Ensemblpanpan1.1panPan2
NID1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.143,935,218 - 4,018,133 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl43,935,223 - 4,017,300 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha43,981,575 - 4,064,476 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.043,955,978 - 4,038,945 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl43,955,982 - 4,038,935 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.143,968,163 - 4,051,014 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.044,085,771 - 4,168,637 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.044,306,838 - 4,389,727 (+)NCBIUU_Cfam_GSD_1.0
Nid1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440934440,456,408 - 40,526,088 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_00493648416,621,601 - 16,691,313 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_00493648416,621,666 - 16,691,304 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
NID1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12573,130,966 - 73,227,385 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl2573,130,448 - 73,227,349 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366605575,181,369 - 75,276,675 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Nid1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462477514,486,145 - 14,563,447 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462477514,486,357 - 14,563,341 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in NID1
3401 total Variants

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 5 4 4 2 2 2
Low 5 3 1 23 1 3
Below cutoff

Sequence


RefSeq Acc Id: ENSSSCT00000011114   ⟹   ENSSSCP00000010826
Type: CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.1 Ensembl1455,239,653 - 55,346,937 (+)Ensembl
RefSeq Acc Id: ENSSSCT00000028752   ⟹   ENSSSCP00000024343
Type: CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.1 Ensembl1455,239,577 - 55,344,036 (+)Ensembl
RefSeq Acc Id: ENSSSCT00000039059   ⟹   ENSSSCP00000057861
Type: CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.1 Ensembl1455,239,577 - 55,390,782 (+)Ensembl
RefSeq Acc Id: XM_021073758   ⟹   XP_020929417
Type: CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.11455,239,327 - 55,346,948 (+)NCBI
Sequence:
RefSeq Acc Id: XM_021073759   ⟹   XP_020929418
Type: CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.11455,239,329 - 55,346,948 (+)NCBI
Sequence:
Protein Sequences
Protein RefSeqs XP_020929417 (Get FASTA)   NCBI Sequence Viewer  
  XP_020929418 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSSSCP00000010826
  ENSSSCP00000010826.4
  ENSSSCP00000024343.4
  ENSSSCP00000057861.2
  ENSSSCP00070029311.1
RefSeq Acc Id: XP_020929417   ⟸   XM_021073758
- Peptide Label: isoform X1
- UniProtKB: A0A4X1UL11 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_020929418   ⟸   XM_021073759
- Peptide Label: isoform X2
- UniProtKB: A0A4X1UL11 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSSSCP00000057861   ⟸   ENSSSCT00000039059
RefSeq Acc Id: ENSSSCP00000010826   ⟸   ENSSSCT00000011114
RefSeq Acc Id: ENSSSCP00000024343   ⟸   ENSSSCT00000028752

Additional Information

Database Acc Id Source(s)
Ensembl Genes ENSSSCG00000026819 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
  ENSSSCG00070017750 UniProtKB/TrEMBL
Ensembl Transcript ENSSSCT00000011114 ENTREZGENE
  ENSSSCT00000011114.5 UniProtKB/TrEMBL
  ENSSSCT00000028752.4 UniProtKB/TrEMBL
  ENSSSCT00000039059.3 UniProtKB/TrEMBL
  ENSSSCT00070035088.1 UniProtKB/TrEMBL
Gene3D-CATH 2.120.10.30 UniProtKB/TrEMBL
  2.40.155.10 UniProtKB/TrEMBL
  4.10.800.10 UniProtKB/TrEMBL
  Laminin UniProtKB/TrEMBL
InterPro 6-blade_b-propeller_TolB-like UniProtKB/TrEMBL
  cEGF UniProtKB/TrEMBL
  EGF-like_Ca-bd_dom UniProtKB/TrEMBL
  EGF-like_dom UniProtKB/TrEMBL
  EGF-type_Asp/Asn_hydroxyl_site UniProtKB/TrEMBL
  EGF_Ca-bd_CS UniProtKB/TrEMBL
  EGF_dom UniProtKB/TrEMBL
  G2_nidogen/fibulin_G2F UniProtKB/TrEMBL
  GFP UniProtKB/TrEMBL
  Growth_fac_rcpt_cys_sf UniProtKB/TrEMBL
  LDLR_classB_rpt UniProtKB/TrEMBL
  NIDO_dom UniProtKB/TrEMBL
  Thyroglobulin_1 UniProtKB/TrEMBL
  Thyroglobulin_1_sf UniProtKB/TrEMBL
NCBI Gene NID1 ENTREZGENE
PANTHER NIDOGEN-1 UniProtKB/TrEMBL
  VITELLOGENIN RECEPTOR-LIKE PROTEIN-RELATED-RELATED UniProtKB/TrEMBL
Pfam cEGF UniProtKB/TrEMBL
  EGF_3 UniProtKB/TrEMBL
  EGF_CA UniProtKB/TrEMBL
  FXa_inhibition UniProtKB/TrEMBL
  G2F UniProtKB/TrEMBL
  Ldl_recept_b UniProtKB/TrEMBL
  NIDO UniProtKB/TrEMBL
  Thyroglobulin_1 UniProtKB/TrEMBL
PROSITE ASX_HYDROXYL UniProtKB/TrEMBL
  EGF_2 UniProtKB/TrEMBL
  EGF_3 UniProtKB/TrEMBL
  EGF_CA UniProtKB/TrEMBL
  LDLRB UniProtKB/TrEMBL
  NIDO UniProtKB/TrEMBL
  NIDOGEN_G2 UniProtKB/TrEMBL
  THYROGLOBULIN_1_1 UniProtKB/TrEMBL
  THYROGLOBULIN_1_2 UniProtKB/TrEMBL
SMART EGF UniProtKB/TrEMBL
  EGF_CA UniProtKB/TrEMBL
  G2F UniProtKB/TrEMBL
  NIDO UniProtKB/TrEMBL
  SM00135 UniProtKB/TrEMBL
  SM00211 UniProtKB/TrEMBL
Superfamily-SCOP EGF/Laminin UniProtKB/TrEMBL
  SSF54511 UniProtKB/TrEMBL
  SSF57184 UniProtKB/TrEMBL
  SSF57610 UniProtKB/TrEMBL
  YWTD domain UniProtKB/TrEMBL
UniProt A0A287BMX9_PIG UniProtKB/TrEMBL
  A0A4X1UL11 ENTREZGENE, UniProtKB/TrEMBL
  F1RGY5_PIG UniProtKB/TrEMBL
  I3LJT1_PIG UniProtKB/TrEMBL
VGNC ID VGNC:90742 ENTREZGENE