DEFB1 (defensin, beta 1) - Rat Genome Database

Send us a Message
Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Search RGD Grant Resources Citing RGD About Us Contact Us
Genes Variants Community Projects QTLs Strains Markers Genome Information Ontologies Cell Lines References Download Submit Data
OntoMate (Literature Search) JBrowse (Genome Browser) Synteny Browser (VCMap) Variant Visualizer Multi-Ontology Enrichment (MOET) Gene-Ortholog Location Finder (GOLF) InterViewer (Protein-Protein Interactions) PhenoMiner (Quatitative Phenotypes) Gene Annotator OLGA (Gene List Generator) AllianceMine GViewer (Genome Viewer)
Aging & Age-Related Disease Cancer & Neoplastic Disease Cardiovascular Disease Coronavirus Disease Developmental Disease Diabetes Hematologic Disease Immune & Inflammatory Disease Infectious Disease Liver Disease Neurological Disease Obesity & Metabolic Syndrome Renal Disease Respiratory Disease Sensory Organ Disease
Find Models   new Genetic Models Autism Models Rat PhenoMiner (Quantitative Phenotypes) Chinchilla PhenoMiner Expected Ranges (Quantitative Phenotype) PhenoMiner Term Comparison Hybrid Rat Diversity Panel Phenotypes Phenotypes in Other Animal Models Animal Husbandry Strain Medical Records Phylogenetics Strain Availability Calendar Rats 101 Submissions Photo Archive
Pathways
Rat Community Forum Directory of Rat Laboratories Video Tutorials News RGD Publications RGD Presentations Archive Nomenclature Guidelines Resource Links Laboratory Resources Employment Resources
Gene: DEFB1 (defensin, beta 1) Sus scrofa
Analyze
Symbol: DEFB1
Name: defensin, beta 1
RGD ID: 13875150
Description: ENCODES a protein that exhibits CCR6 chemokine receptor binding (ortholog); identical protein binding (ortholog); phosphatidylinositol-4,5-bisphosphate binding (ortholog); INVOLVED IN antifungal innate immune response (ortholog); antimicrobial humoral immune response mediated by antimicrobial peptide (ortholog); cAMP-mediated signaling (ortholog); ASSOCIATED WITH bacterial pneumonia (ortholog); common cold (ortholog); cystic fibrosis (ortholog); FOUND IN membrane (ortholog); microvesicle (ortholog); sperm midpiece (ortholog)
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: BD-1; beta-defensin 1; PBD-1; PBD1; prepro-beta-defensin 1
RGD Orthologs
Human
Mouse
Rat
Dog
Alliance Genes
More Info more info ...
Latest Assembly: Sscrofa11.1 - Pig Sscrofa11.1 Assembly
Position:
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1538,076,057 - 38,077,899 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11538,076,057 - 38,077,899 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Pig Cytomap15q14-q15.1NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

References
Additional References at PubMed
PMID:9537511   PMID:10446172   PMID:16552064   PMID:22301074   PMID:23065293   PMID:23220638   PMID:30032202  


Genomics

Comparative Map Data
DEFB1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1538,076,057 - 38,077,899 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11538,076,057 - 38,077,899 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Pig Cytomap15q14-q15.1NCBI
DEFB4A
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh3887,894,677 - 7,896,716 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl87,894,677 - 7,896,716 (+)EnsemblGRCh38hg38GRCh38
GRCh38.p14 Ensembl87,414,855 - 7,416,863 (-)EnsemblGRCh38hg38GRCh38
GRCh3787,752,199 - 7,754,238 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 3687,789,609 - 7,791,647 (+)NCBINCBI36Build 36hg18NCBI36
Build 3487,789,608 - 7,791,647NCBI
Cytogenetic Map8p23.1NCBI
CHM1_187,817,857 - 7,819,910 (+)NCBICHM1_1
T2T-CHM13v2.0812,040,687 - 12,042,691 (+)NCBIT2T-CHM13v2.0
Defb4
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39819,248,720 - 19,251,563 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl819,248,722 - 19,251,561 (+)EnsemblGRCm39 Ensembl
GRCm38819,198,704 - 19,201,547 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl819,198,706 - 19,201,545 (+)EnsemblGRCm38mm10GRCm38
MGSCv37819,198,704 - 19,201,547 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36819,198,683 - 19,201,522 (+)NCBIMGSCv36mm8
Celera819,322,586 - 19,325,383 (+)NCBICelera
Cytogenetic Map8A1.3NCBI
cM Map810.35NCBI
Defb4
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81677,352,911 - 77,356,104 (-)NCBIGRCr8
mRatBN7.21670,650,472 - 70,653,665 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1670,650,472 - 70,653,665 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1675,927,305 - 75,930,496 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01679,390,193 - 79,393,646 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01674,639,631 - 74,643,084 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01675,634,598 - 75,637,789 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1675,634,598 - 75,637,789 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01675,234,830 - 75,238,021 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41675,442,005 - 75,445,196NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera1668,518,128 - 68,521,319 (-)NCBICelera
Cytogenetic Map16q12.5NCBI
DEFB4A
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11658,953,916 - 58,956,407 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1658,953,916 - 58,956,407 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1654,479,009 - 54,481,500 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.01657,091,988 - 57,094,475 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl1657,091,965 - 57,094,519 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.11659,114,878 - 59,117,361 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01655,100,644 - 55,103,128 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01655,475,309 - 55,477,794 (+)NCBIUU_Cfam_GSD_1.0

Variants

.
Variants in DEFB1
43 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 nervous system reproductive system respiratory system
High
Medium 1 1
Low 2 1 5 1
Below cutoff 1 1 2 1 7

Sequence


Reference Sequences
RefSeq Acc Id: ENSSSCT00000024650   ⟹   ENSSSCP00000025388
Type: CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.1 Ensembl1538,076,057 - 38,077,899 (+)Ensembl
RefSeq Acc Id: NM_213838   ⟹   NP_999003
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.11538,076,057 - 38,077,899 (+)NCBI
Sequence:
Reference Protein Sequences
RefSeq Acc Id: NP_999003   ⟸   NM_213838
- Peptide Label: precursor
- UniProtKB: O62697 (UniProtKB/Swiss-Prot),   H9ZGM8 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSSSCP00000025388   ⟸   ENSSSCT00000024650
Protein Domains
Beta/alpha-defensin C-terminal


Additional Information

Database Acc Id Source(s)
Ensembl Genes ENSSSCG00000027555 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
  ENSSSCG00005003519 UniProtKB/Swiss-Prot
  ENSSSCG00015031725 UniProtKB/Swiss-Prot
  ENSSSCG00025002275 UniProtKB/Swiss-Prot
  ENSSSCG00030041522 UniProtKB/Swiss-Prot
  ENSSSCG00035029032 UniProtKB/Swiss-Prot
  ENSSSCG00040064278 UniProtKB/Swiss-Prot
  ENSSSCG00045005153 UniProtKB/Swiss-Prot
  ENSSSCG00050075098 UniProtKB/Swiss-Prot
  ENSSSCG00055000810 UniProtKB/Swiss-Prot
  ENSSSCG00060011864 UniProtKB/Swiss-Prot
  ENSSSCG00065005920 UniProtKB/Swiss-Prot
  ENSSSCG00070027368 UniProtKB/Swiss-Prot
Ensembl Transcript ENSSSCT00000024650 ENTREZGENE
  ENSSSCT00000024650.4 UniProtKB/Swiss-Prot
  ENSSSCT00005005133.1 UniProtKB/Swiss-Prot
  ENSSSCT00015042039.1 UniProtKB/Swiss-Prot
  ENSSSCT00025002948.1 UniProtKB/Swiss-Prot
  ENSSSCT00030057697.1 UniProtKB/Swiss-Prot
  ENSSSCT00035038414.1 UniProtKB/Swiss-Prot
  ENSSSCT00040087755.1 UniProtKB/Swiss-Prot
  ENSSSCT00045008563.1 UniProtKB/Swiss-Prot
  ENSSSCT00050102899.1 UniProtKB/Swiss-Prot
  ENSSSCT00055001408.1 UniProtKB/Swiss-Prot
  ENSSSCT00060015496.1 UniProtKB/Swiss-Prot
  ENSSSCT00065007949.1 UniProtKB/Swiss-Prot
  ENSSSCT00070054902.1 UniProtKB/Swiss-Prot
InterPro Defensin_beta-typ UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Defensin_beta/alpha UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report ssc:396819 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
NCBI Gene DEFB1 ENTREZGENE
PANTHER BETA-DEFENSIN UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  BETA-DEFENSIN 4A UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam Defensin_beta UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART DEFSN UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP Defensin-like UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt DEFB1_PIG UniProtKB/Swiss-Prot
  H9ZGM8 ENTREZGENE, UniProtKB/TrEMBL
  O62697 ENTREZGENE