LOC100522887 (caspase-13) - Rat Genome Database

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Gene: LOC100522887 (caspase-13) Sus scrofa
Analyze
Symbol: LOC100522887
Name: caspase-13
RGD ID: 14203920
Description: ENCODES a protein that exhibits CARD domain binding (ortholog); lipid binding (ortholog); lipopolysaccharide binding (ortholog); INVOLVED IN cellular response to amyloid-beta (ortholog); defense response to bacterium (ortholog); defense response to Gram-positive bacterium (ortholog); ASSOCIATED WITH ataxia telangiectasia (ortholog); Chromosome 11, Partial Trisomy 11q (ortholog); COVID-19 (ortholog); FOUND IN cytosol (ortholog); endoplasmic reticulum (ortholog); mitochondrion (ortholog)
Type: protein-coding
RefSeq Status: MODEL
Previously known as: CASP4; caspase 4, apoptosis-related cysteine peptidase
RGD Orthologs
Human
Mouse
Rat
Bonobo
Dog
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: Sscrofa11.1 - Pig Sscrofa11.1 Assembly
Position:
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1935,167,567 - 35,185,791 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2939,189,534 - 39,208,073 (-)NCBISscrofa10.2Sscrofa10.2susScr3
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

References
Additional References at PubMed
PMID:14681463   PMID:17145712   PMID:22301074   PMID:30032202  


Genomics

Comparative Map Data
LOC100522887
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1935,167,567 - 35,185,791 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2939,189,534 - 39,208,073 (-)NCBISscrofa10.2Sscrofa10.2susScr3
CASP4
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh3811104,942,866 - 104,968,574 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl11104,942,866 - 104,969,366 (-)EnsemblGRCh38hg38GRCh38
GRCh3711104,813,593 - 104,839,301 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 3611104,318,804 - 104,344,535 (-)NCBINCBI36Build 36hg18NCBI36
Build 3411104,318,804 - 104,344,503NCBI
Celera11101,977,781 - 102,003,518 (-)NCBICelera
Cytogenetic Map11q22.3NCBI
HuRef11100,744,534 - 100,770,269 (-)NCBIHuRef
CHM1_111104,696,522 - 104,722,254 (-)NCBICHM1_1
T2T-CHM13v2.011104,946,956 - 104,972,673 (-)NCBIT2T-CHM13v2.0
Casp4
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm3995,308,816 - 5,336,791 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl95,308,828 - 5,336,783 (+)EnsemblGRCm39 Ensembl
GRCm3895,308,849 - 5,336,791 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl95,308,828 - 5,336,783 (+)EnsemblGRCm38mm10GRCm38
MGSCv3795,308,860 - 5,336,791 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv3695,308,874 - 5,336,717 (+)NCBIMGSCv36mm8
Celera3117,367,159 - 117,395,096 (-)NCBICelera
Cytogenetic Map9A1NCBI
cM Map92.46NCBI
Casp4
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8810,883,817 - 10,919,978 (+)NCBIGRCr8
mRatBN7.282,599,017 - 2,635,097 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl82,598,876 - 2,635,092 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx86,570,604 - 6,598,288 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.084,868,372 - 4,896,060 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.082,851,833 - 2,886,754 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.082,616,391 - 2,651,682 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl82,635,851 - 2,651,652 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.082,638,624 - 2,673,915 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.482,038,626 - 2,075,722 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.182,038,610 - 2,075,144 (+)NCBI
Celera84,218,310 - 4,234,223 (+)NCBICelera
Cytogenetic Map8q11NCBI
CASP4
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v29105,734,010 - 105,759,789 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan111106,822,318 - 106,848,104 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01199,883,353 - 99,909,185 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.111103,366,138 - 103,391,849 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl11103,366,138 - 103,391,824 (-)Ensemblpanpan1.1panPan2
CASP4
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1527,133,778 - 27,147,954 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl527,132,565 - 27,149,736 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha527,064,601 - 27,078,777 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0527,170,519 - 27,184,696 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl527,169,891 - 27,186,517 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1527,212,077 - 27,226,245 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0527,098,364 - 27,112,532 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0527,257,464 - 27,271,644 (+)NCBIUU_Cfam_GSD_1.0
LOC103248367
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1196,315,781 - 96,342,057 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl196,315,569 - 96,342,016 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366604329,555,456 - 29,581,392 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Casp4
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_004624918145,661 - 187,006 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in LOC100522887
607 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 10 2 1 5 1 7 3 3
Low 2 2 1 16 2
Below cutoff

Sequence


RefSeq Acc Id: XM_003129812   ⟹   XP_003129860
Type: CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.1935,167,567 - 35,185,791 (-)NCBI
Sequence:
Protein Sequences
Protein RefSeqs XP_003129860 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSSSCP00000015922
  ENSSSCP00000015922.4
  ENSSSCP00035013871.1
  ENSSSCP00040019607.1
  ENSSSCP00050014775.1
  ENSSSCP00055013735.1
GenBank Protein JAG69674 (Get FASTA)   NCBI Sequence Viewer  
RefSeq Acc Id: XP_003129860   ⟸   XM_003129812
- UniProtKB: A0A8D1K9R7 (UniProtKB/TrEMBL)
- Sequence:

Additional Information

Database Acc Id Source(s)
Ensembl Genes ENSSSCG00000014997 ENTREZGENE, UniProtKB/TrEMBL
  ENSSSCG00035026513 UniProtKB/TrEMBL
  ENSSSCG00040034768 UniProtKB/TrEMBL
  ENSSSCG00050026429 UniProtKB/TrEMBL
  ENSSSCG00055008882 UniProtKB/TrEMBL
Ensembl Transcript ENSSSCT00000016361 ENTREZGENE
  ENSSSCT00000016361.5 UniProtKB/TrEMBL
  ENSSSCT00035034992.1 UniProtKB/TrEMBL
  ENSSSCT00040046768.1 UniProtKB/TrEMBL
  ENSSSCT00050035561.1 UniProtKB/TrEMBL
  ENSSSCT00055017371.1 UniProtKB/TrEMBL
Gene3D-CATH 1.10.533.10 UniProtKB/TrEMBL
  3.40.50.1460 UniProtKB/TrEMBL
InterPro CARD UniProtKB/TrEMBL
  Caspase-like_dom_sf UniProtKB/TrEMBL
  Caspase_cys_AS UniProtKB/TrEMBL
  Caspase_his_AS UniProtKB/TrEMBL
  DEATH-like_dom_sf UniProtKB/TrEMBL
  Pept_C14_caspase UniProtKB/TrEMBL
  Pept_C14_p10 UniProtKB/TrEMBL
  Pept_C14_p20 UniProtKB/TrEMBL
  Pept_C14A UniProtKB/TrEMBL
KEGG Report ssc:100522887 UniProtKB/TrEMBL
NCBI Gene LOC100522887 ENTREZGENE
PANTHER CASPASE RECRUITMENT DOMAIN-CONTAINING PROTEIN 18 UniProtKB/TrEMBL
  CASPASE-1 UniProtKB/TrEMBL
Pfam CARD UniProtKB/TrEMBL
  Peptidase_C14 UniProtKB/TrEMBL
PIRSF Caspase_ICE UniProtKB/TrEMBL
PRINTS IL1BCENZYME UniProtKB/TrEMBL
PROSITE CARD UniProtKB/TrEMBL
  CASPASE_CYS UniProtKB/TrEMBL
  CASPASE_HIS UniProtKB/TrEMBL
  CASPASE_P10 UniProtKB/TrEMBL
  CASPASE_P20 UniProtKB/TrEMBL
SMART CARD UniProtKB/TrEMBL
  CASc UniProtKB/TrEMBL
Superfamily-SCOP SSF47986 UniProtKB/TrEMBL
  SSF52129 UniProtKB/TrEMBL
UniProt A0A8D1K9R7 ENTREZGENE, UniProtKB/TrEMBL
  A0A8D1LWG5_PIG UniProtKB/TrEMBL
  F1SV36_PIG UniProtKB/TrEMBL