Samd13 (sterile alpha motif domain containing 13) - Rat Genome Database

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Gene: Samd13 (sterile alpha motif domain containing 13) Rattus norvegicus
Analyze
Symbol: Samd13
Name: sterile alpha motif domain containing 13
RGD ID: 708544
Description: Predicted to enable protein folding chaperone; protein-folding chaperone binding activity; and unfolded protein binding activity. Predicted to be involved in chaperone-mediated protein folding. Predicted to be active in cytoplasm and nucleus. Orthologous to human SAMD13 (sterile alpha motif domain containing 13); INTERACTS WITH acetamide; acrylamide; bisphenol A.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: Djl; dnaj-like protein; LOC56764; rDJL; sterile alpha motif domain-containing protein 13
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr82238,194,962 - 238,200,790 (-)NCBIGRCr8
mRatBN7.22235,534,699 - 235,540,527 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl2235,534,702 - 235,567,615 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx2243,330,300 - 243,336,126 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.02241,220,945 - 241,226,771 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.02236,087,964 - 236,093,790 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.02252,500,143 - 252,537,490 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl2252,500,146 - 252,505,971 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.02271,026,743 - 271,064,476 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42244,844,139 - 244,849,967 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.12244,830,879 - 244,836,707 (-)NCBI
Celera2227,512,995 - 227,518,823 (-)NCBICelera
Cytogenetic Map2q44NCBI
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

Biological Process

Cellular Component
cytoplasm  (IBA)
nucleus  (IBA)

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
2. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
3. GOA pipeline RGD automated data pipeline
Additional References at PubMed
PMID:12477932   PMID:16225871  


Genomics

Comparative Map Data
Samd13
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr82238,194,962 - 238,200,790 (-)NCBIGRCr8
mRatBN7.22235,534,699 - 235,540,527 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl2235,534,702 - 235,567,615 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx2243,330,300 - 243,336,126 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.02241,220,945 - 241,226,771 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.02236,087,964 - 236,093,790 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.02252,500,143 - 252,537,490 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl2252,500,146 - 252,505,971 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.02271,026,743 - 271,064,476 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42244,844,139 - 244,849,967 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.12244,830,879 - 244,836,707 (-)NCBI
Celera2227,512,995 - 227,518,823 (-)NCBICelera
Cytogenetic Map2q44NCBI
SAMD13
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38184,298,538 - 84,350,798 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl184,298,366 - 84,389,957 (+)EnsemblGRCh38hg38GRCh38
GRCh37184,764,221 - 84,816,481 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36184,536,637 - 84,589,067 (+)NCBINCBI36Build 36hg18NCBI36
Celera183,008,265 - 83,060,708 (+)NCBICelera
Cytogenetic Map1p31.1NCBI
HuRef182,874,346 - 82,926,549 (+)NCBIHuRef
CHM1_1184,878,880 - 84,931,314 (+)NCBICHM1_1
T2T-CHM13v2.0184,139,002 - 84,191,273 (+)NCBIT2T-CHM13v2.0
Samd13
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm393146,350,944 - 146,391,555 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl3146,350,948 - 146,357,072 (-)EnsemblGRCm39 Ensembl
GRCm39 Ensembl3146,350,950 - 146,391,347 (-)EnsemblGRCm39 Ensembl
GRCm383146,645,189 - 146,685,892 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl3146,645,193 - 146,651,317 (-)EnsemblGRCm38mm10GRCm38
GRCm38.p6 Ensembl3146,645,195 - 146,685,592 (-)EnsemblGRCm38mm10GRCm38
MGSCv373146,309,223 - 146,314,281 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv363146,587,086 - 146,588,698 (-)NCBIMGSCv36mm8
Celera3153,096,735 - 153,101,791 (-)NCBICelera
Cytogenetic Map3H2NCBI
cM Map372.28NCBI
Samd13
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554239,531,020 - 9,574,621 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554239,531,538 - 9,574,312 (-)NCBIChiLan1.0ChiLan1.0
SAMD13
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21142,592,219 - 142,644,569 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11141,746,675 - 141,799,016 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01116,846,246 - 116,898,678 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1185,707,104 - 85,759,529 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl185,707,104 - 85,759,529 (+)Ensemblpanpan1.1panPan2
SAMD13
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1663,528,376 - 63,587,419 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha666,176,535 - 66,235,733 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0664,068,195 - 64,127,539 (-)NCBIROS_Cfam_1.0
UMICH_Zoey_3.1663,596,127 - 63,655,377 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0663,564,819 - 63,623,986 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0664,070,961 - 64,130,376 (-)NCBIUU_Cfam_GSD_1.0
Samd13
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440505895,009,042 - 95,059,734 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049366081,246,299 - 1,293,865 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049366081,246,299 - 1,296,991 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SAMD13
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl6129,395,698 - 129,440,039 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.16129,395,684 - 129,440,062 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.26119,672,505 - 119,675,351 (-)NCBISscrofa10.2Sscrofa10.2susScr3
SAMD13
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12049,003,525 - 49,053,323 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl2049,003,424 - 49,049,451 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366603368,708,728 - 68,758,403 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Samd13
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462474213,121,244 - 13,162,723 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462474213,121,273 - 13,163,101 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Samd13
30 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:239
Count of miRNA genes:169
Interacting mature miRNAs:196
Transcripts:ENSRNOT00000021984
Prediction methods:Microtar, Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
724534Uae6Urinary albumin excretion QTL 610urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)278665619249053267Rat
1641891Alcrsp17Alcohol response QTL 17response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)2149559561249053267Rat
2317752Glom23Glomerulus QTL 233.6urine protein amount (VT:0005160)urine protein level (CMO:0000591)2193452645245889826Rat
1598835Anxrr18Anxiety related response QTL 182.98body movement coordination trait (VT:0005424)number of rearing movements in an experimental apparatus (CMO:0001752)2200990457245990457Rat
2298479Eau5Experimental allergic uveoretinitis QTL 50.0021uvea integrity trait (VT:0010551)experimental autoimmune uveitis score (CMO:0001504)2202446871237938339Rat
7207490Bss111Bone structure and strength QTL 1116.4femur morphology trait (VT:0000559)femur midshaft cortical cross-sectional area (CMO:0001663)2211744537249053267Rat
7207482Bss107Bone structure and strength QTL 1077femur strength trait (VT:0010010)femur ultimate force (CMO:0001675)2211744537249053267Rat
7207484Bss108Bone structure and strength QTL 1085.3femur strength trait (VT:0010010)femur total energy absorbed before break (CMO:0001677)2211744537249053267Rat
1298075Scl17Serum cholesterol level QTL 173.4blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)2211744537249053267Rat
1549836Bss2Bone structure and strength QTL 27.5femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)2211744537249053267Rat
2317885Alcrsp28Alcohol response QTL 282.10.63response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)2212828222249053267Rat
1300126Bp175Blood pressure QTL 1753.46arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)2214226044247136170Rat
2313073Bmd75Bone mineral density QTL 754.10.0001tibia mineral mass (VT:1000283)total volumetric bone mineral density (CMO:0001728)2215377404237938339Rat
1331767Hrtrt12Heart rate QTL 123.373heart pumping trait (VT:2000009)heart rate (CMO:0000002)2218414747240841241Rat
2293833Kiddil8Kidney dilation QTL 82.9kidney pelvis morphology trait (VT:0004194)hydronephrosis severity score (CMO:0001208)2219753301247136170Rat
2293844Kiddil7Kidney dilation QTL 73.5kidney pelvis morphology trait (VT:0004194)hydronephrosis severity score (CMO:0001208)2219753301247136170Rat
9587428Epfw6Epididymal fat weight QTL 67.470.001epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)2223389739249053267Rat
7411555Bw132Body weight QTL 1320.001body mass (VT:0001259)body weight gain (CMO:0000420)2223389739249053267Rat
631563Hcuc3Hepatic copper content QTL 33.87liver copper amount (VT:0003065)liver copper weight to liver dry weight ratio (CMO:0001512)2229059610249053267Rat


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 exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 8
Low 31 33 21 19 21 8 10 18 27 28 10 8
Below cutoff 2 12 23 19 19 1 56 8 5 1

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000021984   ⟹   ENSRNOP00000021984
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl2235,534,702 - 235,540,527 (-)Ensembl
Rnor_6.0 Ensembl2252,500,146 - 252,505,971 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000102174   ⟹   ENSRNOP00000096914
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl2235,535,603 - 235,567,615 (-)Ensembl
RefSeq Acc Id: NM_020089   ⟹   NP_064474
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr82238,194,962 - 238,200,790 (-)NCBI
mRatBN7.22235,534,699 - 235,540,527 (-)NCBI
Rnor_6.02252,500,143 - 252,505,971 (-)NCBI
Rnor_5.02271,026,743 - 271,064,476 (-)NCBI
RGSC_v3.42244,844,139 - 244,849,967 (-)RGD
Celera2227,512,995 - 227,518,823 (-)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_064474 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAD53061 (Get FASTA)   NCBI Sequence Viewer  
  AAH83558 (Get FASTA)   NCBI Sequence Viewer  
  EDL82432 (Get FASTA)   NCBI Sequence Viewer  
  EDL82433 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000021984
  ENSRNOP00000021984.4
  ENSRNOP00000096914.1
Reference Protein Sequences
RefSeq Acc Id: NP_064474   ⟸   NM_020089
- UniProtKB: Q9QZW8 (UniProtKB/TrEMBL),   F7FMA6 (UniProtKB/TrEMBL),   A6HWE8 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000021984   ⟸   ENSRNOT00000021984
RefSeq Acc Id: ENSRNOP00000096914   ⟸   ENSRNOT00000102174
Protein Domains
J   SAM

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q9QZW8-F1-model_v2 AlphaFold Q9QZW8 1-223 view protein structure

Transcriptome

eQTL   View at Phenogen
WGCNA   View at Phenogen
Tissue/Strain Expression   View at Phenogen

Promoters
RGD ID:13691817
Promoter ID:EPDNEW_R2342
Type:multiple initiation site
Name:Samd13_1
Description:sterile alpha motif domain containing 13
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.02252,505,966 - 252,506,026EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:708544 AgrOrtholog
BioCyc Gene G2FUF-50896 BioCyc
Ensembl Genes ENSRNOG00000016432 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000021984 ENTREZGENE
  ENSRNOT00000021984.5 UniProtKB/TrEMBL
  ENSRNOT00000102174.1 UniProtKB/TrEMBL
Gene3D-CATH 1.10.150.50 UniProtKB/TrEMBL
  1.10.287.110 UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7134067 IMAGE-MGC_LOAD
InterPro DnaJ_dom_sf UniProtKB/TrEMBL
  DnaJ_N UniProtKB/TrEMBL
  DNJB2/6-like UniProtKB/TrEMBL
  Heat_shock_DnaJ_CS UniProtKB/TrEMBL
  SAM UniProtKB/TrEMBL
  SAM/pointed_sf UniProtKB/TrEMBL
KEGG Report rno:56764 UniProtKB/TrEMBL
MGC_CLONE MGC:93471 IMAGE-MGC_LOAD
NCBI Gene 56764 ENTREZGENE
PANTHER DNAJ HOMOLOG SUBFAMILY B MEMBER 2 UniProtKB/TrEMBL
  POLYCOMB GROUP PROTEIN UniProtKB/TrEMBL
  SIMILAR TO DNAJ HOMOLOG SUBFAMILY B MEMBER 6 (HEAT SHOCK PROTEIN J2) (HSJ-2) (MRJ) (MDJ4) UniProtKB/TrEMBL
  STERILE ALPHA MOTIF DOMAIN-CONTAINING 1A UniProtKB/TrEMBL
Pfam DnaJ UniProtKB/TrEMBL
  SAM_1 UniProtKB/TrEMBL
PhenoGen Samd13 PhenoGen
PRINTS JDOMAIN UniProtKB/TrEMBL
PROSITE DNAJ_1 UniProtKB/TrEMBL
  DNAJ_2 UniProtKB/TrEMBL
  SAM_DOMAIN UniProtKB/TrEMBL
RatGTEx ENSRNOG00000016432 RatGTEx
SMART DnaJ UniProtKB/TrEMBL
Superfamily-SCOP DnaJ_N UniProtKB/TrEMBL
  SSF47769 UniProtKB/TrEMBL
UniProt A0A8I6ARW6_RAT UniProtKB/TrEMBL
  A6HWE8 ENTREZGENE, UniProtKB/TrEMBL
  F7FMA6 ENTREZGENE, UniProtKB/TrEMBL
  Q9QZW8 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2017-04-26 Samd13  sterile alpha motif domain containing 13  LOC56764  dnaj-like protein  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-09-30 LOC56764        Symbol and Name status set to provisional 70820 PROVISIONAL