Slc39a13 (solute carrier family 39 member 13) - Rat Genome Database

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Gene: Slc39a13 (solute carrier family 39 member 13) Rattus norvegicus
Analyze
Symbol: Slc39a13
Name: solute carrier family 39 member 13
RGD ID: 1304695
Description: Predicted to enable protein homodimerization activity and zinc ion transmembrane transporter activity. Involved in response to zinc ion. Located in endoplasmic reticulum. Human ortholog(s) of this gene implicated in Ehlers-Danlos syndrome and Ehlers-Danlos syndrome spondylodysplastic type 3. Orthologous to human SLC39A13 (solute carrier family 39 member 13); PARTICIPATES IN Bone morphogenetic proteins signaling pathway; INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 2,3,7,8-Tetrachlorodibenzofuran; 2,6-dinitrotoluene.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: LOC295928; MGC124816; solute carrier family 39 (metal ion transporter), member 13; solute carrier family 39 (zinc transporter), member 13; zinc transporter ZIP13; ZIP-13; zrt- and Irt-like 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
mRatBN7.2377,039,411 - 77,047,536 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl377,037,565 - 77,049,226 (-)Ensembl
Rnor_6.0379,884,524 - 79,892,664 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl379,884,524 - 79,892,429 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0386,593,277 - 86,601,315 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4375,421,153 - 75,429,058 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1375,317,524 - 75,325,349 (-)NCBI
Celera376,248,117 - 76,256,038 (-)NCBICelera
Cytogenetic Map3q24NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
# Reference Title Reference Citation
1. The zinc transporter SLC39A13/ZIP13 is required for connective tissue development; its involvement in BMP/TGF-beta signaling pathways. Fukada T, etal., PLoS One. 2008;3(11):e3642. doi: 10.1371/journal.pone.0003642. Epub 2008 Nov 5.
2. 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.
3. Spondylocheiro dysplastic form of the Ehlers-Danlos syndrome--an autosomal-recessive entity caused by mutations in the zinc transporter gene SLC39A13. Giunta C, etal., Am J Hum Genet. 2008 Jun;82(6):1290-305. doi: 10.1016/j.ajhg.2008.05.001.
4. Over-expression of Zip-13 mRNA in kidney and lung during dietary zinc deficiency in Wistar rats. Guo L, etal., Mol Biol Rep. 2011 Mar;38(3):1869-74. doi: 10.1007/s11033-010-0304-y. Epub 2010 Sep 22.
5. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
6. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
7. GOA pipeline RGD automated data pipeline
8. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
9. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
10. Comprehensive gene review and curation RGD comprehensive gene curation
11. Zinc deficiency mediates alcohol-induced apoptotic cell death in the liver of rats through activating ER and mitochondrial cell death pathways. Sun Q, etal., Am J Physiol Gastrointest Liver Physiol. 2015 May 1;308(9):G757-66. doi: 10.1152/ajpgi.00442.2014. Epub 2015 Mar 12.
Additional References at PubMed
PMID:12477932   PMID:21917916  


Genomics

Comparative Map Data
Slc39a13
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2377,039,411 - 77,047,536 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl377,037,565 - 77,049,226 (-)Ensembl
Rnor_6.0379,884,524 - 79,892,664 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl379,884,524 - 79,892,429 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0386,593,277 - 86,601,315 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4375,421,153 - 75,429,058 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1375,317,524 - 75,325,349 (-)NCBI
Celera376,248,117 - 76,256,038 (-)NCBICelera
Cytogenetic Map3q24NCBI
SLC39A13
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381147,407,276 - 47,416,500 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl1147,407,132 - 47,416,496 (+)EnsemblGRCh38hg38GRCh38
GRCh371147,428,827 - 47,438,051 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361147,386,758 - 47,394,623 (+)NCBINCBI36hg18NCBI36
Build 341147,386,757 - 47,394,622NCBI
Celera1147,571,745 - 47,579,746 (+)NCBI
Cytogenetic Map11p11.2NCBI
HuRef1147,130,928 - 47,137,364 (+)NCBIHuRef
CHM1_11147,429,277 - 47,437,283 (+)NCBICHM1_1
T2T-CHM13v2.01147,566,179 - 47,575,404 (+)NCBI
Slc39a13
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39290,892,126 - 90,900,754 (-)NCBIGRCm39mm39
GRCm39 Ensembl290,892,136 - 90,900,762 (-)Ensembl
GRCm38291,061,781 - 91,070,441 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl291,061,791 - 91,070,417 (-)EnsemblGRCm38mm10GRCm38
MGSCv37290,901,948 - 90,910,378 (-)NCBIGRCm37mm9NCBIm37
MGSCv36290,862,630 - 90,871,060 (-)NCBImm8
Celera292,446,265 - 92,454,697 (-)NCBICelera
Cytogenetic Map2E1NCBI
Slc39a13
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_004955422845,678 - 852,772 (-)EnsemblChiLan1.0
ChiLan1.0NW_004955422845,076 - 852,772 (-)NCBIChiLan1.0ChiLan1.0
SLC39A13
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11147,910,552 - 47,918,014 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1147,910,551 - 47,918,014 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01147,356,465 - 47,364,710 (+)NCBIMhudiblu_PPA_v0panPan3
SLC39A13
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11842,221,311 - 42,229,992 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1842,222,333 - 42,227,361 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1840,951,851 - 40,960,577 (-)NCBI
ROS_Cfam_1.01842,877,035 - 42,885,762 (-)NCBI
ROS_Cfam_1.0 Ensembl1842,877,036 - 42,884,329 (-)Ensembl
UMICH_Zoey_3.11842,363,637 - 42,372,357 (-)NCBI
UNSW_CanFamBas_1.01841,918,606 - 41,927,337 (-)NCBI
UU_Cfam_GSD_1.01842,648,054 - 42,656,786 (-)NCBI
Slc39a13
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494719,699,562 - 19,714,178 (-)NCBI
SpeTri2.0NW_0049365621,811,479 - 1,825,857 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SLC39A13
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl215,193,506 - 15,210,425 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1215,194,028 - 15,202,936 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2216,400,675 - 16,409,565 (-)NCBISscrofa10.2Sscrofa10.2susScr3
SLC39A13
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1117,899,349 - 17,907,165 (-)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl117,899,030 - 17,905,850 (-)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_023666038115,200,824 - 115,208,776 (-)NCBIVero_WHO_p1.0
Slc39a13
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247671,368,965 - 1,375,586 (-)EnsemblHetGla_female_1.0hetGla2
HetGla 1.0NW_0046247671,368,965 - 1,376,378 (-)NCBIHetGla_female_1.0hetGla2

Position Markers
RH130983  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2377,039,514 - 77,039,701 (+)MAPPERmRatBN7.2
Rnor_6.0379,884,628 - 79,884,814NCBIRnor6.0
Rnor_5.0386,593,381 - 86,593,567UniSTSRnor5.0
RGSC_v3.4375,421,257 - 75,421,443UniSTSRGSC3.4
Celera376,248,221 - 76,248,407UniSTS
Cytogenetic Map3q24UniSTS
BE108715  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2377,039,049 - 77,039,218 (+)MAPPERmRatBN7.2
Rnor_6.0379,884,163 - 79,884,331NCBIRnor6.0
Rnor_5.0386,592,916 - 86,593,084UniSTSRnor5.0
RGSC_v3.4375,420,792 - 75,420,960UniSTSRGSC3.4
Celera376,247,756 - 76,247,924UniSTS
Cytogenetic Map3q24UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2290452Scl56Serum cholesterol level QTL 562.26blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)3191609953Rat
1358905Hrtrt17Heart rate QTL 175.90.000014heart pumping trait (VT:2000009)heart rate (CMO:0000002)31086191289878372Rat
1358885Bp251Blood pressure QTL 2513.8arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)314489145121056321Rat
1358888Bp264Blood pressure QTL 2644.43arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)314489145121056321Rat
737818Hcar12Hepatocarcinoma resistance QTL 122.6liver integrity trait (VT:0010547)volume of individual liver tumorous lesion (CMO:0001078)329463235118376539Rat
61419Cia11Collagen induced arthritis QTL 115.6joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)33035677398535386Rat
70216Cm14Cardiac mass QTL 142.1heart mass (VT:0007028)heart wet weight (CMO:0000069)331172320163586636Rat
1354589Bw31Body weight QTL 313.3body mass (VT:0001259)body weight (CMO:0000012)33370334778196190Rat
1354604Bw36Body weight QTL 362.9body mass (VT:0001259)body weight (CMO:0000012)333703347104104347Rat
1358362Srcrt2Stress Responsive Cort QTL 22.78blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)338192233133483320Rat
738019Anxrr10Anxiety related response QTL 103.9exploratory behavior trait (VT:0010471)number of entries into a discrete space in an experimental apparatus (CMO:0000960)33851780383517803Rat
1331777Bw24Body weight QTL 243.503body mass (VT:0001259)body weight (CMO:0000012)33945463789115240Rat
1331795Rf30Renal function QTL 303.708urine potassium amount (VT:0010539)urine potassium level (CMO:0000128)33945463789115240Rat
1354597Kidm13Kidney mass QTL 132.9kidney mass (VT:0002707)right kidney wet weight (CMO:0000082)341874578104104347Rat
2301970Bw81Body weight QTL 815.19body mass (VT:0001259)body weight (CMO:0000012)341874578155617519Rat
2301971Cm71Cardiac mass QTL 714.63heart left ventricle mass (VT:0007031)heart left ventricle weight (CMO:0000776)341874578155617519Rat
1300178Hrtrt4Heart rate QTL 43.74heart pumping trait (VT:2000009)heart rate (CMO:0000002)34382736490905114Rat
1581503Cm58Cardiac mass QTL 582.70.05heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)343827364121056321Rat
1559282Emca5Estrogen-induced mammary cancer QTL 53.9mammary gland integrity trait (VT:0010552)percentage of study population developing mammary tumors during a period of time (CMO:0000948)343827364169034231Rat
2292591Esta4Estrogen-induced thymic atrophy QTL 4thymus mass (VT:0004954)thymus wet weight (CMO:0000855)347233211147415807Rat
1358186Ept2Estrogen-induced pituitary tumorigenesis QTL 28.3pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)347233430110362260Rat
2292613Ept16Estrogen-induced pituitary tumorigenesis QTL 168.3pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)347233430110362260Rat
631665Bw8Body weight QTL 85.5body mass (VT:0001259)body weight (CMO:0000012)350437042119183768Rat
724523Tsu1Thymus enlargement suppressive QTL 13.84thymus mass (VT:0004954)thymus weight to body weight ratio (CMO:0000612)350437504115638231Rat
1582218Bw74Body weight QTL 743.90.0021body mass (VT:0001259)body weight (CMO:0000012)353184593115665732Rat
1582238Bw68Body weight QTL 683.20.0064body mass (VT:0001259)body weight (CMO:0000012)353184593115665732Rat
1582239Epfw1Epididymal fat weight QTL 14.50.0006epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)353184593115665732Rat
61377Edpm3Estrogen-dependent pituitary mass QTL 37.050.038pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)35318469289878207Rat
731180Bp152Blood pressure QTL 1520.03arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)35378111291609953Rat
731180Bp152Blood pressure QTL 1520.03arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)35378111291609953Rat
731180Bp152Blood pressure QTL 1520.03arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)35378111291609953Rat
1581568Rf53Renal function QTL 53total urine protein amount (VT:0000032)urine protein excretion rate to body weight ratio (CMO:0001099)356395968161299569Rat
8662816Vetf4Vascular elastic tissue fragility QTL 44renal artery integrity trait (VT:0010642)number of ruptures of the internal elastic lamina of the renal arteries (CMO:0002563)359242096157323038Rat
1300111Rf12Renal function QTL 123.78renal blood flow trait (VT:2000006)absolute change in renal blood flow rate (CMO:0001168)361017749121056321Rat
631200Cm25Cardiac mass QTL 254.80.0001heart left ventricle mass (VT:0007031)heart left ventricle wet weight (CMO:0000071)36113434889115068Rat
1582210Bw71Body weight QTL 713.30.0012body mass (VT:0001259)body weight (CMO:0000012)364655305115665732Rat
1582221Kidm30Kidney mass QTL 303.50.0008kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)364655305115665732Rat
12879848Bw181Body weght QTL 1810.015body mass (VT:0001259)body weight (CMO:0000012)370348525121056321Rat
2301414Kidm37Kidney mass QTL 370.001kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)370653097121056321Rat
1600376Arunc5Aerobic running capacity QTL 50.21exercise endurance trait (VT:0002332)maximum distance run on treadmill (CMO:0001406)373376539118376539Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:578
Count of miRNA genes:261
Interacting mature miRNAs:327
Transcripts:ENSRNOT00000016191
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.


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 1 35 18 6 13 6 6 9 74 35 41 11 6
Low 2 8 39 35 6 35 2 2 2
Below cutoff

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_001039196 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_001399258 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_001399259 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NR_174175 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NR_174176 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006234501 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006234502 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039104511 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039104512 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039104513 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039104514 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039104515 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039104516 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039104517 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039104518 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039104519 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_005501807 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_005501808 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_005501809 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide BC112321 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH473949 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000118 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000016191   ⟹   ENSRNOP00000016191
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl377,039,400 - 77,047,331 (-)Ensembl
Rnor_6.0 Ensembl379,884,524 - 79,892,429 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000098235   ⟹   ENSRNOP00000096044
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl377,037,565 - 77,047,216 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000105219   ⟹   ENSRNOP00000089562
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl377,039,405 - 77,049,226 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000112322   ⟹   ENSRNOP00000078410
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl377,039,432 - 77,046,457 (-)Ensembl
RefSeq Acc Id: NM_001039196   ⟹   NP_001034285
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2377,039,411 - 77,047,316 (-)NCBI
Rnor_6.0379,884,524 - 79,892,429 (-)NCBI
Rnor_5.0386,593,277 - 86,601,315 (-)NCBI
RGSC_v3.4375,421,153 - 75,429,058 (-)RGD
Celera376,248,117 - 76,256,038 (-)RGD
Sequence:
RefSeq Acc Id: XM_006234501   ⟹   XP_006234563
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2377,039,411 - 77,047,424 (-)NCBI
Rnor_6.0379,884,524 - 79,892,657 (-)NCBI
Rnor_5.0386,593,277 - 86,601,315 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006234502   ⟹   XP_006234564
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2377,039,411 - 77,047,480 (-)NCBI
Rnor_6.0379,884,524 - 79,892,664 (-)NCBI
Rnor_5.0386,593,277 - 86,601,315 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039104511   ⟹   XP_038960439
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2377,039,411 - 77,047,528 (-)NCBI
RefSeq Acc Id: XM_039104512   ⟹   XP_038960440
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2377,039,411 - 77,046,535 (-)NCBI
RefSeq Acc Id: XM_039104513   ⟹   XP_038960441
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2377,039,411 - 77,046,522 (-)NCBI
RefSeq Acc Id: XM_039104514   ⟹   XP_038960442
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2377,039,411 - 77,046,544 (-)NCBI
RefSeq Acc Id: XM_039104515   ⟹   XP_038960443
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2377,039,411 - 77,046,532 (-)NCBI
RefSeq Acc Id: XM_039104516   ⟹   XP_038960444
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2377,041,338 - 77,046,556 (-)NCBI
RefSeq Acc Id: XM_039104517   ⟹   XP_038960445
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2377,041,329 - 77,046,563 (-)NCBI
RefSeq Acc Id: XM_039104518   ⟹   XP_038960446
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2377,041,325 - 77,046,572 (-)NCBI
RefSeq Acc Id: XM_039104519   ⟹   XP_038960447
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2377,039,411 - 77,043,385 (-)NCBI
RefSeq Acc Id: XR_005501807
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2377,039,411 - 77,046,558 (-)NCBI
RefSeq Acc Id: XR_005501808
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2377,039,411 - 77,047,534 (-)NCBI
RefSeq Acc Id: XR_005501809
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2377,039,411 - 77,047,536 (-)NCBI
Reference Sequences
RefSeq Acc Id: NP_001034285   ⟸   NM_001039196
- Peptide Label: precursor
- Sequence:
RefSeq Acc Id: XP_006234564   ⟸   XM_006234502
- Peptide Label: isoform X7
- Sequence:
RefSeq Acc Id: XP_006234563   ⟸   XM_006234501
- Peptide Label: isoform X4
- Sequence:
RefSeq Acc Id: ENSRNOP00000016191   ⟸   ENSRNOT00000016191
RefSeq Acc Id: XP_038960439   ⟸   XM_039104511
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038960442   ⟸   XM_039104514
- Peptide Label: isoform X5
RefSeq Acc Id: XP_038960440   ⟸   XM_039104512
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038960443   ⟸   XM_039104515
- Peptide Label: isoform X6
RefSeq Acc Id: XP_038960441   ⟸   XM_039104513
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038960447   ⟸   XM_039104519
- Peptide Label: isoform X11
RefSeq Acc Id: XP_038960446   ⟸   XM_039104518
- Peptide Label: isoform X10
RefSeq Acc Id: XP_038960445   ⟸   XM_039104517
- Peptide Label: isoform X9
RefSeq Acc Id: XP_038960444   ⟸   XM_039104516
- Peptide Label: isoform X8
RefSeq Acc Id: ENSRNOP00000089562   ⟸   ENSRNOT00000105219
RefSeq Acc Id: ENSRNOP00000078410   ⟸   ENSRNOT00000112322
RefSeq Acc Id: ENSRNOP00000096044   ⟸   ENSRNOT00000098235

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q2M1K6-F1-model_v2 AlphaFold Q2M1K6 1-361 view protein structure

Transcriptome

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

Promoters
RGD ID:13692205
Promoter ID:EPDNEW_R2730
Type:initiation region
Name:Slc39a13_1
Description:solute carrier family 39 member 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_6.0379,892,313 - 79,892,373EPDNEW

Strain Variation

Strain Sequence Variants (MRatBN7.2)
ACI/EurMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN-Lx/CubMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BUF/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH2/CubMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH3/CubMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
DA/OlaHsd (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/DuCrl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/Stm (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE16/Stm (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE18/Stm (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GK/FarMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB10/IpcvMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB2/IpcvMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB20/IpcvMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB31/IpcvMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB4/IpcvMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEW/Crl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF10A/StmMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF11/Stm (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1A/Stm (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1C/Stm (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF2B/Stm (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF3/Stm (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF4/Stm (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LH/MavRrrcAek (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LL/MavRrrcAek (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LN/MavRrrcAek (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/NRrrcMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MR/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MWF/Hsd (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
PVG/Seac (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHR/OlalpcvMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/A3NCrl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SR/JrHsd (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SS/JrHsdMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WAG/RijCrl (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/NCrl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WN/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1304695 AgrOrtholog
BioCyc Gene G2FUF-48752 BioCyc
Ensembl Genes ENSRNOG00000011981 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000078410 ENTREZGENE
  ENSRNOP00000078410.1 UniProtKB/TrEMBL
  ENSRNOP00000089562 ENTREZGENE
  ENSRNOP00000089562.1 UniProtKB/TrEMBL
  ENSRNOP00000096044 ENTREZGENE
  ENSRNOP00000096044.1 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000098235 ENTREZGENE
  ENSRNOT00000098235.1 UniProtKB/TrEMBL
  ENSRNOT00000105219 ENTREZGENE
  ENSRNOT00000105219.1 UniProtKB/TrEMBL
  ENSRNOT00000112322 ENTREZGENE
  ENSRNOT00000112322.1 UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7933412 IMAGE-MGC_LOAD
InterPro ZIP UniProtKB/Swiss-Prot
KEGG Report rno:295928 UniProtKB/Swiss-Prot
MGC_CLONE MGC:124816 IMAGE-MGC_LOAD
NCBI Gene 295928 ENTREZGENE
Pfam Zip UniProtKB/Swiss-Prot
PhenoGen Slc39a13 PhenoGen
UniProt A0A8I6AA51_RAT UniProtKB/TrEMBL
  A0A8I6G1R5_RAT UniProtKB/TrEMBL
  A0A8I6GLF4_RAT UniProtKB/TrEMBL
  Q2M1K6 ENTREZGENE, UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-03-09 Slc39a13  solute carrier family 39 member 13  Slc39a13  solute carrier family 39 (zinc transporter), member 13  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2009-12-16 Slc39a13  solute carrier family 39 (zinc transporter), member 13  Slc39a13  solute carrier family 39 (metal ion transporter), member 13  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-03-07 Slc39a13  solute carrier family 39 (metal ion transporter), member 13  Slc39a13  solute carrier family 39 (zinc transporter), member 13  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-03-07 Slc39a13  solute carrier family 39 (zinc transporter), member 13  Slc39a13_predicted  solute carrier family 39 (zinc transporter), member 13 (predicted)  Symbol and Name status set to approved 1299863 APPROVED
2005-01-12 Slc39a13_predicted  solute carrier family 39 (zinc transporter), member 13 (predicted)      Symbol and Name status set to approved 70820 APPROVED