Slc25a38 (solute carrier family 25, member 38) - Rat Genome Database

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Gene: Slc25a38 (solute carrier family 25, member 38) Rattus norvegicus
Analyze
Symbol: Slc25a38
Name: solute carrier family 25, member 38
RGD ID: 1311914
Description: Predicted to enable glycine transmembrane transporter activity. Predicted to be involved in erythrocyte differentiation and glycine import into mitochondrion. Predicted to be located in mitochondrial inner membrane. Predicted to be active in mitochondrion. Human ortholog(s) of this gene implicated in autosomal recessive pyridoxine-refractory sideroblastic anemia 2. Orthologous to human SLC25A38 (solute carrier family 25 member 38); PARTICIPATES IN heme biosynthetic pathway; INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 6-propyl-2-thiouracil; amitrole.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: LOC301067; MGC124671; mitochondrial glycine transporter; RGD1311914; similar to hypothetical protein MGC18873; solute carrier family 25 member 38
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr88128,713,180 - 128,725,968 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl8128,713,131 - 128,725,966 (+)EnsemblGRCr8
mRatBN7.28119,835,546 - 119,848,334 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl8119,835,634 - 119,848,332 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx8125,416,655 - 125,428,672 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.08123,615,691 - 123,627,708 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.08121,456,372 - 121,468,146 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.08128,790,348 - 128,802,988 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl8128,790,348 - 128,802,989 (+)Ensemblrn6Rnor6.0
Rnor_5.08127,991,043 - 128,003,673 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.48125,084,481 - 125,097,326 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera8118,981,834 - 118,993,323 (+)NCBICelera
RGSC_v3.18125,104,217 - 125,117,063 (+)NCBI
Cytogenetic Map8q32NCBI
JBrowse:




Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component
membrane  (IEA)
mitochondrial inner membrane  (IEA,ISO,ISS)
mitochondrion  (IBA,IEA)

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
# Reference Title Reference Citation
1. Synthesis, delivery and regulation of eukaryotic heme and Fe-S cluster cofactors. Barupala DP, etal., Arch Biochem Biophys. 2016 Feb 15;592:60-75. doi: 10.1016/j.abb.2016.01.010. Epub 2016 Jan 16.
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. Characterization of Human and Yeast Mitochondrial Glycine Carriers with Implications for Heme Biosynthesis and Anemia. Lunetti P, etal., J Biol Chem. 2016 Sep 16;291(38):19746-59. doi: 10.1074/jbc.M116.736876. Epub 2016 Jul 30.
4. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
5. GOA pipeline RGD automated data pipeline
6. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
7. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:12477932   PMID:19412178   PMID:34800366  


Genomics

Comparative Map Data
Slc25a38
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr88128,713,180 - 128,725,968 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl8128,713,131 - 128,725,966 (+)EnsemblGRCr8
mRatBN7.28119,835,546 - 119,848,334 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl8119,835,634 - 119,848,332 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx8125,416,655 - 125,428,672 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.08123,615,691 - 123,627,708 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.08121,456,372 - 121,468,146 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.08128,790,348 - 128,802,988 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl8128,790,348 - 128,802,989 (+)Ensemblrn6Rnor6.0
Rnor_5.08127,991,043 - 128,003,673 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.48125,084,481 - 125,097,326 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera8118,981,834 - 118,993,323 (+)NCBICelera
RGSC_v3.18125,104,217 - 125,117,063 (+)NCBI
Cytogenetic Map8q32NCBI
SLC25A38
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38339,383,370 - 39,397,351 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl339,383,370 - 39,397,351 (+)Ensemblhg38GRCh38
GRCh37339,424,861 - 39,438,842 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36339,399,819 - 39,413,823 (+)NCBIBuild 36Build 36hg18NCBI36
Celera339,366,402 - 39,380,406 (+)NCBICelera
Cytogenetic Map3p22.1NCBI
HuRef339,468,155 - 39,482,157 (+)NCBIHuRef
CHM1_1339,375,927 - 39,389,932 (+)NCBICHM1_1
T2T-CHM13v2.0339,396,296 - 39,410,278 (+)NCBIT2T-CHM13v2.0
Slc25a38
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm399119,939,428 - 119,953,570 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl9119,939,440 - 119,953,570 (+)EnsemblGRCm39 EnsemblGRCm39
GRCm389120,110,377 - 120,126,093 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl9120,110,374 - 120,124,504 (+)Ensemblmm10GRCm38
MGSCv379120,019,517 - 120,033,439 (+)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv369119,959,097 - 119,973,019 (+)NCBIMGSCv36mm8
Celera9120,580,001 - 120,593,558 (+)NCBICelera
Cytogenetic Map9F4NCBI
cM Map971.4NCBI
Slc25a38
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495542029,988,147 - 29,996,486 (-)Ensembl
ChiLan1.0NW_00495542029,988,147 - 29,996,485 (-)NCBIChiLan1.0ChiLan1.0
SLC25A38
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2239,343,608 - 39,357,136 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1339,348,032 - 39,361,898 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0339,287,934 - 39,301,810 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1339,567,737 - 39,581,966 (+)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 Ensembl339,567,737 - 39,581,957 (+)EnsemblpanPan2panpan1.1
SLC25A38
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1239,031,984 - 9,045,781 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl239,032,000 - 9,045,788 (+)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha239,067,493 - 9,079,760 (+)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.0239,316,688 - 9,328,967 (+)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl239,316,722 - 9,328,968 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1239,130,095 - 9,142,148 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0239,272,686 - 9,284,973 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0239,266,297 - 9,278,567 (+)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Slc25a38
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405118195,464,571 - 195,482,113 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_00493647328,603,445 - 28,621,355 (+)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_00493647328,602,920 - 28,621,024 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SLC25A38
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1324,030,653 - 24,044,782 (+)EnsemblsusScr11Sscrofa11.1
Sscrofa11.11324,030,571 - 24,043,866 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21326,291,188 - 26,304,483 (+)NCBISscrofa10.2Sscrofa10.2susScr3
SLC25A38
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11539,051 - 53,170 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1538,881 - 52,775 (-)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_0236660638,764,051 - 8,778,508 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Slc25a38
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462473078,818,069 - 78,832,091 (-)NCBIHetGla 1.0HetGla 1.0hetGla2

Variants

.
Variants in Slc25a38
87 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:293
Count of miRNA genes:195
Interacting mature miRNAs:214
Transcripts:ENSRNOT00000025142
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 (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
738011Anxrr9Anxiety related response QTL 96.1exploratory behavior trait (VT:0010471)number of entries into a discrete space in an experimental apparatus (CMO:0000960)893535351123900184Rat
724539Cm19Cardiac mass QTL 192.6heart mass (VT:0007028)calculated heart weight (CMO:0000073)8100149864120994388Rat
1358903Bp252Blood pressure QTL 25270.0001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)893965141123900184Rat
738014Anxrr15Anxiety related response QTL 153.60.005locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)895718998123900184Rat
2300182Bmd56Bone mineral density QTL 565.4femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)895718998123900184Rat
1554321Bmd3Bone mineral density QTL 37.90.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)840952565123900184Rat
2300181Bmd55Bone mineral density QTL 555.70.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)876468691121468691Rat
1358893Bp263Blood pressure QTL 2635.01arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)893965141123900184Rat
61437Cia6Collagen induced arthritis QTL 6joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)882460758122812818Rat

Markers in Region
RH141766  
Rat AssemblyChrPosition (strand)SourceJBrowse
GRCr88128,725,735 - 128,725,930 (+)Marker Load Pipeline
mRatBN7.28119,848,101 - 119,848,296 (+)MAPPERmRatBN7.2
Rnor_6.08128,802,756 - 128,802,950NCBIRnor6.0
Rnor_5.08128,003,441 - 128,003,635UniSTSRnor5.0
RGSC_v3.48125,097,096 - 125,097,290UniSTSRGSC3.4
Celera8118,993,093 - 118,993,287UniSTS
Cytogenetic Map8q32UniSTS


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
musculoskeletal system
nervous system
renal system
reproductive system
respiratory system
sensory system
visual system
23 13 74 196 91 90 59 136 59 6 439 246 15 179 103 117 31 30 30

Sequence


Ensembl Acc Id: ENSRNOT00000025142   ⟹   ENSRNOP00000025142
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl8128,713,131 - 128,725,966 (+)Ensembl
mRatBN7.2 Ensembl8119,835,634 - 119,848,332 (+)Ensembl
Rnor_6.0 Ensembl8128,790,348 - 128,802,986 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000083329   ⟹   ENSRNOP00000071588
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl8128,715,538 - 128,725,966 (+)Ensembl
mRatBN7.2 Ensembl8119,836,081 - 119,848,332 (+)Ensembl
Rnor_6.0 Ensembl8128,792,707 - 128,802,989 (+)Ensembl
RefSeq Acc Id: NM_001030032   ⟹   NP_001025203
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr88128,713,180 - 128,725,966 (+)NCBI
mRatBN7.28119,835,546 - 119,848,332 (+)NCBI
Rnor_6.08128,790,348 - 128,802,986 (+)NCBI
Rnor_5.08127,991,043 - 128,003,673 (+)NCBI
RGSC_v3.48125,084,481 - 125,097,326 (+)RGD
Celera8118,981,834 - 118,993,323 (+)RGD
Sequence:
RefSeq Acc Id: XM_006244089   ⟹   XP_006244151
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr88128,713,671 - 128,725,968 (+)NCBI
mRatBN7.28119,837,857 - 119,848,334 (+)NCBI
Rnor_6.08128,790,858 - 128,802,988 (+)NCBI
Rnor_5.08127,991,043 - 128,003,673 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039081301   ⟹   XP_038937229
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr88128,715,491 - 128,725,968 (+)NCBI
mRatBN7.28119,837,861 - 119,848,334 (+)NCBI
RefSeq Acc Id: XM_039081302   ⟹   XP_038937230
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr88128,713,267 - 128,725,968 (+)NCBI
mRatBN7.28119,835,574 - 119,848,334 (+)NCBI
RefSeq Acc Id: XM_039081304   ⟹   XP_038937232
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr88128,715,493 - 128,725,968 (+)NCBI
mRatBN7.28119,837,862 - 119,848,334 (+)NCBI
RefSeq Acc Id: XM_039081305   ⟹   XP_038937233
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr88128,715,493 - 128,725,968 (+)NCBI
mRatBN7.28119,837,862 - 119,848,334 (+)NCBI
RefSeq Acc Id: NP_001025203   ⟸   NM_001030032
- UniProtKB: Q499U1 (UniProtKB/Swiss-Prot),   G3V8E7 (UniProtKB/Swiss-Prot),   A0A8L2QD79 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006244151   ⟸   XM_006244089
- Peptide Label: isoform X1
- UniProtKB: A0A0G2K0U7 (UniProtKB/TrEMBL),   A0A8L2QD79 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000071588   ⟸   ENSRNOT00000083329
Ensembl Acc Id: ENSRNOP00000025142   ⟸   ENSRNOT00000025142
RefSeq Acc Id: XP_038937230   ⟸   XM_039081302
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038937229   ⟸   XM_039081301
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038937232   ⟸   XM_039081304
- Peptide Label: isoform X3
- UniProtKB: A6I3Z2 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038937233   ⟸   XM_039081305
- Peptide Label: isoform X3
- UniProtKB: A6I3Z2 (UniProtKB/TrEMBL)

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q499U1-F1-model_v2 AlphaFold Q499U1 1-326 view protein structure

Transcriptome

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

Promoters
RGD ID:13696383
Promoter ID:EPDNEW_R6905
Type:initiation region
Name:Slc25a38_1
Description:solute carrier family 25, member 38
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_6.08128,790,341 - 128,790,401EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1311914 AgrOrtholog
BioCyc Gene G2FUF-28760 BioCyc
Ensembl Genes ENSRNOG00000018552 Ensembl, ENTREZGENE
Ensembl Transcript ENSRNOT00000025142 ENTREZGENE
  ENSRNOT00000083329 ENTREZGENE
Gene3D-CATH 1.50.40.10 UniProtKB/Swiss-Prot
IMAGE_CLONE IMAGE:7930329 IMAGE-MGC_LOAD
InterPro Hem25/SLC25A38 UniProtKB/Swiss-Prot
  Mit_carrier UniProtKB/Swiss-Prot
  Mitochondrial_sb/sol_carrier UniProtKB/Swiss-Prot
  Mt_carrier_dom_sf UniProtKB/Swiss-Prot
KEGG Report rno:301067 UniProtKB/Swiss-Prot
MGC_CLONE MGC:124671 IMAGE-MGC_LOAD
NCBI Gene 301067 ENTREZGENE
PANTHER MITOCHONDRIAL GLYCINE TRANSPORTER UniProtKB/Swiss-Prot
  MITOCHONDRIAL GLYCINE TRANSPORTER UniProtKB/Swiss-Prot
Pfam Mito_carr UniProtKB/Swiss-Prot
PhenoGen Slc25a38 PhenoGen
PRINTS MITOCARRIER UniProtKB/Swiss-Prot
PROSITE SOLCAR UniProtKB/Swiss-Prot
RatGTEx ENSRNOG00000018552 RatGTEx
Superfamily-SCOP SSF103506 UniProtKB/Swiss-Prot
UniProt A0A0G2K0U7 ENTREZGENE, UniProtKB/TrEMBL
  A0A8L2QD79 ENTREZGENE, UniProtKB/TrEMBL
  A6I3Z2 ENTREZGENE, UniProtKB/TrEMBL
  G3V8E7 ENTREZGENE
  Q499U1 ENTREZGENE, UniProtKB/Swiss-Prot
UniProt Secondary G3V8E7 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-02-27 Slc25a38  solute carrier family 25, member 38  RGD1311914  similar to hypothetical protein MGC18873  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-12-06 RGD1311914  similar to hypothetical protein MGC18873  RGD1311914_predicted  similar to hypothetical protein MGC18873 (predicted)  Symbol and Name updated 1559027 APPROVED
2005-01-20 RGD1311914_predicted  similar to hypothetical protein MGC18873 (predicted)  LOC301067_predicted    Symbol and Name status set to approved 1331353 APPROVED
2005-01-12 LOC301067_predicted  similar to hypothetical protein MGC18873 (predicted)      Symbol and Name status set to provisional 70820 PROVISIONAL