Gramd4 (GRAM domain containing 4) - Rat Genome Database

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Gene: Gramd4 (GRAM domain containing 4) Rattus norvegicus
Analyze
Symbol: Gramd4
Name: GRAM domain containing 4
RGD ID: 1309983
Description: Predicted to be involved in negative regulation of toll-like receptor 9 signaling pathway and positive regulation of apoptotic process. Predicted to be located in endoplasmic reticulum membrane and mitochondrial membrane. Predicted to be active in mitochondrion. Orthologous to human GRAMD4 (GRAM domain containing 4); INTERACTS WITH 6-propyl-2-thiouracil; amphetamine; atrazine.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: death-inducing-protein; Dip; GRAM domain-containing protein 4; LOC315203; RGD1309983; similar to hypothetical protein 9930016O13
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Black Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr87119,030,225 - 119,103,875 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl7119,030,225 - 119,103,875 (+)EnsemblGRCr8
mRatBN7.27117,150,398 - 117,224,056 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl7117,150,374 - 117,224,053 (+)EnsemblmRatBN7.2
Rnor_6.07126,939,819 - 127,013,455 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl7126,939,925 - 127,013,486 (+)Ensemblrn6Rnor6.0
Rnor_5.07126,650,776 - 126,723,990 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.47124,062,507 - 124,134,558 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera7113,441,339 - 113,514,781 (+)NCBICelera
RGSC_v3.17124,095,596 - 124,168,395 (+)NCBI
Cytogenetic Map7q34NCBI
JBrowse:




Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

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. GOA pipeline RGD automated data pipeline
3. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:15565177   PMID:25917084  


Genomics

Comparative Map Data
Gramd4
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr87119,030,225 - 119,103,875 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl7119,030,225 - 119,103,875 (+)EnsemblGRCr8
mRatBN7.27117,150,398 - 117,224,056 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl7117,150,374 - 117,224,053 (+)EnsemblmRatBN7.2
Rnor_6.07126,939,819 - 127,013,455 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl7126,939,925 - 127,013,486 (+)Ensemblrn6Rnor6.0
Rnor_5.07126,650,776 - 126,723,990 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.47124,062,507 - 124,134,558 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera7113,441,339 - 113,514,781 (+)NCBICelera
RGSC_v3.17124,095,596 - 124,168,395 (+)NCBI
Cytogenetic Map7q34NCBI
GRAMD4
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh382246,575,744 - 46,682,756 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl2246,575,644 - 46,679,790 (+)Ensemblhg38GRCh38
GRCh372246,972,985 - 47,078,653 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 362245,401,322 - 45,454,352 (+)NCBIBuild 36Build 36hg18NCBI36
Celera2230,928,417 - 30,991,380 (+)NCBICelera
Cytogenetic Map22q13.31NCBI
HuRef2229,967,301 - 30,020,467 (+)NCBIHuRef
CHM1_12246,981,380 - 47,034,369 (+)NCBICHM1_1
T2T-CHM13v2.02247,062,971 - 47,170,713 (+)NCBIT2T-CHM13v2.0
Gramd4
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391585,941,896 - 86,021,837 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1585,941,896 - 86,021,835 (+)EnsemblGRCm39 EnsemblGRCm39
GRCm381586,057,695 - 86,137,636 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1586,057,695 - 86,137,634 (+)Ensemblmm10GRCm38
MGSCv371585,888,137 - 85,968,064 (+)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv361585,885,473 - 85,965,310 (+)NCBIMGSCv36mm8
Celera1588,199,972 - 88,280,152 (+)NCBICelera
Cytogenetic Map15E2NCBI
cM Map1540.48NCBI
Gramd4
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495541330,603,580 - 30,656,940 (+)Ensembl
ChiLan1.0NW_00495541330,603,820 - 30,656,940 (+)NCBIChiLan1.0ChiLan1.0
GRAMD4
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v22356,411,020 - 56,551,530 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan12259,104,712 - 59,243,675 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v02226,789,989 - 26,877,172 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.12245,693,067 - 45,745,520 (+)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2245,687,833 - 45,745,518 (+)EnsemblpanPan2panpan1.1
GRAMD4
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11019,608,037 - 19,643,294 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1019,605,955 - 19,661,694 (-)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha1019,525,704 - 19,599,170 (-)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.01020,339,831 - 20,413,366 (-)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl1020,339,835 - 20,413,366 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.11020,057,889 - 20,131,258 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01020,369,996 - 20,443,394 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01020,551,661 - 20,625,250 (-)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Gramd4
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_0244049453,347,466 - 3,398,624 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049366293,346,495 - 3,432,096 (-)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_0049366293,348,461 - 3,431,975 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
GRAMD4
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl52,873,428 - 2,947,785 (-)EnsemblsusScr11Sscrofa11.1
Sscrofa11.152,873,466 - 2,947,804 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
GRAMD4
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11929,068,166 - 29,175,646 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1929,070,023 - 29,172,977 (+)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_02366604596,360,766 - 96,701,961 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Gramd4
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247523,330,905 - 3,400,977 (-)EnsemblHetGla_female_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_0046247523,328,132 - 3,401,027 (-)NCBIHetGla 1.0HetGla 1.0hetGla2
Gramd4
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v11255,438,325 - 255,481,269 (+)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Gramd4
385 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:94
Count of miRNA genes:72
Interacting mature miRNAs:76
Transcripts:ENSRNOT00000022746, ENSRNOT00000045635
Prediction methods:Microtar, Miranda, Rnahybrid
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
1300179Kidm5Kidney mass QTL 53.51kidney mass (VT:0002707)left kidney wet weight (CMO:0000083)792388565119280177Rat
1331728Bp214Blood pressure QTL 2142.825arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)782111245123048330Rat
1331731Bp216Blood pressure QTL 2162.851arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)7104186212135371468Rat
631687Hcas1Hepatocarcinoma susceptibility QTL 13.90.001liver integrity trait (VT:0010547)liver tumorous lesion volume to total liver volume ratio (CMO:0001082)793302009131686183Rat
61397Bw17Body weight QTL 176.3body mass (VT:0001259)body weight (CMO:0000012)795485047137014596Rat
1358914Bp266Blood pressure QTL 266arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)7115313999136544683Rat
631504Cm27Cardiac mass QTL 273.45heart left ventricle mass (VT:0007031)heart left ventricle wet weight (CMO:0000071)746307490127866166Rat
634322Bw12Body weight QTL 120body mass (VT:0001259)body weight (CMO:0000012)785043242130043242Rat
70173Niddm19Non-insulin dependent diabetes mellitus QTL 194.330.00005blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)785497398130497398Rat
1549899Stresp8Stress response QTL 84.370.0008stress-related behavior trait (VT:0010451)defensive burying duration (CMO:0001961)792362341137014596Rat
2317052Aia17Adjuvant induced arthritis QTL 172.13joint integrity trait (VT:0010548)left rear ankle joint diameter (CMO:0002149)783626689128626689Rat
631529Tls2T-lymphoma susceptibility QTL 200.001thymus integrity trait (VT:0010555)percentage of study population developing T-cell lymphomas during a period of time (CMO:0001911)782111382132099989Rat
731176Glom5Glomerulus QTL 52.50.0035kidney glomerulus morphology trait (VT:0005325)count of superficial glomeruli not directly contacting the kidney surface (CMO:0001002)798549867137014596Rat
7411607Foco15Food consumption QTL 150.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)777807807122807807Rat
1331768Kidm10Kidney mass QTL 104.62096kidney mass (VT:0002707)left kidney wet weight (CMO:0000083)782111245123048330Rat
61357Bp38Blood pressure QTL 381.60.052arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)740540077123682549Rat
1331748Bp215Blood pressure QTL 2154.043arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)7110725024135371468Rat
61428Scl3Serum cholesterol level QTL 33.2blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)7100548246137014596Rat
1331746Kidm9Kidney mass QTL 93.934kidney mass (VT:0002707)right kidney wet weight (CMO:0000082)782111245134948181Rat
7411654Foco25Food consumption QTL 259.30.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)777807807122807807Rat
1582240Sffal1Serum free fatty acids level QTL 13.40.0021blood free fatty acid amount (VT:0001553)serum free fatty acids level (CMO:0000547)7118556868125929417Rat
2299163Iddm34Insulin dependent diabetes mellitus QTL 342.71blood glucose amount (VT:0000188)age at onset/diagnosis of type 1 diabetes mellitus (CMO:0001140)7116269196132020414Rat
10402855Bp379Blood pressure QTL 3790.21arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)778682549123682549Rat
631540Bw9Body weight QTL 94.5body mass (VT:0001259)body weight (CMO:0000012)771621154119349044Rat
1358891Bp265Blood pressure QTL 2652.21arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)771827901136544683Rat

Markers in Region
AU047797  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.27117,170,753 - 117,170,854 (+)MAPPERmRatBN7.2
Rnor_6.07126,960,157 - 126,960,257NCBIRnor6.0
Rnor_5.07126,670,704 - 126,670,804UniSTSRnor5.0
RGSC_v3.47124,083,091 - 124,083,191UniSTSRGSC3.4
Celera7113,461,479 - 113,461,579UniSTS
Cytogenetic Map7q34UniSTS


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
16 12 67 165 91 90 59 92 59 6 356 192 11 144 81 92 31 17 17

Sequence


Ensembl Acc Id: ENSRNOT00000022746   ⟹   ENSRNOP00000022746
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl7119,030,225 - 119,103,875 (+)Ensembl
mRatBN7.2 Ensembl7117,150,374 - 117,224,053 (+)Ensembl
Rnor_6.0 Ensembl7126,939,925 - 127,013,486 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000095265   ⟹   ENSRNOP00000094040
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl7119,040,479 - 119,103,875 (+)Ensembl
mRatBN7.2 Ensembl7117,175,931 - 117,224,050 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000111804   ⟹   ENSRNOP00000084782
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl7119,046,108 - 119,103,875 (+)Ensembl
mRatBN7.2 Ensembl7117,166,010 - 117,224,053 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000172490   ⟹   ENSRNOP00000102987
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl7119,059,733 - 119,103,875 (+)Ensembl
RefSeq Acc Id: NM_001427302   ⟹   NP_001414231
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr87119,030,225 - 119,103,875 (+)NCBI
RefSeq Acc Id: XM_017595281   ⟹   XP_017450770
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr87119,030,527 - 119,103,875 (+)NCBI
mRatBN7.27117,150,684 - 117,224,056 (+)NCBI
Rnor_6.07126,940,207 - 127,013,455 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017595282   ⟹   XP_017450771
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr87119,056,595 - 119,103,875 (+)NCBI
mRatBN7.27117,176,772 - 117,224,056 (+)NCBI
Rnor_6.07126,965,570 - 127,013,455 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039080319   ⟹   XP_038936247
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr87119,060,064 - 119,103,875 (+)NCBI
mRatBN7.27117,180,135 - 117,224,056 (+)NCBI
RefSeq Acc Id: XP_017450770   ⟸   XM_017595281
- Peptide Label: isoform X1
- UniProtKB: A0A8I6GKJ8 (UniProtKB/TrEMBL),   F1LYJ8 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_017450771   ⟸   XM_017595282
- Peptide Label: isoform X1
- UniProtKB: A0A8I6GKJ8 (UniProtKB/TrEMBL),   F1LYJ8 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000022746   ⟸   ENSRNOT00000022746
RefSeq Acc Id: XP_038936247   ⟸   XM_039080319
- Peptide Label: isoform X1
- UniProtKB: A0A8I6GKJ8 (UniProtKB/TrEMBL),   F1LYJ8 (UniProtKB/TrEMBL)
Ensembl Acc Id: ENSRNOP00000084782   ⟸   ENSRNOT00000111804
Ensembl Acc Id: ENSRNOP00000094040   ⟸   ENSRNOT00000095265
RefSeq Acc Id: NP_001414231   ⟸   NM_001427302
- UniProtKB: F1LYJ8 (UniProtKB/TrEMBL)
Ensembl Acc Id: ENSRNOP00000102987   ⟸   ENSRNOT00000172490
Protein Domains
GRAM

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-F1LYJ8-F1-model_v2 AlphaFold F1LYJ8 1-608 view protein structure

Transcriptome

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


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1309983 AgrOrtholog
BioCyc Gene G2FUF-32520 BioCyc
Ensembl Genes ENSRNOG00000016968 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000022746 ENTREZGENE
  ENSRNOT00000022746.10 UniProtKB/TrEMBL
  ENSRNOT00000095265 ENTREZGENE
  ENSRNOT00000095265.2 UniProtKB/TrEMBL
  ENSRNOT00000111804.2 UniProtKB/TrEMBL
  ENSRNOT00000172490 ENTREZGENE
  ENSRNOT00000172490.1 UniProtKB/TrEMBL
Gene3D-CATH 2.30.29.30 UniProtKB/TrEMBL
InterPro GRAM UniProtKB/TrEMBL
  GRAMDC4 UniProtKB/TrEMBL
  GRAMDC4_PH-GRAM UniProtKB/TrEMBL
  PH-like_dom_sf UniProtKB/TrEMBL
NCBI Gene 315203 ENTREZGENE
PANTHER GRAM DOMAIN-CONTAINING PROTEIN 4 UniProtKB/TrEMBL
  PTHR37402 UniProtKB/TrEMBL
Pfam GRAM UniProtKB/TrEMBL
PhenoGen Gramd4 PhenoGen
RatGTEx ENSRNOG00000016968 RatGTEx
SMART GRAM UniProtKB/TrEMBL
UniProt A0A8I6A0A6_RAT UniProtKB/TrEMBL
  A0A8I6GKJ8 ENTREZGENE, UniProtKB/TrEMBL
  A0ABK0L2H7_RAT UniProtKB/TrEMBL
  F1LYJ8 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-05-08 Gramd4  GRAM domain containing 4  Dip  death-inducing-protein  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-02-26 Dip  death-inducing-protein  RGD1309983_predicted  similar to hypothetical protein 9930016O13 (predicted)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-01-20 RGD1309983_predicted  similar to hypothetical protein 9930016O13 (predicted)  LOC315203_predicted    Symbol and Name status set to approved 1331353 APPROVED
2005-01-12 LOC315203_predicted  similar to hypothetical protein 9930016O13 (predicted)      Symbol and Name status set to provisional 70820 PROVISIONAL