THUMPD3 (THUMP domain containing 3) - Rat Genome Database

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Gene: THUMPD3 (THUMP domain containing 3) Canis lupus familiaris
Analyze
Symbol: THUMPD3
Name: THUMP domain containing 3
RGD ID: 12338272
Description: ENCODES a protein that exhibits methyltransferase activity (inferred); RNA binding (inferred); tRNA (guanine(6)-N2)-methyltransferase activity (inferred); INVOLVED IN methylation (inferred); RNA processing (inferred); tRNA methylation (inferred); ASSOCIATED WITH 3p deletion syndrome (ortholog); Atrioventricular Septal Defect 2 (ortholog); long QT syndrome (ortholog); FOUND IN cytoplasm (inferred); cytosol (inferred); nucleolus (inferred)
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: THUMP domain-containing protein 3; tRNA (guanine(6)-N2)-methyltransferase THUMP3
RGD Orthologs
Human
Mouse
Rat
Chinchilla
Bonobo
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Related Pseudogenes: LOC475972  
Latest Assembly: CanFam3.1 - Dog CanFam3.1 Assembly
Position:
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1208,779,442 - 8,802,286 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl208,779,442 - 8,802,215 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha208,811,833 - 8,834,603 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0208,808,906 - 8,831,764 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl208,808,289 - 8,831,654 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1208,530,804 - 8,553,575 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0208,876,208 - 8,898,976 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0208,849,544 - 8,872,338 (-)NCBIUU_Cfam_GSD_1.0
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  (IEA)
cytosol  (IEA)
nucleolus  (IEA)

Molecular Function

References
Additional References at PubMed
PMID:16723480   PMID:22301074   PMID:30032202  


Genomics

Comparative Map Data
THUMPD3
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1208,779,442 - 8,802,286 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl208,779,442 - 8,802,215 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha208,811,833 - 8,834,603 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0208,808,906 - 8,831,764 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl208,808,289 - 8,831,654 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1208,530,804 - 8,553,575 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0208,876,208 - 8,898,976 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0208,849,544 - 8,872,338 (-)NCBIUU_Cfam_GSD_1.0
THUMPD3
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh3839,363,054 - 9,386,791 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl39,362,971 - 9,386,791 (+)EnsemblGRCh38hg38GRCh38
GRCh3739,404,738 - 9,428,475 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 3639,379,736 - 9,402,412 (+)NCBINCBI36Build 36hg18NCBI36
Build 3439,379,735 - 9,402,412NCBI
Celera39,339,426 - 9,363,176 (+)NCBICelera
Cytogenetic Map3p25.3NCBI
HuRef39,341,480 - 9,365,230 (+)NCBIHuRef
CHM1_139,354,927 - 9,378,706 (+)NCBICHM1_1
T2T-CHM13v2.039,354,825 - 9,378,730 (+)NCBIT2T-CHM13v2.0
Thumpd3
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm396113,023,292 - 113,045,239 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl6113,023,186 - 113,045,234 (+)EnsemblGRCm39 Ensembl
GRCm386113,046,302 - 113,068,278 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl6113,046,225 - 113,068,273 (+)EnsemblGRCm38mm10GRCm38
MGSCv376112,996,321 - 113,018,267 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv366113,012,104 - 113,034,050 (+)NCBIMGSCv36mm8
Celera6114,875,220 - 114,897,164 (+)NCBICelera
Cytogenetic Map6E3NCBI
cM Map652.73NCBI
Thumpd3
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr84147,741,288 - 147,764,254 (+)NCBIGRCr8
mRatBN7.24146,185,422 - 146,209,802 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl4146,185,503 - 146,211,246 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx4151,569,798 - 151,592,778 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.04147,350,610 - 147,373,590 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.04145,972,021 - 145,994,999 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.04144,985,850 - 145,010,164 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl4144,985,880 - 145,008,831 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.04208,284,202 - 208,308,521 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.44148,918,100 - 148,941,045 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera4134,744,697 - 134,767,664 (+)NCBICelera
Cytogenetic Map4q42NCBI
Thumpd3
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_004955561933,173 - 956,457 (+)EnsemblChiLan1.0
ChiLan1.0NW_004955561933,168 - 956,457 (+)NCBIChiLan1.0ChiLan1.0
THUMPD3
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v229,374,529 - 9,397,487 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan139,379,287 - 9,402,245 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v039,315,275 - 9,338,096 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.139,557,642 - 9,581,157 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl39,557,894 - 9,581,157 (+)Ensemblpanpan1.1panPan2
Thumpd3
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494215,220,520 - 15,245,355 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049366023,661,967 - 3,689,159 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049366023,664,354 - 3,689,130 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
THUMPD3
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1365,721,475 - 65,747,076 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11365,720,556 - 65,747,989 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21372,863,112 - 72,885,873 (+)NCBISscrofa10.2Sscrofa10.2susScr3
THUMPD3
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12245,355,889 - 45,378,134 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl2245,355,579 - 45,377,941 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_023666041121,179,371 - 121,203,965 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Thumpd3
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247314,052,631 - 4,077,486 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046247314,052,618 - 4,078,639 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in THUMPD3
207 total Variants

Expression

RNA-SEQ Expression

adipose tissue
alimentary part of gastrointestinal system
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
nervous system
reproductive system
respiratory system
6 5 5 23 22 16 6 6 6 6 33 22 12 14 10

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_001252173 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_005632045 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_005632046 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_022406262 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_022406263 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_038426511 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_038426512 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AAEX04000020 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CF409766 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CX001790 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  DT536470 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  GR896512 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JAAHUQ010000232 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JAAQRD010000058 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JAAUVH010000291 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  REHQ01000020 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Ensembl Acc Id: ENSCAFT00000035640   ⟹   ENSCAFP00000030923
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.1 Ensembl208,779,442 - 8,802,215 (-)Ensembl
Ensembl Acc Id: ENSCAFT00845017895   ⟹   ENSCAFP00845013940
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
ROS_Cfam_1.0 Ensembl208,808,289 - 8,831,654 (-)Ensembl
RefSeq Acc Id: NM_001252173   ⟹   NP_001239102
RefSeq Status: VALIDATED
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.1208,779,442 - 8,802,215 (-)NCBI
Dog10K_Boxer_Tasha208,811,833 - 8,834,603 (-)NCBI
ROS_Cfam_1.0208,808,910 - 8,831,683 (-)NCBI
UMICH_Zoey_3.1208,530,804 - 8,553,575 (-)NCBI
UNSW_CanFamBas_1.0208,876,208 - 8,898,976 (-)NCBI
UU_Cfam_GSD_1.0208,849,544 - 8,872,338 (-)NCBI
Sequence:
RefSeq Acc Id: XM_038426511   ⟹   XP_038282439
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
ROS_Cfam_1.0208,808,906 - 8,831,764 (-)NCBI
RefSeq Acc Id: XM_038426512   ⟹   XP_038282440
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
ROS_Cfam_1.0208,808,906 - 8,831,764 (-)NCBI
RefSeq Acc Id: NP_001239102   ⟸   NM_001252173
- UniProtKB: A0A8C0TWU7 (UniProtKB/TrEMBL),   A0A8C0QXL9 (UniProtKB/TrEMBL),   A0A8I3NEC2 (UniProtKB/TrEMBL),   A0A8P0NN69 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSCAFP00000030923   ⟸   ENSCAFT00000035640
RefSeq Acc Id: XP_038282440   ⟸   XM_038426512
- Peptide Label: isoform X2
- UniProtKB: A0A8P0NN69 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038282439   ⟸   XM_038426511
- Peptide Label: isoform X1
- UniProtKB: A0A8P0NN69 (UniProtKB/TrEMBL)
Ensembl Acc Id: ENSCAFP00845013940   ⟸   ENSCAFT00845017895
Protein Domains
THUMP

Promoters
RGD ID:13686791
Promoter ID:EPDNEW_C4861
Type:initiation region
Name:THUMPD3_1
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.1208,802,186 - 8,802,246EPDNEW

Additional Information

Database Acc Id Source(s)
Ensembl Genes ENSCAFG00000005499 Ensembl, UniProtKB/TrEMBL
  ENSCAFG00000008060 UniProtKB/TrEMBL
  ENSCAFG00030008815 UniProtKB/TrEMBL
  ENSCAFG00040025111 UniProtKB/TrEMBL
  ENSCAFG00845010175 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSCAFT00000012854.5 UniProtKB/TrEMBL
  ENSCAFT00000035640.3 UniProtKB/TrEMBL
  ENSCAFT00030016270.1 UniProtKB/TrEMBL
  ENSCAFT00040046817.1 UniProtKB/TrEMBL
  ENSCAFT00845017895 ENTREZGENE
  ENSCAFT00845017895.1 UniProtKB/TrEMBL
Gene3D-CATH 3.30.2130.30 UniProtKB/TrEMBL
  3.40.50.150 UniProtKB/TrEMBL
InterPro RlmKL-like_Mtase_CS UniProtKB/TrEMBL
  RNA_methylase_dom UniProtKB/TrEMBL
  SAM-dependent_MTases UniProtKB/TrEMBL
  THUMP_dom UniProtKB/TrEMBL
KEGG Report cfa:610222 UniProtKB/TrEMBL
NCBI Gene THUMPD3 ENTREZGENE
PANTHER THUMP DOMAIN-CONTAINING UniProtKB/TrEMBL
  THUMP DOMAIN-CONTAINING PROTEIN 3 UniProtKB/TrEMBL
Pfam THUMP UniProtKB/TrEMBL
  UPF0020 UniProtKB/TrEMBL
PROSITE THUMP UniProtKB/TrEMBL
  UPF0020 UniProtKB/TrEMBL
SMART THUMP UniProtKB/TrEMBL
Superfamily-SCOP SSF53335 UniProtKB/TrEMBL
  THUMP domain-like UniProtKB/TrEMBL
UniProt A0A8C0QXL9 ENTREZGENE
  A0A8C0TWU7 ENTREZGENE, UniProtKB/TrEMBL
  A0A8I3NEC2 ENTREZGENE, UniProtKB/TrEMBL
  A0A8P0NN69 ENTREZGENE, UniProtKB/TrEMBL