RIMKLA (ribosomal modification protein rimK like family member A) - Rat Genome Database

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Gene: RIMKLA (ribosomal modification protein rimK like family member A) Canis lupus familiaris
Analyze
Symbol: RIMKLA
Name: ribosomal modification protein rimK like family member A
RGD ID: 12401640
Description: ENCODES a protein that exhibits ATP binding (inferred); metal ion binding (inferred); N-acetyl-L-aspartate-L-glutamate ligase activity (inferred); INVOLVED IN protein modification process (inferred); ASSOCIATED WITH Charcot-Marie-Tooth disease dominant intermediate C (ortholog); genetic disease (ortholog); FOUND IN cytoplasm (inferred)
Type: protein-coding
RefSeq Status: MODEL
Previously known as: N-acetylaspartylglutamate synthase A
RGD Orthologs
Human
Mouse
Rat
Chinchilla
Bonobo
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: CanFam3.1 - Dog CanFam3.1 Assembly
Position:
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.115853,705 - 888,721 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl15856,719 - 889,138 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha151,108,525 - 1,143,813 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.015935,312 - 970,597 (-)NCBIROS_Cfam_1.0
UMICH_Zoey_3.115844,536 - 879,796 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.015906,054 - 941,309 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.015921,178 - 956,452 (-)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)

Molecular Function

References
Additional References at PubMed
PMID:22301074   PMID:30032202  


Genomics

Comparative Map Data
RIMKLA
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.115853,705 - 888,721 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl15856,719 - 889,138 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha151,108,525 - 1,143,813 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.015935,312 - 970,597 (-)NCBIROS_Cfam_1.0
UMICH_Zoey_3.115844,536 - 879,796 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.015906,054 - 941,309 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.015921,178 - 956,452 (-)NCBIUU_Cfam_GSD_1.0
RIMKLA
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38142,380,792 - 42,424,232 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl142,380,792 - 42,424,232 (+)EnsemblGRCh38hg38GRCh38
GRCh37142,846,463 - 42,889,903 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36142,619,064 - 42,653,437 (+)NCBINCBI36Build 36hg18NCBI36
Celera141,128,424 - 41,171,853 (+)NCBICelera
Cytogenetic Map1p34.2NCBI
HuRef140,966,574 - 41,009,995 (+)NCBIHuRef
CHM1_1142,963,386 - 43,006,757 (+)NCBICHM1_1
T2T-CHM13v2.0142,251,175 - 42,294,608 (+)NCBIT2T-CHM13v2.0
Rimkla
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm394119,322,480 - 119,349,795 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl4119,322,480 - 119,349,825 (-)EnsemblGRCm39 Ensembl
GRCm384119,465,283 - 119,492,598 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl4119,465,283 - 119,492,628 (-)EnsemblGRCm38mm10GRCm38
MGSCv374119,137,888 - 119,165,203 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv364118,963,215 - 118,990,511 (-)NCBIMGSCv36mm8
Celera4118,196,499 - 118,223,900 (-)NCBICelera
Cytogenetic Map4D2.1NCBI
cM Map455.4NCBI
Rimkla
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr85138,357,463 - 138,384,132 (-)NCBIGRCr8
mRatBN7.25133,072,179 - 133,098,840 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl5133,073,960 - 133,098,792 (-)EnsemblmRatBN7.2 Ensembl
Rnor_6.05138,518,559 - 138,545,577 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl5138,521,340 - 138,545,404 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.05142,324,385 - 142,350,390 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.45140,060,901 - 140,085,824 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.15140,067,034 - 140,090,967 (-)NCBI
Celera5131,595,800 - 131,622,259 (-)NCBICelera
Cytogenetic Map5q36NCBI
Rimkla
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555371,992,670 - 2,021,340 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049555371,992,660 - 2,024,331 (+)NCBIChiLan1.0ChiLan1.0
RIMKLA
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21184,389,708 - 184,431,363 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11183,531,601 - 183,573,319 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0141,680,447 - 41,722,087 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1143,061,769 - 43,103,043 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl143,061,769 - 43,095,443 (+)Ensemblpanpan1.1panPan2
Rimkla
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440505857,975,850 - 58,009,557 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_00493647423,800,642 - 23,824,145 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_00493647423,800,632 - 23,827,184 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
RIMKLA
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl6168,916,725 - 168,950,046 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.16168,909,477 - 168,949,921 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.26156,332,262 - 156,352,608 (+)NCBISscrofa10.2Sscrofa10.2susScr3
RIMKLA
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12090,511,003 - 90,549,400 (-)NCBIChlSab1.1ChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366603326,360,426 - 26,403,424 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Rimkla
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248921,696,182 - 1,724,848 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046248921,696,275 - 1,731,905 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in RIMKLA
218 total Variants

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 reproductive system respiratory system adipose tissue
High
Medium 6 2
Low 5 5 16 6 6 6 8 8 6
Below cutoff 6 6 6 6

Sequence


RefSeq Acc Id: ENSCAFT00000004034   ⟹   ENSCAFP00000003727
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.1 Ensembl15856,719 - 889,138 (-)Ensembl
RefSeq Acc Id: ENSCAFT00000036945   ⟹   ENSCAFP00000032380
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.1 Ensembl15856,719 - 889,138 (-)Ensembl
RefSeq Acc Id: XM_038451790   ⟹   XP_038307718
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
Dog10K_Boxer_Tasha151,108,525 - 1,143,373 (-)NCBI
RefSeq Acc Id: XM_038495341   ⟹   XP_038351269
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UMICH_Zoey_3.115844,536 - 879,796 (-)NCBI
RefSeq Acc Id: XM_038495342   ⟹   XP_038351270
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UMICH_Zoey_3.115844,536 - 879,356 (-)NCBI
RefSeq Acc Id: XM_038557688   ⟹   XP_038413616
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UU_Cfam_GSD_1.015921,178 - 956,452 (-)NCBI
RefSeq Acc Id: XM_038557689   ⟹   XP_038413617
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UU_Cfam_GSD_1.015921,178 - 956,012 (-)NCBI
RefSeq Acc Id: XM_038621578   ⟹   XP_038477506
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UNSW_CanFamBas_1.015906,054 - 941,309 (-)NCBI
RefSeq Acc Id: XM_038621579   ⟹   XP_038477507
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UNSW_CanFamBas_1.015906,054 - 940,869 (-)NCBI
RefSeq Acc Id: XM_038687348   ⟹   XP_038543276
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
ROS_Cfam_1.015935,312 - 970,597 (-)NCBI
RefSeq Acc Id: XM_038687349   ⟹   XP_038543277
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
ROS_Cfam_1.015935,312 - 970,157 (-)NCBI
RefSeq Acc Id: XM_539562   ⟹   XP_539562
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.115853,705 - 888,721 (-)NCBI
Dog10K_Boxer_Tasha151,108,525 - 1,143,813 (-)NCBI
Sequence:
RefSeq Acc Id: XP_539562   ⟸   XM_539562
- Peptide Label: isoform X1
- UniProtKB: A0A8C0RRR9 (UniProtKB/TrEMBL),   A0A8P0TPP9 (UniProtKB/TrEMBL),   A0A8C0PFC6 (UniProtKB/TrEMBL),   A0A8P0PJC1 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSCAFP00000003727   ⟸   ENSCAFT00000004034
RefSeq Acc Id: ENSCAFP00000032380   ⟸   ENSCAFT00000036945
RefSeq Acc Id: XP_038351269   ⟸   XM_038495341
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038351270   ⟸   XM_038495342
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038477506   ⟸   XM_038621578
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038477507   ⟸   XM_038621579
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038543276   ⟸   XM_038687348
- Peptide Label: isoform X1
- UniProtKB: A0A8C0RRR9 (UniProtKB/TrEMBL),   A0A8P0TPP9 (UniProtKB/TrEMBL),   A0A8C0PFC6 (UniProtKB/TrEMBL),   A0A8P0PJC1 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038543277   ⟸   XM_038687349
- Peptide Label: isoform X2
- UniProtKB: A0A8C0PFC6 (UniProtKB/TrEMBL),   A0A8P0PJC1 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038307718   ⟸   XM_038451790
- Peptide Label: isoform X2
- UniProtKB: A0A8C0PFC6 (UniProtKB/TrEMBL),   A0A8P0PJC1 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038413616   ⟸   XM_038557688
- Peptide Label: isoform X1
- UniProtKB: A0A8C0PFC6 (UniProtKB/TrEMBL),   A0A8C0RRR9 (UniProtKB/TrEMBL),   A0A8P0PJC1 (UniProtKB/TrEMBL),   A0A8P0TPP9 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038413617   ⟸   XM_038557689
- Peptide Label: isoform X2
- UniProtKB: A0A8C0PFC6 (UniProtKB/TrEMBL),   A0A8P0PJC1 (UniProtKB/TrEMBL)
Protein Domains
ATP-grasp


Additional Information

Database Acc Id Source(s)
Ensembl Genes ENSCAFG00000002557 Ensembl
  ENSCAFG00000052708 UniProtKB/TrEMBL
  ENSCAFG00030023328 UniProtKB/TrEMBL
  ENSCAFG00040010332 UniProtKB/TrEMBL
  ENSCAFG00845017232 UniProtKB/TrEMBL
Ensembl Transcript ENSCAFT00000096582.1 UniProtKB/TrEMBL
  ENSCAFT00000102547.1 UniProtKB/TrEMBL
  ENSCAFT00030042879.1 UniProtKB/TrEMBL
  ENSCAFT00030042898.1 UniProtKB/TrEMBL
  ENSCAFT00040019121.1 UniProtKB/TrEMBL
  ENSCAFT00040019164.1 UniProtKB/TrEMBL
  ENSCAFT00845030478.1 UniProtKB/TrEMBL
  ENSCAFT00845030522.1 UniProtKB/TrEMBL
Gene3D-CATH 3.30.1490.20 UniProtKB/TrEMBL
  3.40.50.20 UniProtKB/TrEMBL
  ATP-grasp fold, B domain UniProtKB/TrEMBL
InterPro ATP-grasp UniProtKB/TrEMBL
  ATP-grasp_RimK-type UniProtKB/TrEMBL
  ATP_grasp_subdomain_1 UniProtKB/TrEMBL
  RpS6_RimK/Lys_biosynth_LsyX UniProtKB/TrEMBL
NCBI Gene RIMKLA ENTREZGENE
PANTHER N-ACETYLASPARTYLGLUTAMATE SYNTHASE A UniProtKB/TrEMBL
  RIBOSOMAL PROTEIN S6 MODIFICATION PROTEIN UniProtKB/TrEMBL
Pfam RimK UniProtKB/TrEMBL
PROSITE ATP_GRASP UniProtKB/TrEMBL
Superfamily-SCOP Glutathione synthetase ATP-binding domain-like UniProtKB/TrEMBL
UniProt A0A8C0PFC6 ENTREZGENE, UniProtKB/TrEMBL
  A0A8C0RRR9 ENTREZGENE, UniProtKB/TrEMBL
  A0A8I3NX83_CANLF UniProtKB/TrEMBL
  A0A8I3P1Y2_CANLF UniProtKB/TrEMBL
  A0A8P0PJC1 ENTREZGENE
  A0A8P0TPP9 ENTREZGENE
UniProt Secondary A0A8P0PJC1 UniProtKB/TrEMBL
  A0A8P0TPP9 UniProtKB/TrEMBL
VGNC ID VGNC:45580 ENTREZGENE