Pam16 (presequence translocase associated motor 16) - Rat Genome Database

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Gene: Pam16 (presequence translocase associated motor 16) Rattus norvegicus
Analyze
Symbol: Pam16
Name: presequence translocase associated motor 16
RGD ID: 1598163
Description: Involved in negative regulation of apoptotic DNA fragmentation and negative regulation of release of cytochrome c from mitochondria. Predicted to be located in mitochondrial matrix. Predicted to be part of PAM complex, Tim23 associated import motor. Predicted to colocalize with matrix side of mitochondrial inner membrane. Human ortholog(s) of this gene implicated in spondylometaphyseal dysplasia Megarbane-Dagher-Melike type. Orthologous to human PAM16 (presequence translocase associated motor 16); PARTICIPATES IN presequence pathway of mitochondrial protein import; INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 3-chloropropane-1,2-diol; 6-propyl-2-thiouracil.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: LOC679907; Magmas; mitochondria-associated granulocyte macrophage CSF signaling molecule; mitochondria-associated protein involved in granulocyte-macrophage colony-stimulating factor signal transduction; mitochondrial import inner membrane translocase subunit TIM16; presequence translocase associated motor 16 homolog; presequence translocase-associated motor 16 homolog; presequence translocase-associated motor 16 homolog (S. cerevisiae); similar to mitochondria-associated granulocyte macrophage CSF signaling molecule
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Related Pseudogenes: Magmas-ps1  
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81011,449,316 - 11,457,071 (+)NCBIGRCr8
mRatBN7.21010,942,534 - 10,950,654 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1010,943,001 - 10,950,649 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1015,651,764 - 15,659,342 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01015,140,582 - 15,148,160 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01010,809,734 - 10,817,306 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01011,146,359 - 11,153,936 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1011,146,359 - 11,153,936 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0109,911,717 - 9,919,294 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41011,072,402 - 11,079,980 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera109,905,330 - 9,912,908 (+)NCBICelera
Cytogenetic Map10q12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
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. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
3. Comprehensive gene review and curation RGD comprehensive gene curation
4. Unlocking the presequence import pathway. Schulz C, etal., Trends Cell Biol. 2015 May;25(5):265-75. doi: 10.1016/j.tcb.2014.12.001. Epub 2014 Dec 23.
5. Magmas overexpression inhibits staurosporine induced apoptosis in rat pituitary adenoma cell lines. Tagliati F, etal., PLoS One. 2013 Sep 17;8(9):e75194. doi: 10.1371/journal.pone.0075194. eCollection 2013.
Additional References at PubMed
PMID:8889548   PMID:12704206   PMID:12865426   PMID:15632090   PMID:15984936   PMID:18614015   PMID:19564938   PMID:20053669   PMID:20719856   PMID:24786642  


Genomics

Comparative Map Data
Pam16
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81011,449,316 - 11,457,071 (+)NCBIGRCr8
mRatBN7.21010,942,534 - 10,950,654 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1010,943,001 - 10,950,649 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1015,651,764 - 15,659,342 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01015,140,582 - 15,148,160 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01010,809,734 - 10,817,306 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01011,146,359 - 11,153,936 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1011,146,359 - 11,153,936 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0109,911,717 - 9,919,294 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41011,072,402 - 11,079,980 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera109,905,330 - 9,912,908 (+)NCBICelera
Cytogenetic Map10q12NCBI
PAM16
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38164,340,251 - 4,351,321 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl164,331,549 - 4,355,607 (-)EnsemblGRCh38hg38GRCh38
GRCh37164,390,252 - 4,401,322 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36164,330,253 - 4,341,301 (-)NCBINCBI36Build 36hg18NCBI36
Celera164,597,200 - 4,610,208 (-)NCBICelera
Cytogenetic Map16p13.3NCBI
HuRef164,357,104 - 4,368,547 (-)NCBIHuRef
CHM1_1164,390,188 - 4,401,147 (-)NCBICHM1_1
T2T-CHM13v2.0164,367,543 - 4,380,493 (-)NCBIT2T-CHM13v2.0
Pam16
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39164,434,330 - 4,442,810 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl164,434,328 - 4,442,852 (-)EnsemblGRCm39 Ensembl
GRCm38164,616,466 - 4,624,946 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl164,616,464 - 4,624,988 (-)EnsemblGRCm38mm10GRCm38
MGSCv37164,616,466 - 4,624,946 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36164,531,694 - 4,540,174 (-)NCBIMGSCv36mm8
Celera165,245,931 - 5,254,413 (-)NCBICelera
Cytogenetic Map16A1NCBI
cM Map162.45NCBI
Pam16
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495544213,087,092 - 13,097,048 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495544213,087,082 - 13,097,048 (+)NCBIChiLan1.0ChiLan1.0
PAM16
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2184,847,319 - 4,883,025 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1168,631,732 - 8,675,724 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0163,243,435 - 3,248,815 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PAM16
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1637,040,484 - 37,047,708 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha638,368,787 - 38,376,010 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0637,244,809 - 37,252,032 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl637,184,569 - 37,252,759 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1637,039,040 - 37,046,262 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0636,932,206 - 36,939,429 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0637,333,506 - 37,340,730 (+)NCBIUU_Cfam_GSD_1.0
Pam16
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024409344106,547,828 - 106,555,515 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_004936694153,959 - 161,635 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_004936694153,958 - 161,635 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
LOC100513346
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl337,928,096 - 37,985,151 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1337,928,098 - 38,005,619 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2338,983,207 - 39,040,262 (+)NCBISscrofa10.2Sscrofa10.2susScr3
PAM16
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.154,020,116 - 4,031,233 (-)NCBIChlSab1.1ChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366606826,660,330 - 26,671,448 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Pam16
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462474618,235,774 - 18,237,603 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Pam16
51 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:81
Count of miRNA genes:72
Interacting mature miRNAs:75
Transcripts:ENSRNOT00000006314
Prediction methods:Microtar, 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 (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
634329Pia15Pristane induced arthritis QTL 153.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)10124158324Rat
2293680Bss40Bone structure and strength QTL 405.660.0001femur strength trait (VT:0010010)femur total energy absorbed before break (CMO:0001677)10135225947Rat
634327Hc4Hypercalciuria QTL 42.4urine calcium amount (VT:0002985)urine calcium excretion rate (CMO:0000763)10138328221Rat
7411611Foco17Food consumption QTL 1718.70.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)10142315980Rat
70223Bp57Blood pressure QTL 575arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)10180676123Rat
10401803Kidm50Kidney mass QTL 50kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)1041834445418344Rat
631554Bp133Blood pressure QTL 1330.005arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1074336463851208Rat
1576304Schws7Schwannoma susceptibility QTL 70.0115nervous system integrity trait (VT:0010566)percentage of study population developing trigeminal nerve neurilemmomas during a period of time (CMO:0002017)10476552719816042Rat
631828Alc5Alcohol consumption QTL 52.4consumption behavior trait (VT:0002069)ethanol drink intake rate (CMO:0001407)10514402717245662Rat
737820Alc9Alcohol consumption QTL 92.2consumption behavior trait (VT:0002069)ethanol drink intake rate (CMO:0001407)10514402719233348Rat
2313064Bmd71Bone mineral density QTL 710.90.0001tibia mineral mass (VT:1000283)compact volumetric bone mineral density (CMO:0001730)10538701450387014Rat
2313066Bss63Bone structure and strength QTL 631.40.0001tibia strength trait (VT:1000284)bone polar moment of inertia (CMO:0001558)10538701450387014Rat
2313081Bss64Bone structure and strength QTL 641.30.0001tibia strength trait (VT:1000284)tibia total energy absorbed before break (CMO:0001736)10538701450387014Rat
2313095Bss62Bone structure and strength QTL 621.50.0001tibia size trait (VT:0100001)tibia midshaft cross-sectional area (CMO:0001717)10538701450387014Rat
2313104Bss61Bone structure and strength QTL 610.90.0001tibia area (VT:1000281)tibia midshaft cross-sectional area (CMO:0001717)10538701450387014Rat
2298544Neuinf9Neuroinflammation QTL 94.6nervous system integrity trait (VT:0010566)spinal cord complement component 1, q subcomponent, B chain mRNA level (CMO:0002126)10580199062146030Rat
631660Hcar1Hepatocarcinoma resistance QTL 13.40.0001liver integrity trait (VT:0010547)volume of individual liver tumorous lesion (CMO:0001078)10615418215990232Rat
8662860Vetf10Vascular elastic tissue fragility QTL 10artery integrity trait (VT:0010639)number of ruptures of the internal elastic lamina of the abdominal aorta and iliac arteries (CMO:0002562)10615418273453136Rat
61427Cia16Collagen induced arthritis QTL 163.2joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)10635789696121100Rat
1578761Stresp21Stress response QTL 213.3thymus mass (VT:0004954)thymus wet weight (CMO:0000855)10637574651375746Rat
2303118Mamtr7Mammary tumor resistance QTL 70.003mammary gland integrity trait (VT:0010552)mammary tumor growth rate (CMO:0000344)109658275104670812Rat

Markers in Region
AV006767  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21088,602,624 - 88,602,766 (+)MAPPERmRatBN7.2
mRatBN7.21010,949,961 - 10,950,518 (+)MAPPERmRatBN7.2
Rnor_6.01011,153,249 - 11,153,805NCBIRnor6.0
Rnor_6.01091,753,106 - 91,753,247NCBIRnor6.0
Rnor_5.0109,918,607 - 9,919,163UniSTSRnor5.0
Rnor_5.01091,519,598 - 91,519,739UniSTSRnor5.0
RGSC_v3.41092,847,314 - 92,847,455UniSTSRGSC3.4
RGSC_v3.41011,079,293 - 11,079,849UniSTSRGSC3.4
Celera109,912,221 - 9,912,777UniSTS
Celera1087,302,071 - 87,302,212UniSTS
Cytogenetic Map10q12UniSTS
Cytogenetic Map10q32.1UniSTS


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 3 43 57 41 19 41 8 11 74 35 41 11 8
Low
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000006314   ⟹   ENSRNOP00000006314
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1010,943,012 - 10,950,612 (+)Ensembl
Rnor_6.0 Ensembl1011,146,359 - 11,153,936 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000106238   ⟹   ENSRNOP00000078930
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1010,949,131 - 10,950,649 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000117581   ⟹   ENSRNOP00000095881
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1010,943,001 - 10,950,649 (+)Ensembl
RefSeq Acc Id: NM_001100136   ⟹   NP_001093606
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81011,449,492 - 11,457,070 (+)NCBI
mRatBN7.21010,943,071 - 10,950,649 (+)NCBI
Rnor_6.01011,146,359 - 11,153,936 (+)NCBI
Rnor_5.0109,911,717 - 9,919,294 (+)NCBI
RGSC_v3.41011,072,402 - 11,079,980 (+)RGD
Celera109,905,330 - 9,912,908 (+)RGD
Sequence:
RefSeq Acc Id: XM_039086817   ⟹   XP_038942745
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81011,449,316 - 11,457,071 (+)NCBI
mRatBN7.21010,942,534 - 10,950,654 (+)NCBI
Reference Protein Sequences
RefSeq Acc Id: NP_001093606   ⟸   NM_001100136
- UniProtKB: D3ZZV1 (UniProtKB/TrEMBL),   A6K4S2 (UniProtKB/TrEMBL),   A0A8I5ZMD9 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000006314   ⟸   ENSRNOT00000006314
RefSeq Acc Id: XP_038942745   ⟸   XM_039086817
- Peptide Label: isoform X1
RefSeq Acc Id: ENSRNOP00000095881   ⟸   ENSRNOT00000117581
RefSeq Acc Id: ENSRNOP00000078930   ⟸   ENSRNOT00000106238

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZZV1-F1-model_v2 AlphaFold D3ZZV1 1-125 view protein structure

Transcriptome

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

Promoters
RGD ID:13696976
Promoter ID:EPDNEW_R7501
Type:initiation region
Name:Pam16_1
Description:presequence translocase associated motor 16
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_6.01011,146,347 - 11,146,407EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1598163 AgrOrtholog
BioCyc Gene G2FUF-26032 BioCyc
Ensembl Genes ENSRNOG00000004608 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000006314 ENTREZGENE
  ENSRNOT00000006314.6 UniProtKB/TrEMBL
  ENSRNOT00000106238.1 UniProtKB/TrEMBL
  ENSRNOT00000117581.1 UniProtKB/TrEMBL
Gene3D-CATH 1.10.287.110 UniProtKB/TrEMBL
InterPro DnaJ_dom_sf UniProtKB/TrEMBL
  Protein_transpt UniProtKB/TrEMBL
KEGG Report rno:679907 UniProtKB/TrEMBL
NCBI Gene 679907 ENTREZGENE
PANTHER MITOCHONDRIAL IMPORT INNER MEMBRANE TRANSLOCASE SUBUNIT TIM16 UniProtKB/TrEMBL
  Protein_transpt UniProtKB/TrEMBL
Pfam Pam16 UniProtKB/TrEMBL
PhenoGen Pam16 PhenoGen
RatGTEx ENSRNOG00000004608 RatGTEx
UniProt A0A8I5ZMD9 ENTREZGENE, UniProtKB/TrEMBL
  A0A8I6AUB7_RAT UniProtKB/TrEMBL
  A6K4S2 ENTREZGENE, UniProtKB/TrEMBL
  D3ZZV1 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2017-08-23 Pam16  presequence translocase associated motor 16  Pam16  presequence translocase associated motor 16 homolog  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2016-07-27 Pam16  presequence translocase associated motor 16 homolog  Pam16  presequence translocase-associated motor 16 homolog (S. cerevisiae)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2013-05-24 Pam16  presequence translocase-associated motor 16 homolog (S. cerevisiae)  LOC687579  similar to mitochondria-associated granulocyte macrophage CSF signaling molecule  Data merged from RGD:1584186 1643240 APPROVED
2013-01-22 Pam16  presequence translocase-associated motor 16 homolog (S. cerevisiae)  Magmas  mitochondria-associated protein involved in granulocyte-macrophage colony-stimulating factor signal transduction  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-03-05 Magmas  mitochondria-associated protein involved in granulocyte-macrophage colony-stimulating factor signal transduction  LOC679907  similar to mitochondria-associated granulocyte macrophage CSF signaling molecule  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-11-20 LOC679907  similar to mitochondria-associated granulocyte macrophage CSF signaling molecule      Symbol and Name status set to provisional 70820 PROVISIONAL
2006-11-19 LOC687579  similar to mitochondria-associated granulocyte macrophage CSF signaling molecule      Symbol and Name status set to provisional 70820 PROVISIONAL