Smc5 (structural maintenance of chromosomes 5) - Rat Genome Database

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Gene: Smc5 (structural maintenance of chromosomes 5) Rattus norvegicus
Analyze
Symbol: Smc5
Name: structural maintenance of chromosomes 5
RGD ID: 1307492
Description: Predicted to enable single-stranded DNA binding activity. Predicted to be involved in DNA recombination; cellular senescence; and positive regulation of cell cycle process. Predicted to act upstream of or within several processes, including chromosome condensation; internal peptidyl-lysine acetylation; and protein localization to chromosome, centromeric region. Predicted to be located in several cellular components, including cell junction; chromosome; and nuclear body. Predicted to be part of Smc5-Smc6 complex. Predicted to be active in nucleus. Orthologous to human SMC5 (structural maintenance of chromosomes 5); INTERACTS WITH 2,2',4,4'-Tetrabromodiphenyl ether; 2,3,7,8-tetrachlorodibenzodioxine; bisphenol A.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: LOC293967; SMC5 structural maintenance of chromosomes 5-like 1; SMC5 structural maintenance of chromosomes 5-like 1 (yeast); Smc5l1; structural maintenance of chromosomes protein 5
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21220,769,366 - 220,839,138 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1220,769,366 - 220,839,096 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1229,208,668 - 229,273,287 (-)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.01236,138,728 - 236,203,341 (-)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.01228,956,773 - 229,021,389 (-)NCBIRnor_WKY
Rnor_6.01240,977,898 - 241,046,273 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1240,977,898 - 241,046,256 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01248,263,018 - 248,331,371 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41226,494,137 - 226,566,143 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11226,660,743 - 226,730,160 (-)NCBI
Celera1217,985,830 - 218,055,270 (-)NCBICelera
Cytogenetic Map1q51NCBI
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

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:11408570   PMID:16810316   PMID:17589526   PMID:18086888   PMID:19502785   PMID:19793919   PMID:20339383   PMID:25931565  


Genomics

Comparative Map Data
Smc5
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21220,769,366 - 220,839,138 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1220,769,366 - 220,839,096 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1229,208,668 - 229,273,287 (-)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.01236,138,728 - 236,203,341 (-)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.01228,956,773 - 229,021,389 (-)NCBIRnor_WKY
Rnor_6.01240,977,898 - 241,046,273 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1240,977,898 - 241,046,256 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01248,263,018 - 248,331,371 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41226,494,137 - 226,566,143 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11226,660,743 - 226,730,160 (-)NCBI
Celera1217,985,830 - 218,055,270 (-)NCBICelera
Cytogenetic Map1q51NCBI
SMC5
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38970,258,978 - 70,354,873 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl970,258,978 - 70,354,873 (+)EnsemblGRCh38hg38GRCh38
GRCh37972,873,894 - 72,969,789 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36972,063,698 - 72,159,609 (+)NCBINCBI36Build 36hg18NCBI36
Build 34970,103,458 - 70,196,886NCBI
Celera943,464,262 - 43,560,152 (+)NCBICelera
Cytogenetic Map9q21.12NCBI
HuRef942,713,635 - 42,809,515 (+)NCBIHuRef
CHM1_1973,020,407 - 73,116,329 (+)NCBICHM1_1
T2T-CHM13v2.0982,425,826 - 82,521,669 (+)NCBIT2T-CHM13v2.0
Smc5
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391923,183,805 - 23,251,286 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1923,183,815 - 23,251,261 (-)EnsemblGRCm39 Ensembl
GRCm381923,206,441 - 23,273,922 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1923,206,451 - 23,273,897 (-)EnsemblGRCm38mm10GRCm38
MGSCv371923,283,221 - 23,348,367 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361923,275,828 - 23,340,974 (-)NCBIMGSCv36mm8
Celera1923,941,397 - 24,012,767 (-)NCBICelera
Cytogenetic Map19BNCBI
Smc5
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554342,742,373 - 2,848,337 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554342,742,276 - 2,848,384 (-)NCBIChiLan1.0ChiLan1.0
SMC5
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1969,016,716 - 69,112,550 (+)NCBIpanpan1.1PanPan1.1panPan2
Mhudiblu_PPA_v0954,446,863 - 54,543,249 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
SMC5
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1187,192,988 - 87,285,678 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl187,194,867 - 87,285,606 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha187,664,171 - 87,757,137 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0187,744,103 - 87,837,243 (-)NCBIROS_Cfam_1.0
UMICH_Zoey_3.1187,398,935 - 87,491,806 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0187,104,843 - 87,197,796 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0187,862,299 - 87,955,619 (-)NCBIUU_Cfam_GSD_1.0
Smc5
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024404947134,689,708 - 134,784,451 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365036,388,487 - 6,483,333 (+)EnsemblSpeTri2.0
SpeTri2.0NW_0049365036,388,556 - 6,483,293 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SMC5
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.11223,560,271 - 223,653,370 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21250,125,007 - 250,145,640 (-)NCBISscrofa10.2Sscrofa10.2susScr3
SMC5
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11281,317,689 - 81,426,196 (+)NCBIChlSab1.1ChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366603869,734,993 - 69,843,464 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Smc5
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247362,700,161 - 2,803,439 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046247362,697,764 - 2,803,501 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Smc5
155 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:218
Count of miRNA genes:150
Interacting mature miRNAs:171
Transcripts:ENSRNOT00000067796
Prediction methods:Miranda
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
7794788Mcs32Mammary carcinoma susceptibility QTL 322.61mammary gland integrity trait (VT:0010552)mammary tumor incidence/prevalence measurement (CMO:0000946)1115540693238914717Rat
7421630Bp362Blood pressure QTL 3620.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1118608292241799120Rat
737828Hcas3Hepatocarcinoma susceptibility QTL 34.9liver integrity trait (VT:0010547)liver tumorous lesion volume to total liver volume ratio (CMO:0001082)1144267353222987745Rat
2302378Insul11Insulin level QTL 113.25blood insulin amount (VT:0001560)serum insulin level (CMO:0000358)1144267353251128347Rat
7771612Cm80Cardiac mass QTL 808.4heart left ventricle mass (VT:0007031)heart left ventricle weight (CMO:0000776)1149448574221264292Rat
724531Uae5Urinary albumin excretion QTL 54urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)1150700142252085212Rat
1578759Uae30Urinary albumin excretion QTL 303.30.003urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)1150700247252085048Rat
1578778Pur4Proteinuria QTL 43.30.003urine total protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)1150700247252085048Rat
1354610Bw34Body weight QTL 344.1body mass (VT:0001259)body weight (CMO:0000012)1151162512256448636Rat
1354646Kidm18Kidney mass QTL 185.7kidney mass (VT:0002707)calculated kidney weight (CMO:0000160)1151162512256448636Rat
1354661Bw33Body weight QTL 335.2body mass (VT:0001259)body weight (CMO:0000012)1151162512256448636Rat
1358886Bp260Blood pressure QTL 2603.67arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1151162766225824951Rat
1549837Hcar15Hepatocarcinoma resistance QTL 150.05liver integrity trait (VT:0010547)liver tumorous lesion number (CMO:0001068)1153136852260522016Rat
1354580Scort1Serum corticosterone level QTL 13.4blood corticosterone amount (VT:0005345)blood corticosterone level (CMO:0001172)1156677124256448636Rat
2292220Bp306Blood pressure QTL 3063.470.00087arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1164310393243914901Rat
738032Hcas5Hepatocarcinoma susceptibility QTL 53.12liver integrity trait (VT:0010547)liver tumorous lesion number (CMO:0001068)1176426412257976495Rat
1600380Niddm70Non-insulin dependent diabetes mellitus QTL 703.10.0008blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)1176550523221550523Rat
10059600Bp378Blood pressure QTL 3783.080.05arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1176869060221869060Rat
1354624Cm35Cardiac mass QTL355.7heart left ventricle mass (VT:0007031)calculated heart weight (CMO:0000073)1177227632256448636Rat
1354652Kidm20Kidney mass QTL 204.3kidney mass (VT:0002707)calculated kidney weight (CMO:0000160)1177227632256448636Rat
1558658Bw59Body weight QTL 593.50.0003body mass (VT:0001259)body weight (CMO:0000012)1178784622223784622Rat
634321Hc1Hypercalciuria QTL 12.91urine calcium amount (VT:0002985)urine calcium excretion rate (CMO:0000763)1178810256240830002Rat
1578763Kidm29Kidney mass QTL 293.30.0001kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)1179567751260522016Rat
737977Bp160Blood pressure QTL 1600.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1181133855226133855Rat
2293083Iddm25Insulin dependent diabetes mellitus QTL 254.18blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)1181829673224569684Rat
8655655Arrd2Age-related retinal degeneration QTL 27.79retinal layer morphology trait (VT:0003727)percentage of study population developing retinopathy during a period of time (CMO:0002453)1183970203243914901Rat
8655855Arrd3Age-related retinal degeneration QTL 33.07lens clarity trait (VT:0001304)cataract incidence/prevalence measurement (CMO:0001585)1183970203243914901Rat
631838Niddm36Non-insulin dependent diabetes mellitus QTL 360.01insulin secretion trait (VT:0003564)calculated pancreatic islet insulin release measurement (CMO:0001217)1184550676229550676Rat
1300145Rf7Renal function QTL 72.96urine creatinine amount (VT:0010540)urine creatinine level (CMO:0000125)1185145134221264292Rat
2312564Glom18Glomerulus QTL 182.40.003kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)1185356336231689108Rat
1582206Kidm33Kidney mass QTL 336.9kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)1188377360224054420Rat
1358898Bp255Blood pressure QTL 2553.6arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1191019702246062233Rat
10059590Kidm44Kidney mass QTL 443.420.025kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)1191033875236033875Rat
1358191Ept10Estrogen-induced pituitary tumorigenesis QTL 103.8pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)1192825253243914732Rat
8552891Epfw5Epididymal fat weight QTL 54.4epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)1193113876238113876Rat
1600388Niddm67Non-insulin dependent diabetes mellitus QTL 675.840.000004blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)1195804352257091168Rat
1600395Niddm69Non-insulin dependent diabetes mellitus QTL 694.140.0002blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)1195804352257091168Rat
1600396Niddm68Non-insulin dependent diabetes mellitus QTL 684.970.0003blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)1195804352257091168Rat
631658Cm7Cardiac mass QTL 75.320.0001aorta mass (VT:0002845)aorta weight (CMO:0000076)1196248093241248093Rat
1358292Cm37Cardiac mass QTL 376.20.00000081heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)1196248093241248093Rat
1600374Mcs17Mammary carcinoma susceptibility QTL 173mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)1197670404242670404Rat
1641926Teswt2Testicular weight QTL 22.82testis mass (VT:1000644)both testes wet weight (CMO:0000175)1197697768238755659Rat
2302375Bw83Body weight QTL 834.870.0002body mass (VT:0001259)body weight (CMO:0000012)1197697768242697768Rat
61376Bp42Blood pressure QTL 4223.4arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1197814409242814409Rat
1298084Thym4Thymus enlargement QTL 410.68thymus mass (VT:0004954)thymus weight to body weight ratio (CMO:0000612)1197814409242814409Rat
1357335Bw39Body weight QTL 393.3body mass (VT:0001259)body weight (CMO:0000012)1197814409242814409Rat
1331790Bp201Blood pressure QTL 2013.127arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1198211513225126682Rat
634313Niddm43Non-insulin dependent diabetes mellitus QTL 43blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)1199050459259647894Rat
2292218Kidm35Kidney mass QTL 35kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)1199368955224569684Rat
2293694Bss38Bone structure and strength QTL 387.050.0001femur strength trait (VT:0010010)femur stiffness (CMO:0001674)1201554356246554356Rat
7394701Uae46Urinary albumin excretion QTL 463.60.0056urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)1201554356246554356Rat
2300175Bmd40Bone mineral density QTL 4015.40.0001femur mineral mass (VT:0010011)bone mineral density (CMO:0001226)1201554356246554356Rat
2293655Bss36Bone structure and strength QTL 3610.660.0001femur strength trait (VT:0010010)femur ultimate force (CMO:0001675)1201554356246554356Rat
2293674Bss39Bone structure and strength QTL 397.10.0001femur strength trait (VT:0010010)femur total energy absorbed before break (CMO:0001677)1201554356246554356Rat
10059587Bw173Body weight QTL 1733.230.025body mass (VT:0001259)body weight (CMO:0000012)1202069611247069611Rat
1600363Hc6Hypercalciuria QTL 62.7urine calcium amount (VT:0002985)urine calcium excretion rate (CMO:0000763)1203995416244113296Rat
1600397Edcs4Endometrial carcinoma susceptibility QTL 42.2uterus morphology trait (VT:0001120)percentage of study population developing endometrioid carcinoma during a period of time (CMO:0001759)1206081677251081677Rat
61403Niddm4Non-insulin dependent diabetes mellitus QTL 4blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)1206329708222745518Rat
1357399Bw45Body weight QTL 453.05body mass (VT:0001259)body mass index (BMI) (CMO:0000105)1206329708251329708Rat
1357404Bw42Body weight QTL 424.490.0001body mass (VT:0001259)body weight (CMO:0000012)1206329708251329708Rat
1300168Bp170Blood pressure QTL 1702.76arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1207702246228581766Rat
1358916Kidm22Kidney mass QTL 223.32kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)1210702053240947965Rat
1358890Bp259Blood pressure QTL 2593.06arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1210702053260522016Rat
2292216Bw80Body weight QTL 803.230.0019body mass (VT:0001259)body weight (CMO:0000012)1213533809243914901Rat
724538Kidm1Kidney mass QTL 13.2kidney mass (VT:0002707)calculated kidney weight (CMO:0000160)1213707201252085212Rat
734768Niddm59Non-insulin dependent diabetes mellitus QTL 59body mass (VT:0001259)body weight (CMO:0000012)1213843987258843987Rat
634340Hcar5Hepatocarcinoma resistance QTL 58liver integrity trait (VT:0010547)liver tumorous lesion number (CMO:0001068)1214537555226660468Rat
61455Niddm7Non-insulin dependent diabetes mellitus QTL 75.5blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)1214537555238757011Rat
70211Niddm24Non-insulin dependent diabetes mellitus QTL 243.79blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)1214647894259647894Rat
1549910Bw54Body weight QTL 540.05body mass (VT:0001259)body weight (CMO:0000012)1214647894259647894Rat
61327Eae7Experimental allergic encephalomyelitis QTL 75.6body mass (VT:0001259)change in body weight (CMO:0002045)1216255568260522016Rat
2302040Pia35Pristane induced arthritis QTL 353.80.001blood immunoglobulin amount (VT:0002460)serum immunoglobulin G1 level (CMO:0002115)1216255568260522016Rat
5508828Leukc3Leukocyte quantity QTL 3eosinophil quantity (VT:0002602)blood eosinophil count (CMO:0000033)1218108584224054420Rat
1598821Rf55Renal function QTL 556.3renal blood flow trait (VT:2000006)ratio of change in renal blood flow to change in renal perfusion pressure (CMO:0001239)1218748008257976495Rat
61400Niddm1Non-insulin dependent diabetes mellitus QTL 111blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)1218753689245907899Rat
724533Rf51Renal function QTL 515.30.0002kidney plasma flow trait (VT:0005524)renal plasma flow (CMO:0001914)1218753816256448513Rat

Markers in Region
AU048250  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21220,833,136 - 220,833,377 (+)MAPPERmRatBN7.2
Rnor_6.01241,040,292 - 241,040,530NCBIRnor6.0
Rnor_5.01248,325,412 - 248,325,650UniSTSRnor5.0
RGSC_v3.41226,560,186 - 226,560,424UniSTSRGSC3.4
Celera1218,049,319 - 218,049,551UniSTS
Cytogenetic Map1q51UniSTS
RH142597  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21220,772,000 - 220,773,196 (+)MAPPERmRatBN7.2
Rnor_6.01240,980,582 - 240,981,886NCBIRnor6.0
Rnor_5.01248,265,702 - 248,267,006UniSTSRnor5.0
RGSC_v3.41226,496,772 - 226,497,997UniSTSRGSC3.4
Celera1217,988,467 - 217,989,662UniSTS
RH 3.4 Map11613.7UniSTS
Cytogenetic Map1q51UniSTS
AA946375  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21220,769,832 - 220,770,077 (+)MAPPERmRatBN7.2
Rnor_6.01240,978,414 - 240,978,658NCBIRnor6.0
Rnor_5.01248,263,534 - 248,263,778UniSTSRnor5.0
RGSC_v3.41226,494,604 - 226,494,848UniSTSRGSC3.4
Celera1217,986,299 - 217,986,543UniSTS
RH 3.4 Map11615.31UniSTS
Cytogenetic Map1q51UniSTS


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 2 30 32 16 19 16 2 2 74 28 41 11 2
Low 1 13 25 25 25 6 9 7 6
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000067796   ⟹   ENSRNOP00000061357
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1220,769,366 - 220,839,096 (-)Ensembl
Rnor_6.0 Ensembl1240,977,898 - 241,046,249 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000081866   ⟹   ENSRNOP00000073164
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1220,770,128 - 220,839,083 (-)Ensembl
Rnor_6.0 Ensembl1240,980,418 - 241,046,256 (-)Ensembl
RefSeq Acc Id: NM_001106357   ⟹   NP_001099827
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21220,769,366 - 220,839,096 (-)NCBI
Rnor_6.01240,977,898 - 241,046,249 (-)NCBI
Rnor_5.01248,263,018 - 248,331,371 (-)NCBI
RGSC_v3.41226,494,137 - 226,566,143 (-)RGD
Celera1217,985,830 - 218,055,270 (-)RGD
Sequence:
RefSeq Acc Id: XM_006231183   ⟹   XP_006231245
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21220,770,109 - 220,839,138 (-)NCBI
Rnor_6.01240,978,695 - 241,046,273 (-)NCBI
Rnor_5.01248,263,018 - 248,331,371 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006231184   ⟹   XP_006231246
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21220,770,109 - 220,839,138 (-)NCBI
Rnor_6.01240,978,695 - 241,046,273 (-)NCBI
Rnor_5.01248,263,018 - 248,331,371 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039108980   ⟹   XP_038964908
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21220,796,887 - 220,839,138 (-)NCBI
RefSeq Acc Id: XR_005504103
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21220,780,734 - 220,839,138 (-)NCBI
Protein Sequences
Protein RefSeqs NP_001099827 (Get FASTA)   NCBI Sequence Viewer  
  XP_006231245 (Get FASTA)   NCBI Sequence Viewer  
  XP_006231246 (Get FASTA)   NCBI Sequence Viewer  
  XP_038964908 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDM13015 (Get FASTA)   NCBI Sequence Viewer  
  EDM13016 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_001099827   ⟸   NM_001106357
- UniProtKB: D4A9F0 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006231245   ⟸   XM_006231183
- Peptide Label: isoform X1
- UniProtKB: A0A0G2K4T5 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006231246   ⟸   XM_006231184
- Peptide Label: isoform X2
- UniProtKB: A0A0G2K4T5 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000061357   ⟸   ENSRNOT00000067796
RefSeq Acc Id: ENSRNOP00000073164   ⟸   ENSRNOT00000081866
RefSeq Acc Id: XP_038964908   ⟸   XM_039108980
- Peptide Label: isoform X3
Protein Domains
SMC_N

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-A0A0G2K4T5-F1-model_v2 AlphaFold A0A0G2K4T5 1-1102 view protein structure

Transcriptome

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

Promoters
RGD ID:13690831
Promoter ID:EPDNEW_R1344
Type:multiple initiation site
Name:Smc5_1
Description:structural maintenance of chromosomes 5
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_6.01241,046,269 - 241,046,329EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1307492 AgrOrtholog
BioCyc Gene G2FUF-56118 BioCyc
Ensembl Genes ENSRNOG00000030572 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000061357 ENTREZGENE
  ENSRNOP00000061357.1 UniProtKB/TrEMBL
  ENSRNOP00000073164 ENTREZGENE
  ENSRNOP00000073164.2 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000067796 ENTREZGENE
  ENSRNOT00000067796.3 UniProtKB/TrEMBL
  ENSRNOT00000081866 ENTREZGENE
  ENSRNOT00000081866.2 UniProtKB/TrEMBL
Gene3D-CATH 3.40.50.300 UniProtKB/TrEMBL
InterPro P-loop_NTPase UniProtKB/TrEMBL
  RecF/RecN/SMC_N UniProtKB/TrEMBL
  SMC5 UniProtKB/TrEMBL
KEGG Report rno:293967 UniProtKB/TrEMBL
NCBI Gene 293967 ENTREZGENE
PANTHER PTHR45916 UniProtKB/TrEMBL
Pfam SMC_N UniProtKB/TrEMBL
PhenoGen Smc5 PhenoGen
Superfamily-SCOP SSF52540 UniProtKB/TrEMBL
UniProt A0A0G2K4T5 ENTREZGENE, UniProtKB/TrEMBL
  D4A9F0 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-03-07 Smc5  structural maintenance of chromosomes 5  Smc5l1_predicted  SMC5 structural maintenance of chromosomes 5-like 1 (yeast) (predicted)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-01-12 Smc5l1_predicted  SMC5 structural maintenance of chromosomes 5-like 1 (yeast) (predicted)      Symbol and Name status set to approved 70820 APPROVED