Swi5 (SWI5 homologous recombination repair protein) - Rat Genome Database

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Gene: Swi5 (SWI5 homologous recombination repair protein) Rattus norvegicus
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Symbol: Swi5
Name: SWI5 homologous recombination repair protein
RGD ID: 1559966
Description: Predicted to be involved in cellular response to ionizing radiation and double-strand break repair via homologous recombination. Predicted to be located in nucleus. Predicted to be part of Swi5-Sfr1 complex and Swi5-Swi2 complex. Orthologous to human SWI5 (SWI5 homologous recombination repair protein); INTERACTS WITH 17alpha-ethynylestradiol; 2,3,7,8-tetrachlorodibenzodioxine; 4,4'-sulfonyldiphenol.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: DNA repair protein SWI5 homolog; LOC499779; protein SAE3 homolog; similar to RIKEN cDNA 2900010J23; SWI5 recombination repair homolog; SWI5 recombination repair homolog (yeast)
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
GRCr8335,972,436 - 35,981,658 (-)NCBIGRCr8
mRatBN7.2315,574,687 - 15,583,760 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl315,564,715 - 15,583,805 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx318,643,571 - 18,652,494 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0327,228,564 - 27,237,487 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0325,479,160 - 25,488,237 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0311,307,981 - 11,317,049 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl311,307,981 - 11,317,049 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0316,656,849 - 16,665,919 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4311,402,738 - 11,411,870 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera310,319,249 - 10,328,317 (-)NCBICelera
Cytogenetic Map3p12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
nucleus  (ISO,ISS)
Swi5-Sfr1 complex  (IBA,IEA,ISO,ISS)
Swi5-Swi2 complex  (IBA,IEA)

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. 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. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, etal., Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16899-903. Epub 2002 Dec 11.
Additional References at PubMed
PMID:20976249   PMID:21252223   PMID:23754376  


Genomics

Comparative Map Data
Swi5
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8335,972,436 - 35,981,658 (-)NCBIGRCr8
mRatBN7.2315,574,687 - 15,583,760 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl315,564,715 - 15,583,805 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx318,643,571 - 18,652,494 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0327,228,564 - 27,237,487 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0325,479,160 - 25,488,237 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0311,307,981 - 11,317,049 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl311,307,981 - 11,317,049 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0316,656,849 - 16,665,919 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4311,402,738 - 11,411,870 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera310,319,249 - 10,328,317 (-)NCBICelera
Cytogenetic Map3p12NCBI
SWI5
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh389128,275,356 - 128,288,989 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl9128,275,379 - 128,316,123 (+)EnsemblGRCh38hg38GRCh38
GRCh379131,037,635 - 131,051,268 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 369130,078,246 - 130,091,089 (+)NCBINCBI36Build 36hg18NCBI36
Build 349128,118,054 - 128,130,821NCBI
Celera9101,689,329 - 101,702,173 (+)NCBICelera
Cytogenetic Map9q34.11NCBI
HuRef9100,651,879 - 100,664,564 (+)NCBIHuRef
CHM1_19131,189,448 - 131,202,290 (+)NCBICHM1_1
T2T-CHM13v2.09140,482,470 - 140,496,104 (+)NCBIT2T-CHM13v2.0
Swi5
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39232,168,817 - 32,178,154 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl232,168,828 - 32,178,087 (-)EnsemblGRCm39 Ensembl
GRCm38232,278,805 - 32,288,136 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl232,278,816 - 32,288,075 (-)EnsemblGRCm38mm10GRCm38
MGSCv37232,134,336 - 32,143,588 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36232,100,826 - 32,110,022 (-)NCBIMGSCv36mm8
Celera231,983,292 - 31,992,544 (-)NCBICelera
Cytogenetic Map2BNCBI
cM Map222.09NCBI
Swi5
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_004955570799,332 - 808,368 (+)EnsemblChiLan1.0
ChiLan1.0NW_004955570799,332 - 808,368 (+)NCBIChiLan1.0ChiLan1.0
SWI5
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21111,064,403 - 11,078,004 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1911,056,102 - 11,079,639 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0999,396,439 - 99,410,054 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.19128,065,237 - 128,078,380 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl9128,064,569 - 128,078,380 (+)Ensemblpanpan1.1panPan2
SWI5
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1955,229,510 - 55,234,645 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl955,229,550 - 55,234,489 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha954,424,421 - 54,429,643 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0956,151,581 - 56,156,803 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl956,151,593 - 56,156,938 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1954,911,478 - 54,916,705 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0955,226,120 - 55,231,344 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0955,317,624 - 55,322,848 (-)NCBIUU_Cfam_GSD_1.0
Swi5
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024404947196,045,921 - 196,054,256 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_00493648715,814,102 - 15,823,311 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_00493648715,814,463 - 15,822,783 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SWI5
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1268,720,355 - 268,726,521 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11268,720,232 - 268,726,527 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21302,710,680 - 302,716,860 (+)NCBISscrofa10.2Sscrofa10.2susScr3
SWI5
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1129,840,286 - 9,852,397 (-)NCBIChlSab1.1ChlSab1.1chlSab2
Vero_WHO_p1.0NW_0236660796,380,808 - 6,394,649 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Swi5
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247606,581,575 - 6,588,233 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046247606,581,471 - 6,588,294 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Swi5
72 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:52
Count of miRNA genes:45
Interacting mature miRNAs:48
Transcripts:ENSRNOT00000030558
Prediction methods:Miranda, 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
70202Alc19Alcohol consumption QTL 192.5drinking behavior trait (VT:0001422)ethanol intake volume to total fluid intake volume ratio (CMO:0001591)3127494778Rat
631679Cm10Cardiac mass QTL 107.340.0001heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)3131158234Rat
631831Alc8Alcohol consumption QTL 82.7consumption behavior trait (VT:0002069)calculated ethanol drink intake rate (CMO:0001615)3133230976Rat
61468Bp15Blood pressure QTL 154.4blood pressure trait (VT:0000183)diastolic blood pressure (CMO:0000005)3133278763Rat
61468Bp15Blood pressure QTL 154.4blood pressure trait (VT:0000183)systolic blood pressure (CMO:0000004)3133278763Rat
61468Bp15Blood pressure QTL 154.4blood pressure trait (VT:0000183)pulse pressure (CMO:0000292)3133278763Rat
631545Bp85Blood pressure QTL 853.1arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3133278763Rat
4889966Bss95Bone structure and strength QTL 954.4tibia area (VT:1000281)tibia-fibula cross-sectional area (CMO:0001718)3136847613Rat
2312664Scl62Serum cholesterol level QTL 620.05blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)3138710544Rat
631568Bp92Blood pressure QTL 922.20.005arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3139874793Rat
2290452Scl56Serum cholesterol level QTL 562.26blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)3191609953Rat
1298526Arunc3Aerobic running capacity QTL 32.2exercise endurance trait (VT:0002332)maximum distance run on treadmill (CMO:0001406)3822719433703538Rat
10401810Kidm53Kidney mass QTL 53kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)3822719447233430Rat
70203Gcr2Gastric cancer resistance QTL 22.6stomach morphology trait (VT:0000470)stomach tumor susceptibility score (CMO:0002043)3865816227494778Rat
1358357Srcrtb1Stress Responsive Cort Basal QTL 16.360.002blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)3865816227494778Rat
6893355Bw101Body weight QTL 1010.40.38body mass (VT:0001259)body weight (CMO:0000012)31077870430357018Rat
6893363Bw105Body weight QTL 1052.60.0036body mass (VT:0001259)body weight (CMO:0000012)31077870430357018Rat
1558654Bw56Body weight QTL 564.50.0000171body mass (VT:0001259)body weight (CMO:0000012)31077870430357018Rat
70191BpQTLcluster4Blood pressure QTL cluster 43arterial blood pressure trait (VT:2000000)absolute change in mean arterial blood pressure (CMO:0000533)31077870450302886Rat
70191BpQTLcluster4Blood pressure QTL cluster 43arterial blood pressure trait (VT:2000000)absolute change in systolic blood pressure (CMO:0000607)31077870450302886Rat
1558647Cm46Cardiac mass QTL 465.40.0000055heart mass (VT:0007028)heart wet weight (CMO:0000069)31077882330356773Rat
1558650Cm48Cardiac mass QTL 4840.0001heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)31077882330356773Rat
1558657Cm43Cardiac mass QTL 436.60.0000000293heart mass (VT:0007028)heart wet weight (CMO:0000069)31077882330356773Rat
1358905Hrtrt17Heart rate QTL 175.90.000014heart pumping trait (VT:2000009)heart rate (CMO:0000002)31086191289878372Rat
1358885Bp251Blood pressure QTL 2513.8arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)314489145121056321Rat
1358888Bp264Blood pressure QTL 2644.43arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)314489145121056321Rat
2298542Neuinf11Neuroinflammation QTL 113.9nervous system integrity trait (VT:0010566)spinal cord complement component 1, q subcomponent, B chain mRNA level (CMO:0002126)31500542276927699Rat

Markers in Region
RH128826  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2315,574,718 - 15,574,903 (+)MAPPERmRatBN7.2
mRatBN7.25145,014,037 - 145,014,224 (+)MAPPERmRatBN7.2
Rnor_6.05150,994,442 - 150,994,628NCBIRnor6.0
Rnor_6.0311,308,009 - 11,308,193NCBIRnor6.0
Rnor_5.0316,656,879 - 16,657,063UniSTSRnor5.0
Rnor_5.05154,662,188 - 154,662,374UniSTSRnor5.0
RGSC_v3.4311,402,769 - 11,402,953UniSTSRGSC3.4
Celera5143,437,909 - 143,438,095UniSTS
Celera310,319,277 - 10,319,461UniSTS
Cytogenetic Map5q36UniSTS
Cytogenetic Map3p11UniSTS


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


RefSeq Acc Id: ENSRNOT00000030558   ⟹   ENSRNOP00000029603
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl315,564,715 - 15,583,805 (-)Ensembl
Rnor_6.0 Ensembl311,307,981 - 11,317,049 (-)Ensembl
RefSeq Acc Id: NM_001246661   ⟹   NP_001233590
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8335,972,436 - 35,981,504 (-)NCBI
mRatBN7.2315,574,691 - 15,583,760 (-)NCBI
Rnor_6.0311,307,981 - 11,317,049 (-)NCBI
Rnor_5.0316,656,849 - 16,665,919 (-)NCBI
Celera310,319,249 - 10,328,317 (-)NCBI
Sequence:
RefSeq Acc Id: XM_063284351   ⟹   XP_063140421
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8335,972,436 - 35,981,658 (-)NCBI
Protein Sequences
Protein RefSeqs NP_001233590 (Get FASTA)   NCBI Sequence Viewer  
  XP_063140421 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAH82799 (Get FASTA)   NCBI Sequence Viewer  
  EDL93247 (Get FASTA)   NCBI Sequence Viewer  
  EDL93248 (Get FASTA)   NCBI Sequence Viewer  
  EDL93250 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000029603.4
GenBank Protein Q63ZV7 (Get FASTA)   NCBI Sequence Viewer  
RefSeq Acc Id: NP_001233590   ⟸   NM_001246661
- UniProtKB: Q63ZV7 (UniProtKB/Swiss-Prot),   A6JU49 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000029603   ⟸   ENSRNOT00000030558
RefSeq Acc Id: XP_063140421   ⟸   XM_063284351
- Peptide Label: isoform X1

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q63ZV7-F1-model_v2 AlphaFold Q63ZV7 1-89 view protein structure

Transcriptome

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

Promoters
RGD ID:13691980
Promoter ID:EPDNEW_R2505
Type:initiation region
Name:Swi5_1
Description:SWI5 homologous recombination repair protein
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_6.0311,317,068 - 11,317,128EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1559966 AgrOrtholog
BioCyc Gene G2FUF-50148 BioCyc
Ensembl Genes ENSRNOG00000022860 Ensembl, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000030558.6 UniProtKB/TrEMBL
Gene3D-CATH 1.20.5.170 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7304460 IMAGE-MGC_LOAD
InterPro DNA-repair_Swi5 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:499779 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
MGC_CLONE MGC:105672 IMAGE-MGC_LOAD
NCBI Gene 499779 ENTREZGENE
PANTHER DNA REPAIR PROTEIN SWI5 HOMOLOG UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PTHR28529 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam Swi5 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Swi5 PhenoGen
RatGTEx ENSRNOG00000022860 RatGTEx
UniProt A0A8L2QIG3_RAT UniProtKB/TrEMBL
  A6JU49 ENTREZGENE, UniProtKB/TrEMBL
  Q63ZV7 ENTREZGENE, UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2015-07-09 Swi5  SWI5 homologous recombination repair protein  Swi5  SWI5 recombination repair homolog (yeast)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2011-08-16 Swi5  SWI5 recombination repair homolog (yeast)  LOC499779  similar to RIKEN cDNA 2900010J23  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-02-09 LOC499779  similar to RIKEN cDNA 2900010J23      Symbol and Name status set to provisional 70820 PROVISIONAL