Rnf38 (ring finger protein 38) - Rat Genome Database
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Gene: Rnf38 (ring finger protein 38) Rattus norvegicus
Analyze
Symbol: Rnf38
Name: ring finger protein 38
RGD ID: 621856
Description: Predicted to have ubiquitin protein ligase activity. Involved in male gonad development. Localizes to sperm flagellum. Orthologous to human RNF38 (ring finger protein 38); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 2,4-dinitrotoluene; ammonium chloride.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: E3 ubiquitin-protein ligase RNF38; MGC93195; Oip1; RING finger protein OIP1
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rnor_6.0559,604,783 - 59,713,108 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl559,607,476 - 59,647,633 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0564,128,873 - 64,235,392 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4560,600,918 - 60,631,312 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1560,601,097 - 60,631,491 (-)NCBI
Celera556,940,197 - 56,970,567 (-)NCBICelera
Cytogenetic Map5q22NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component
nucleoplasm  (IEA,ISO)
nucleus  (ISO)
sperm flagellum  (IDA)

Molecular Function

References

Additional References at PubMed
PMID:12477932   PMID:23973461  


Genomics

Comparative Map Data
Rnf38
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rnor_6.0559,604,783 - 59,713,108 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl559,607,476 - 59,647,633 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0564,128,873 - 64,235,392 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4560,600,918 - 60,631,312 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1560,601,097 - 60,631,491 (-)NCBI
Celera556,940,197 - 56,970,567 (-)NCBICelera
Cytogenetic Map5q22NCBI
RNF38
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl936,336,396 - 36,487,548 (-)EnsemblGRCh38hg38GRCh38
GRCh38936,336,398 - 36,487,384 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh37936,336,395 - 36,487,568 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36936,326,397 - 36,391,195 (-)NCBINCBI36hg18NCBI36
Build 34936,326,392 - 36,391,195NCBI
Celera936,269,750 - 36,334,476 (-)NCBI
Cytogenetic Map9p13.2NCBI
HuRef936,289,333 - 36,353,868 (-)NCBIHuRef
CHM1_1936,336,870 - 36,401,614 (-)NCBICHM1_1
Rnf38
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39444,126,210 - 44,233,929 (-)NCBIGRCm39mm39
GRCm38444,126,210 - 44,233,905 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl444,126,210 - 44,233,789 (-)EnsemblGRCm38mm10GRCm38
MGSCv37444,139,084 - 44,181,155 (-)NCBIGRCm37mm9NCBIm37
MGSCv36444,147,310 - 44,189,439 (-)NCBImm8
Celera444,147,772 - 44,189,740 (-)NCBICelera
Cytogenetic Map4B1NCBI
Rnf38
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495541929,993,358 - 30,063,705 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495541929,903,917 - 30,063,705 (+)NCBIChiLan1.0ChiLan1.0
RNF38
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1936,985,427 - 37,134,188 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl936,985,433 - 37,048,013 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0936,185,284 - 36,335,915 (-)NCBIMhudiblu_PPA_v0panPan3
RNF38
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 Ensembl1152,764,220 - 52,901,983 (-)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.11152,764,216 - 52,827,993 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Rnf38
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_0049365244,281,124 - 4,359,378 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
RNF38
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1237,111,010 - 237,240,348 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11237,111,002 - 237,240,311 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21264,874,672 - 265,047,458 (-)NCBISscrofa10.2Sscrofa10.2susScr3
RNF38
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11244,083,814 - 44,224,206 (+)NCBI
ChlSab1.1 Ensembl1244,185,500 - 44,225,491 (+)Ensembl
Rnf38
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462493037,327 - 180,038 (-)NCBI


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2316959Gluco59Glucose level QTL 594.7blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)535661945117554267Rat
1298067Scl15Serum cholesterol level QTL 154.80.001blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)53440240979402409Rat
6903292Stl28Serum triglyceride level QTL 282.60.0073blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)52964166174641661Rat
6903306Scl35Serum cholesterol QTL 352.60.0073blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)52964166174641661Rat
9589025Epfw7Epididymal fat weight QTL 720.660.001epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)55180442696804426Rat
634305Mamtr1Mammary tumor resistance QTL 10.0001mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)512651967117554267Rat
8552954Pigfal14Plasma insulin-like growth factor 1 level QTL 149blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)52190436366904363Rat
7411561Bw134Body weight QTL 134240.001body mass (VT:0001259)body weight gain (CMO:0000420)55180442696804426Rat
8662454Vetf3Vascular elastic tissue fragility QTL 327.4artery integrity trait (VT:0010639)number of ruptures of the internal elastic lamina of the abdominal aorta and iliac arteries (CMO:0002562)5166658771552720Rat
7394712Emca13Estrogen-induced mammary cancer QTL 13mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)59514842103580403Rat
1358353Srcrtb2Stress Responsive Cort Basal QTL 23.480.003blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)51884791376608178Rat
1331756Rf34Renal function QTL 344.16275kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)5193273395Rat
1331771Rf35Renal function QTL 354.36965kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)5189432042Rat
1331773Scl26Serum cholesterol level QTL 263.065blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)54440427689432042Rat
1331801Rf33Renal function QTL 334.149kidney blood vessel physiology trait (VT:0100012)absolute change in renal vascular resistance (CMO:0001900)544404276134502294Rat
1300115Hrtrt7Heart rate QTL 72.76heart pumping trait (VT:2000009)heart rate (CMO:0000002)54872203893587756Rat
1549845Scl44Serum cholesterol level QTL 446blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)540777918154732375Rat
1641912Alcrsp18Alcohol response QTL 18response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)535788756147487820Rat
1641922Alcrsp8Alcohol response QTL 8alcohol metabolism trait (VT:0015089)blood ethanol level (CMO:0000535)53578875670742105Rat
1576312Emca8Estrogen-induced mammary cancer QTL 84.1mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)551418671147487820Rat
1576314Eutr1Estrogen induced uterine response QTL 1uterus integrity trait (VT:0010575)pyometritis severity score (CMO:0002009)5152509878720537Rat
1576317Eutr2Estrogen induced uterine response QTL 20.01uterus integrity trait (VT:0010575)pyometritis severity score (CMO:0002009)535225432108092802Rat
1578766Tcas11Tongue tumor susceptibility QTL 114.12tongue integrity trait (VT:0010553)number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)547745646167946134Rat
1578767Stresp17Stress response QTL 174.30.01blood aldosterone amount (VT:0005346)plasma aldosterone level (CMO:0000551)52907889974078899Rat
1578776Stresp18Stress response QTL 182.9thymus mass (VT:0004954)thymus wet weight (CMO:0000855)52907889974078899Rat
61359EaexExperimental allergic encephalomyelitis QTL x3nervous system integrity trait (VT:0010566)post-insult time to onset of experimental autoimmune encephalomyelitis (CMO:0001422)556902367101902367Rat
1598807Glom12Glomerulus QTL 122.7kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)53440240979402409Rat
70189Mcs5Mammary carcinoma susceptibility QTL 510.51mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)556991667137729065Rat
70212Niddm25Non-insulin dependent diabetes mellitus QTL 253.54blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)51136640934Rat
2290448Scl54Serum cholesterol level QTL 542.93blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)531926122136640934Rat
2303574Gluco42Glucose level QTL 422blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)555903593100903593Rat
2303615Vencon7Ventilatory control QTL 70.001respiration trait (VT:0001943)respiration rate (CMO:0000289)55330956898309568Rat
1600358Mamtr5Mammary tumor resistance QTL 5mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)51884791363847913Rat
1302786Kidm8Kidney mass QTL 828.15kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)53440240979402409Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:145
Count of miRNA genes:111
Interacting mature miRNAs:118
Transcripts:ENSRNOT00000060203
Prediction methods:Microtar, 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.


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 31 37 22 19 22 73 34 41 11
Low 12 20 19 19 8 11 1 1 8
Below cutoff

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_134467 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006238012 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006238014 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006238015 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006238016 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006238017 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006238018 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006238020 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008763664 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008763665 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008763666 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008763667 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008763668 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017593138 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017593139 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017593140 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AABR07048062 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AABR07073108 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01036425 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AC127935 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AF480444 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC083548 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH473962 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000060203   ⟹   ENSRNOP00000056951
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl559,607,992 - 59,638,385 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000077367   ⟹   ENSRNOP00000074615
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl559,607,476 - 59,638,492 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000091944   ⟹   ENSRNOP00000072089
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl559,608,035 - 59,647,633 (-)Ensembl
RefSeq Acc Id: NM_134467   ⟹   NP_604462
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0559,607,991 - 59,638,385 (-)NCBI
Rnor_5.0564,128,873 - 64,235,392 (-)NCBI
RGSC_v3.4560,600,918 - 60,631,312 (-)RGD
Celera556,940,197 - 56,970,567 (-)RGD
Sequence:
RefSeq Acc Id: XM_006238012   ⟹   XP_006238074
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0559,604,783 - 59,646,904 (-)NCBI
Rnor_5.0564,128,873 - 64,235,392 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006238014   ⟹   XP_006238076
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0559,604,783 - 59,646,904 (-)NCBI
Rnor_5.0564,128,873 - 64,235,392 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006238015   ⟹   XP_006238077
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0559,604,783 - 59,646,904 (-)NCBI
Rnor_5.0564,128,873 - 64,235,392 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006238016   ⟹   XP_006238078
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0559,604,783 - 59,647,546 (-)NCBI
Rnor_5.0564,128,873 - 64,235,392 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006238017   ⟹   XP_006238079
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0559,604,783 - 59,648,837 (-)NCBI
Rnor_5.0564,128,873 - 64,235,392 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006238018   ⟹   XP_006238080
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0559,604,783 - 59,647,252 (-)NCBI
Rnor_5.0564,128,873 - 64,235,392 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006238020   ⟹   XP_006238082
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0559,604,783 - 59,713,108 (-)NCBI
Rnor_5.0564,128,873 - 64,235,392 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008763664   ⟹   XP_008761886
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0559,604,783 - 59,639,271 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008763665   ⟹   XP_008761887
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0559,604,783 - 59,639,271 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008763666   ⟹   XP_008761888
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0559,604,783 - 59,639,271 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008763667   ⟹   XP_008761889
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0559,604,783 - 59,713,108 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008763668   ⟹   XP_008761890
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0559,604,783 - 59,647,252 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017593138   ⟹   XP_017448627
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0559,604,783 - 59,646,904 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017593139   ⟹   XP_017448628
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0559,604,783 - 59,713,108 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017593140   ⟹   XP_017448629
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0559,604,783 - 59,647,065 (-)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_604462   ⟸   NM_134467
- UniProtKB: Q8R4E3 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006238082   ⟸   XM_006238020
- Peptide Label: isoform X8
- UniProtKB: Q5XIX1 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006238079   ⟸   XM_006238017
- Peptide Label: isoform X8
- UniProtKB: Q5XIX1 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006238078   ⟸   XM_006238016
- Peptide Label: isoform X8
- UniProtKB: Q5XIX1 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006238080   ⟸   XM_006238018
- Peptide Label: isoform X8
- UniProtKB: Q5XIX1 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006238077   ⟸   XM_006238015
- Peptide Label: isoform X7
- Sequence:
RefSeq Acc Id: XP_006238076   ⟸   XM_006238014
- Peptide Label: isoform X6
- Sequence:
RefSeq Acc Id: XP_006238074   ⟸   XM_006238012
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_008761889   ⟸   XM_008763667
- Peptide Label: isoform X8
- UniProtKB: Q5XIX1 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_008761890   ⟸   XM_008763668
- Peptide Label: isoform X8
- UniProtKB: Q5XIX1 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_008761888   ⟸   XM_008763666
- Peptide Label: isoform X4
- Sequence:
RefSeq Acc Id: XP_008761887   ⟸   XM_008763665
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: XP_008761886   ⟸   XM_008763664
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_017448628   ⟸   XM_017593139
- Peptide Label: isoform X8
- UniProtKB: Q5XIX1 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_017448629   ⟸   XM_017593140
- Peptide Label: isoform X8
- UniProtKB: Q5XIX1 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_017448627   ⟸   XM_017593138
- Peptide Label: isoform X5
- Sequence:
RefSeq Acc Id: ENSRNOP00000074615   ⟸   ENSRNOT00000077367
RefSeq Acc Id: ENSRNOP00000056951   ⟸   ENSRNOT00000060203
RefSeq Acc Id: ENSRNOP00000072089   ⟸   ENSRNOT00000091944
Protein Domains
RING-type

Transcriptome

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

Promoters
RGD ID:13693695
Promoter ID:EPDNEW_R4215
Type:single initiation site
Name:Rnf38_1
Description:ring finger protein 38
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_6.0559,647,704 - 59,647,764EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN/SsN (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Buf/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
F344/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
FHH/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
GH/OmrMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/Ox (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LE/Stm (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
M520/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MHS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
SBH/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHRSP/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:621856 AgrOrtholog
Ensembl Genes ENSRNOG00000013956 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000056951 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000072089 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000074615 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000060203 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000077367 UniProtKB/TrEMBL
  ENSRNOT00000091944 ENTREZGENE, UniProtKB/TrEMBL
Gene3D-CATH 3.30.40.10 UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7134112 IMAGE-MGC_LOAD
InterPro Znf_RING UniProtKB/TrEMBL
  Znf_RING/FYVE/PHD UniProtKB/TrEMBL
KEGG Report rno:171501 UniProtKB/TrEMBL
MGC_CLONE MGC:93195 IMAGE-MGC_LOAD
NCBI Gene 171501 ENTREZGENE
Pfam zf-RING_2 UniProtKB/TrEMBL
PhenoGen Rnf38 PhenoGen
PROSITE ZF_RING_2 UniProtKB/TrEMBL
SMART RING UniProtKB/TrEMBL
UniGene Rn.82699 ENTREZGENE
UniProt Q5XIX1 ENTREZGENE, UniProtKB/TrEMBL
  Q8R4E3 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2005-01-20 Rnf38  ring finger protein 38  Oip1  RING finger protein OIP1  Symbol and Name updated 1299863 APPROVED
2002-08-07 Oip1  RING finger protein OIP1      Symbol and Name status set to provisional 70820 PROVISIONAL

RGD Curation Notes
Note Type Note Reference
gene_domains contains a RING finger domain 633521
gene_expression expressed in round spermatids, spermatocytes, and several somatic tissues 633521