Mouse Gene Gm28043 (ENSMUST00000130871.1) from GENCODE VM23 Comprehensive Transcript Set (only Basic displayed by default)
  Description: Mus musculus predicted gene, 28043 (Gm28043), long non-coding RNA. (from RefSeq NR_132314)
RefSeq Summary (NR_132314): This locus represents naturally occurring readthrough transcription between the neighboring Rnf8 (ring finger protein 8) and Cmtr1 (cap methyltransferase 1) genes on chromosome 17. The readthrough transcript is a candidate for nonsense-mediated mRNA decay (NMD), and is unlikely to produce a protein product. [provided by RefSeq, Jul 2015]. Sequence Note: The RefSeq transcript and protein were derived from genomic sequence to make the sequence consistent with the reference genome assembly. The genomic coordinates used for the transcript record was based on AK172991.1, which retains an intron.
Gencode Transcript: ENSMUST00000130871.1
Gencode Gene: ENSMUSG00000098374.1
Transcript (Including UTRs)
   Position: mm10 chr17:29,614,876-29,703,359 Size: 88,484 Total Exon Count: 28 Strand: +
Coding Region
   Position: mm10 chr17:29,614,968-29,685,974 Size: 71,007 Coding Exon Count: 14 

Page IndexSequence and LinksUniProtKB CommentsPrimersRNA StructureProtein Structure
Other SpeciesGO AnnotationsmRNA DescriptionsPathwaysOther NamesModel Information
Methods
Data last updated at UCSC: 2019-09-20

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr17:29,614,876-29,703,359)mRNA (may differ from genome)Protein (719 aa)
Gene SorterGenome BrowserOther Species FASTATable SchemaAlphaFoldBioGPS
EnsemblEntrez GeneExonPrimerGeneCardsMGIPubMed
ReactomeSOURCEUniProtKB

-  Comments and Description Text from UniProtKB
  ID: E0CXC2_MOUSE
DESCRIPTION: SubName: Full=E3 ubiquitin-protein ligase RNF8;
CAUTION: The sequence shown here is derived from an Ensembl automatic analysis pipeline and should be considered as preliminary data.

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -33.7092-0.366 Picture PostScript Text
3' UTR -1447.304269-0.339 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR000253 - FHA_dom
IPR000467 - G_patch_dom
IPR008984 - SMAD_FHA_domain
IPR001841 - Znf_RING
IPR013083 - Znf_RING/FYVE/PHD
IPR017907 - Znf_RING_CS

Pfam Domains:
PF00097 - Zinc finger, C3HC4 type (RING finger)
PF00498 - FHA domain
PF01585 - G-patch domain
PF13445 - RING-type zinc-finger
PF13639 - Ring finger domain
PF13920 - Zinc finger, C3HC4 type (RING finger)
PF13923 - Zinc finger, C3HC4 type (RING finger)

SCOP Domains:
46966 - Spectrin repeat
49879 - SMAD/FHA domain
52540 - P-loop containing nucleoside triphosphate hydrolases
57850 - RING/U-box

ModBase Predicted Comparative 3D Structure on E0CXC2
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The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
HumanRatZebrafishD. melanogasterC. elegansS. cerevisiae
Genome BrowserGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
GenBankRGD    
Protein SequenceProtein Sequence    
AlignmentAlignment    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003676 nucleic acid binding
GO:0003682 chromatin binding
GO:0004842 ubiquitin-protein transferase activity
GO:0016740 transferase activity
GO:0042393 histone binding
GO:0043130 ubiquitin binding
GO:0046872 metal ion binding

Biological Process:
GO:0006281 DNA repair
GO:0006302 double-strand break repair
GO:0006325 chromatin organization
GO:0006974 cellular response to DNA damage stimulus
GO:0007049 cell cycle
GO:0010212 response to ionizing radiation
GO:0016567 protein ubiquitination
GO:0033522 histone H2A ubiquitination
GO:0033523 histone H2B ubiquitination
GO:0045739 positive regulation of DNA repair
GO:0051301 cell division

Cellular Component:
GO:0000151 ubiquitin ligase complex
GO:0000781 chromosome, telomeric region
GO:0005634 nucleus
GO:0005694 chromosome
GO:0005737 cytoplasm
GO:0030496 midbody


-  Descriptions from all associated GenBank mRNAs
  AJ242721 - Mus musculus mRNA for partial AIP37 protein.
AK147168 - Mus musculus 13 days embryo liver cDNA, RIKEN full-length enriched library, clone:I920193E04 product:Ubiquitin ligase protein RNF8 (EC 6.3.2.-) (RING finger protein 8) (AIP37) (ActA-interacting protein 37) (LaXp180), full insert sequence.
BC021778 - Mus musculus ring finger protein 8, mRNA (cDNA clone MGC:28682 IMAGE:4239442), complete cds.
AK076180 - Mus musculus 18 days pregnant adult female placenta and extra embryonic tissue cDNA, RIKEN full-length enriched library, clone:3830404E21 product:similar to NEW ZINC FINGER PROTEIN (DJ744I24.1) (KIAA0646 (NEW ZINC FINGER PROTEIN)) (RING FINGER PROTEIN (C3HC4 TYPE) 8) [Homo sapiens], full insert sequence.
AK172991 - Mus musculus mRNA for mKIAA0646 protein.
CT010295 - Mus musculus full open reading frame cDNA clone RZPDo836A0852D for gene Rnf8, Ring finger protein 8; complete cds, incl. stopcodon.
AK219887 - Mus musculus cDNA, clone:Y2G0150A09, strand:plus, reference:ENSEMBL:Mouse-Transcript-ENST:ENSMUST00000058395, based on BLAT search.
AK190624 - Mus musculus cDNA, clone:Y1G0103F04, strand:plus, reference:ENSEMBL:Mouse-Transcript-ENST:ENSMUST00000024817, based on BLAT search.
AK135331 - Mus musculus 12 days embryo male wolffian duct includes surrounding region cDNA, RIKEN full-length enriched library, clone:6720481I24 product:unclassifiable, full insert sequence.
AK080379 - Mus musculus 3 days neonate thymus cDNA, RIKEN full-length enriched library, clone:A630084I01 product:hypothetical D111/G-patch domain/WW/rsp5/WWP domain profile/WW / rsp5 / WWP domain/FtsJ cell division protein containing protein, full insert sequence.
AK049190 - Mus musculus ES cells cDNA, RIKEN full-length enriched library, clone:C330012A18 product:hypothetical D111/G-patch domain/WW/rsp5/WWP domain profile/WW / rsp5 / WWP domain/FtsJ cell division protein containing protein, full insert sequence.
AK154773 - Mus musculus NOD-derived CD11c +ve dendritic cells cDNA, RIKEN full-length enriched library, clone:F630106F20 product:1300018I05Rik protein (RIKEN cDNA 1300018I05 gene) (Hypothetical D111/G-patch domain/WW/rsp5/WWP domain profile/WW/rsp5/WWP domain/FtsJ cell division protein containing protein), full insert sequence.
AK042060 - Mus musculus 3 days neonate thymus cDNA, RIKEN full-length enriched library, clone:A630055B13 product:hypothetical D111/G-patch domain/WW/rsp5/WWP domain profile/WW / rsp5 / WWP domain/FtsJ cell division protein containing protein, full insert sequence.
AK043733 - Mus musculus 10 days neonate cortex cDNA, RIKEN full-length enriched library, clone:A830026H07 product:hypothetical D111/G-patch domain/WW/rsp5/WWP domain profile/WW / rsp5 / WWP domain/FtsJ cell division protein containing protein, full insert sequence.
AK088624 - Mus musculus 2 days neonate thymus thymic cells cDNA, RIKEN full-length enriched library, clone:E430021L17 product:hypothetical D111/G-patch domain/WW / rsp5 / WWP domain/FtsJ cell division protein containing protein, full insert sequence.
AK150392 - Mus musculus bone marrow macrophage cDNA, RIKEN full-length enriched library, clone:I830006J02 product:hypothetical Ribosomal RNA methyltransferase RrmJ/FtsJ containing protein, full insert sequence.
AK151194 - Mus musculus bone marrow macrophage cDNA, RIKEN full-length enriched library, clone:I830026K12 product:hypothetical Ribosomal RNA methyltransferase RrmJ/FtsJ containing protein, full insert sequence.
AK152276 - Mus musculus bone marrow macrophage cDNA, RIKEN full-length enriched library, clone:I830058B13 product:hypothetical Ribosomal RNA methyltransferase RrmJ/FtsJ containing protein, full insert sequence.
AK152799 - Mus musculus bone marrow macrophage cDNA, RIKEN full-length enriched library, clone:I830086G13 product:hypothetical D111/G-patch domain/WW/Rsp5/WWP domain/Ribosomal RNA methyltransferase RrmJ/FtsJ/G-patch domain profile containing protein, full insert sequence.
AK153021 - Mus musculus bone marrow macrophage cDNA, RIKEN full-length enriched library, clone:I830119C20 product:hypothetical Ribosomal RNA methyltransferase RrmJ/FtsJ containing protein, full insert sequence.
AK153066 - Mus musculus bone marrow macrophage cDNA, RIKEN full-length enriched library, clone:I830120J01 product:hypothetical Ribosomal RNA methyltransferase RrmJ/FtsJ containing protein, full insert sequence.
BC024691 - Mus musculus RIKEN cDNA 1300018I05 gene, mRNA (cDNA clone MGC:30380 IMAGE:3668655), complete cds.
AK005044 - Mus musculus adult male liver cDNA, RIKEN full-length enriched library, clone:1300018I05 product:hypothetical D111/G-patch domain/WW / rsp5 / WWP domain/FtsJ cell division protein containing protein, full insert sequence.
AK152452 - Mus musculus bone marrow macrophage cDNA, RIKEN full-length enriched library, clone:I830072O11 product:1300018I05Rik protein (RIKEN cDNA 1300018I05 gene) (Hypothetical D111/G-patch domain/WW/rsp5/WWP domain profile/WW/rsp5/WWP domain/FtsJ cell division protein containing protein), full insert sequence.
AK172883 - Mus musculus premature mRNA for mKIAA0082 protein.
AK182191 - Mus musculus cDNA, clone:Y0G0121C10, strand:plus, reference:ENSEMBL:Mouse-Transcript-ENST:ENSMUST00000024816, based on BLAT search.
AK186244 - Mus musculus cDNA, clone:Y0G0136L15, strand:minus, reference:ENSEMBL:Mouse-Transcript-ENST:ENSMUST00000024816, based on BLAT search.
AK212192 - Mus musculus cDNA, clone:Y2G0124C16, strand:plus, reference:ENSEMBL:Mouse-Transcript-ENST:ENSMUST00000024816, based on BLAT search.
AK047104 - Mus musculus 10 days neonate cerebellum cDNA, RIKEN full-length enriched library, clone:B930020M14 product:RIKEN cDNA 1300018I05 gene, full insert sequence.
AK179199 - Mus musculus cDNA, clone:Y0G0109H11, strand:plus, reference:ENSEMBL:Mouse-Transcript-ENST:ENSMUST00000024816, based on BLAT search.
AK180034 - Mus musculus cDNA, clone:Y0G0112K17, strand:plus, reference:ENSEMBL:Mouse-Transcript-ENST:ENSMUST00000024816, based on BLAT search.
AK183017 - Mus musculus cDNA, clone:Y0G0124H12, strand:plus, reference:ENSEMBL:Mouse-Transcript-ENST:ENSMUST00000024816, based on BLAT search.
LF200999 - JP 2014500723-A/8502: Polycomb-Associated Non-Coding RNAs.
AK183115 - Mus musculus cDNA, clone:Y0G0124M03, strand:minus, reference:ENSEMBL:Mouse-Transcript-ENST:ENSMUST00000024816, based on BLAT search.
AK196080 - Mus musculus cDNA, clone:Y1G0120K05, strand:plus, reference:ENSEMBL:Mouse-Transcript-ENST:ENSMUST00000024816, based on BLAT search.
LF251148 - JP 2014500723-A/58651: Polycomb-Associated Non-Coding RNAs.
LF251150 - JP 2014500723-A/58653: Polycomb-Associated Non-Coding RNAs.
LF251151 - JP 2014500723-A/58654: Polycomb-Associated Non-Coding RNAs.
LF251152 - JP 2014500723-A/58655: Polycomb-Associated Non-Coding RNAs.
LF251154 - JP 2014500723-A/58657: Polycomb-Associated Non-Coding RNAs.
AK197536 - Mus musculus cDNA, clone:Y1G0125G09, strand:plus, reference:ENSEMBL:Mouse-Transcript-ENST:ENSMUST00000024816, based on BLAT search.
AK212706 - Mus musculus cDNA, clone:Y2G0125N13, strand:minus, reference:ENSEMBL:Mouse-Transcript-ENST:ENSMUST00000024816, based on BLAT search.
LF251156 - JP 2014500723-A/58659: Polycomb-Associated Non-Coding RNAs.
AK206456 - Mus musculus cDNA, clone:Y2G0104O19, strand:plus, reference:ENSEMBL:Mouse-Transcript-ENST:ENSMUST00000024816, based on BLAT search.
LF251157 - JP 2014500723-A/58660: Polycomb-Associated Non-Coding RNAs.
LF251159 - JP 2014500723-A/58662: Polycomb-Associated Non-Coding RNAs.
AK179043 - Mus musculus cDNA, clone:Y0G0108P05, strand:plus, reference:ENSEMBL:Mouse-Transcript-ENST:ENSMUST00000024816, based on BLAT search.
AK194398 - Mus musculus cDNA, clone:Y1G0115D12, strand:plus, reference:ENSEMBL:Mouse-Transcript-ENST:ENSMUST00000024816, based on BLAT search.
AK179293 - Mus musculus cDNA, clone:Y0G0109M16, strand:plus, reference:ENSEMBL:Mouse-Transcript-ENST:ENSMUST00000024816, based on BLAT search.
AK215709 - Mus musculus cDNA, clone:Y2G0135O18, strand:minus, reference:ENSEMBL:Mouse-Transcript-ENST:ENSMUST00000024816, based on BLAT search.
LF251160 - JP 2014500723-A/58663: Polycomb-Associated Non-Coding RNAs.
MA436576 - JP 2018138019-A/8502: Polycomb-Associated Non-Coding RNAs.
MA486725 - JP 2018138019-A/58651: Polycomb-Associated Non-Coding RNAs.
MA486727 - JP 2018138019-A/58653: Polycomb-Associated Non-Coding RNAs.
MA486728 - JP 2018138019-A/58654: Polycomb-Associated Non-Coding RNAs.
MA486729 - JP 2018138019-A/58655: Polycomb-Associated Non-Coding RNAs.
MA486731 - JP 2018138019-A/58657: Polycomb-Associated Non-Coding RNAs.
MA486733 - JP 2018138019-A/58659: Polycomb-Associated Non-Coding RNAs.
MA486734 - JP 2018138019-A/58660: Polycomb-Associated Non-Coding RNAs.
MA486736 - JP 2018138019-A/58662: Polycomb-Associated Non-Coding RNAs.
MA486737 - JP 2018138019-A/58663: Polycomb-Associated Non-Coding RNAs.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein E0CXC2 (Reactome details) participates in the following event(s):

R-MMU-5682588 RNF8 binds phosphorylated MDC1 at DNA DSBs
R-MMU-5682586 HERC2 and PIAS4 are recruited to DNA DSBs
R-MMU-5682607 PIAS4 SUMOylates HERC2 with SUMO1 at DNA DSBs
R-MMU-5682598 ATM phosphorylates HERC2
R-MMU-5693566 TP53BP1 associates with H4K20Me2 at DNA DSBs
R-MMU-5683077 RNF8 and RNF168 ubiquitinate KDM4A,B
R-MMU-5682863 RNF168 binds DNA DSBs
R-MMU-5682858 RNF8 and RNF168 ubiquitinate H2AFX
R-MMU-5683384 UIMC1 and FAM175A bind DNA DSBs
R-MMU-5683405 PPP5C dephosphorylates TP53BP1
R-MMU-5683425 ATM phosphorylates TP53BP1 at DNA DSBs
R-MMU-5683735 CHEK2 is recruited to DNA DSBs
R-MMU-5683801 CHEK2 phosphorylates BRCA1
R-MMU-69891 Phosphorylation and activation of CHEK2 by ATM
R-MMU-5693551 Phosphorylation of BRCA1-A complex at multiple sites by ATM
R-MMU-5683385 Formation of BRCA1-A complex at DNA DSBs
R-MMU-5686685 RIF1 and PAX1IP bind TP53BP1 at DNA DSBs
R-MMU-5686900 TP53BP1 recruits DCLRE1C to ATM
R-MMU-5686704 Activated ATM phosphorylates DCLRE1C
R-MMU-5693565 Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks
R-MMU-5693606 DNA Double Strand Break Response
R-MMU-5693532 DNA Double-Strand Break Repair
R-MMU-73894 DNA Repair
R-MMU-69473 G2/M DNA damage checkpoint
R-MMU-5693571 Nonhomologous End-Joining (NHEJ)
R-MMU-69481 G2/M Checkpoints
R-MMU-69620 Cell Cycle Checkpoints
R-MMU-1640170 Cell Cycle

-  Other Names for This Gene
  Alternate Gene Symbols: E0CXC2, E0CXC2_MOUSE, NR_132314, Rnf8, uc289jld.1
UCSC ID: uc289jld.1
RefSeq Accession: NR_132314
Protein: E0CXC2

-  Gene Model Information
  Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.