RetrogeneDB ID: | retro_rnor_2430 | ||
Retrocopy location | Organism: | Rat (Rattus norvegicus) | |
| Coordinates: | 7:17348360..17349181(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Pcgf6 | ||
| Ensembl ID: | ENSRNOG00000020250 | ||
| Aliases: | Pcgf6, Rnf134 | ||
| Description: | Polycomb group RING finger protein 6 [Source:UniProtKB/Swiss-Prot;Acc:Q5XI70] |
Retrocopy-Parental alignment summary:
>retro_rnor_2430
CCCCTGGAGTTGGAGCCAGAGCACAGTCTGGGCCTCTTGTGAGTCCACTTCGAGAACTATGATGAGGAGTTGGAAGAAGA
TTAGGAGATGGAGGAGGAGAAAGACCAGGAGGAAGAGATGAGCCACTTCTCTCTGAGTCTGGAGTCCGGATGTGCAAACT
CCTAGGACCAGGAGAAGAGCCTGATGAACCTGACTGAGCTGACGCCCTACATCTTGTGCTCCATTCGCAAAGGTTAATTG
ATACATGCCACCACTATTGCAGAATGTCTCCACACCTTTTGTAAAAGCTGCATTGTGAGACATTTTTACTATAGCAACAG
ATGCCCCAAATGCAACATAGTAGTCCACCAGACTCAGCCTCTTTATAATATAAGGTTGGACCGGCAGTTACAAGACAAAG
TATATAAATTAGTAATCAATCTAGCGGAAAGAGGAAAAAAGCAAAAGCACGACTTCTATAAAGAAAGAGGTCTAGAAGTC
CCTAAGCCTGCTCTTACACAGCCAGTCGCTGCAAACAAAGGAAGAACCCAGAAAATCCTAGAGTCAGTGTTTTGTATTCC
ACCTGATGTTTTATTGATGTTGAGTTCATTGATGCTAATGAAGACAGAGGACATTTTAAGCCATTGGAAAAGAAGTTTGT
GCATGTTTCAGGAGAAGCAACTACTGGGTATGTAGAAAAATTTCTTGGAAGAAAATTGTGTCTTGATCCAGCTTGTCAGG
TAGATAACATCTGTGGGGATCACTTATTGGAGCGGTACCAAACTCTGCAGGAAATCCGATGTTCAATACGTGACACAGCA
ATGCAGGATGGTCTACCTGTT
ORF - retro_rnor_2430 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 80.14 % |
| Parental protein coverage: | 78.63 % |
| Number of stop codons detected: | 4 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | PPELEPERSLGRLRGRFEDYDEELEEDEEMEEEEEEEEEMSHFSLRLESGRADSEDEEERLINLVELTPY |
| P.ELEPE.SLG.L...FE.YDEELEED.EMEEE...EEEMSHFSL.LESG.A.S.D.E..L.NL.ELTPY | |
| Retrocopy | PLELEPEHSLGLL*VHFENYDEELEED*EMEEEKDQEEEMSHFSLSLESGCANS*DQEKSLMNLTELTPY |
| Parental | ILCSICKGYLIDATTITECLHTFCKSCIVRHFYYSNRCPKCNIVVHQTQPLYNIRLDRQLQDIVYKLVVN |
| ILCSI.KG.LI.ATTI.ECLHTFCKSCIVRHFYYSNRCPKCNIVVHQTQPLYNIRLDRQLQD.VYKLV.N | |
| Retrocopy | ILCSIRKG*LIHATTIAECLHTFCKSCIVRHFYYSNRCPKCNIVVHQTQPLYNIRLDRQLQDKVYKLVIN |
| Parental | LEEREKKQMHDFYKERGLEVPKPAVPQPVPASKGRTKKALESVFRIPPELDVSLLL-EFIGANEDTGHFK |
| L.ER.KKQ.HDFYKERGLEVPKPA..QPV.A.KGRT.K.LESVF.IPP..DV.L.L.EFI.ANED.GHFK | |
| Retrocopy | LAERGKKQKHDFYKERGLEVPKPALTQPVAANKGRTQKILESVFCIPP--DVLLML<EFIDANEDRGHFK |
| Parental | PLEKKFVRVSGEATIGHVEKFLRRKMGLDPACQVDIICGDHLLERYQTLREIRRAIGDTAMQDGLLV |
| PLEKKFV.VSGEAT.G.VEKFL.RK..LDPACQVD.ICGDHLLERYQTL.EIR..I.DTAMQDGL.V | |
| Retrocopy | PLEKKFVHVSGEATTGYVEKFLGRKLCLDPACQVDNICGDHLLERYQTLQEIRCSIRDTAMQDGLPV |
Legend:
| * | Stop codon |
| > | Forward frameshift by one nucleotide |
| < | Reverse frameshift by one nucleotide |
(Hint: click retrocopy or parental gene accession number on the plot's legend, to show / hide expression level values)
Expression validation based on RNA-Seq data:
| Library | Retrocopy expression | Parental gene expression |
|---|---|---|
| SRP017611_brain | 0 .00 RPM | 11 .29 RPM |
| SRP017611_kidney | 0 .00 RPM | 6 .28 RPM |
| SRP017611_liver | 0 .00 RPM | 7 .06 RPM |
Rattus norvegicus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_rnor_2430 retrocopy.
Rattus norvegicus was not studied using FANTOM5 data.
retro_rnor_2430 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_rnor_2430 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 3 parental genes, and 4 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Echinops telfairi | ENSETEG00000004417 | 1 retrocopy | |
| Myotis lucifugus | ENSMLUG00000004985 | 1 retrocopy | |
| Rattus norvegicus | ENSRNOG00000020250 | 2 retrocopies |
retro_rnor_2429, retro_rnor_2430 ,
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