RetrogeneDB ID: retro_rnor_1887

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 3:57275475..57275892(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSRNOG00000027084
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Pddc1
• Ensembl ID: ENSRNOG00000046382
• Aliases: None
• Description: Parkinson disease 7 domain-containing protein 1 [Source:RefSeq peptide;Acc:NP_001101033]

Sequence

>retro_rnor_1887
CTGCCCAGCTTGTCAGCTGATCTCCTGATGGACAGCAGTGCTTCTGAAGGATCAACCCAGTCCTTCTTCCATTGCTACAC
ATTGGCCAGTGGTGCTTTCAACCTACAGGTGGCCACCTCAAGGAGAAAGGCCATGGACTTTGTGCATGTGACTGAGAACA
GTGACTATTGGGTACAAAGGTTCTGCCTCAAGGCATATACCAGGCCTACTAAGCTTGAATCCACAGACAGTGACCAGTAC
CATGATCTTCTGATTCCCAGCTGTTTTGGTATTCTGGATGACCTTGCCAACAATGGGTCCTTGGCTCAAATACGGCAGCA
TTTCCTCTCTGAGAACAAACCCACCTCTGCCATTGGCCATGGTATTGCTGGCCTATGCTACGCTACCAGTGAAGATGGGT
CCTGGGTTTTCAAGGGA

Alignment

ORF - retro_rnor_1887 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.86 %
• Parental protein coverage: 63.64 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LPSRPACLLVASGASEGVSAQSFVHCFTLASAAFNLQVATPGGKAMDFVDVTENNARWVQDFRLKAYASP
          LPS..A.LL..S.ASEG.S.QSF.HC.TLAS.AFNLQVAT...KAMDFV.VTEN...WVQ.F.LKAY..P
Retrocopy LPSLSADLLMDSSASEG-STQSFFHCYTLASGAFNLQVATSRRKAMDFVHVTENSDYWVQRFCLKAYTRP

Parental  AKLESIDGARYHALLIPSCPGALTDLASSGSLARILQHFHSESKPICAIGHGVAALCCATNEDRSWVFQG
          .KLES.D...YH.LLIPSC.G.L.DLA..GSLA.I.QHF.SE.KP..AIGHG.A.LC.AT.ED.SWVF.G
Retrocopy TKLESTDSDQYHDLLIPSCFGILDDLANNGSLAQIRQHFLSENKPTSAIGHGIAGLCYATSEDGSWVFKG

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP017611_brain	0.00 RPM	0.00 RPM
SRP017611_kidney	0.00 RPM	0.00 RPM
SRP017611_liver	0.00 RPM	0.00 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1887 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1887 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1887 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Mus musculus	retro_mmus_2040

---

Parental genes homology:

Parental genes homology involve 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Macropus eugenii	ENSMEUG00000005033	1 retrocopy	retro_meug_954,
Myotis lucifugus	ENSMLUG00000017584	1 retrocopy	retro_mluc_2267,
Mus musculus	ENSMUSG00000051007	1 retrocopy	retro_mmus_2040,
Rattus norvegicus	ENSRNOG00000046382	1 retrocopy	retro_rnor_1887 ,
Sarcophilus harrisii	ENSSHAG00000003122	1 retrocopy	retro_shar_496,