RetrogeneDB ID: retro_mmus_2040

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 2:64570241..64570640(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000081065
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Pddc1
• Ensembl ID: ENSMUSG00000051007
• Aliases: Pddc1, BC023835, D230016J19Rik
• Description: Parkinson disease 7 domain containing 1 [Source:MGI Symbol;Acc:MGI:2387178]

Sequence

>retro_mmus_2040
ATGGTGTTGGACTGGCTGCCCAGCAGGTCAGCTGCTCTCCTGGTGGGCAACGGAGCTTCTGAAGGGTCAGCCCCGTCCTT
CTTCAATTGCTACACAGTGGCCAGTGGTGCCTTCAACCTACAGGTAGCCACCCTAGGGAAAAAGGCCATGGAGTTTGTGC
ATATGACTGAGACCAGTTCATGTTGGGTACAAAGCTTCTGCCTCAAGGCATATGCCAGCCCTACAAAGCTTGAATCCACA
GATAGTGACTCTTACCATGACTTCCCGATTCCCAGCTGTCCTGGAACCCTGGCTGACCCTGACAACAGTGGGTCCTTGAC
TCTAGTGCTGTAGGACTTCCTCTCTGAGAGCAAACCCATCTGTGCCCCTGGCCATGGTATTGCTGGCCTGTGCTGTGCA

Alignment

ORF - retro_mmus_2040 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.43 %
• Parental protein coverage: 60.91 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MASERLPSRPACLLVASGASEGVSAQSFVHCFTLASAAFNLQVATPGGKAIDFVDVTESNARWVQDFRLK
          M....LPSR.A.LLV..GASEG.SA.SF..C.T.AS.AFNLQVAT.G.KA..FV..TE....WVQ.F.LK
Retrocopy MVLDWLPSRSAALLVGNGASEG-SAPSFFNCYTVASGAFNLQVATLGKKAMEFVHMTETSSCWVQSFCLK

Parental  AYASPAKLESIDGARYHALLIPSCPGALTDLASSGSLARILQHFRSESKPICAIGHGVAALCCA
          AYASP.KLES.D...YH...IPSCPG.L.D...SGSL...L..F.SESKPICA.GHG.A.LCCA
Retrocopy AYASPTKLESTDSDSYHDFPIPSCPGTLADPDNSGSLTLVL*DFLSESKPICAPGHGIAGLCCA

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
SRP007412_brain	0.00 RPM	21.31 RPM
SRP007412_cerebellum	0.00 RPM	14.42 RPM
SRP007412_heart	0.00 RPM	7.25 RPM
SRP007412_kidney	0.00 RPM	12.96 RPM
SRP007412_liver	0.00 RPM	9.78 RPM
SRP007412_testis	0.00 RPM	7.00 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_2040 was not detected

EST

No EST(s) were mapped for retro_mmus_2040 retrocopy.

TSS

No TSS is located nearby retro_mmus_2040 retrocopy 5' end.

Lab

retro_mmus_2040 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2040 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Rattus norvegicus	retro_rnor_1887

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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,