RetrogeneDB ID: retro_mmus_3709

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: X:146652217..146652514(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000084147
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Ppih
• Ensembl ID: ENSMUSG00000060288
• Aliases: Ppih, 1100001J08Rik, 2010111B15Rik, 4833408F11Rik, AI464484, CYP-20, CYPH, D4Wsu43e
• Description: peptidyl prolyl isomerase H [Source:MGI Symbol;Acc:MGI:106499]

Sequence

>retro_mmus_3709
ATAGTGGTGGAGAATTCTAGATCACTCAACCCTGTATTTTTCTCTGATGTTAGCATTGACAGCCAGGAAGTTGGTGGCAT
GAAGACTGAGATGTTTGCTAATGTGATGTCTAAGACGGAAGAGAAGTTTAGGAAATTCTGCAGTTGAGAGTTCAGAAAGG
ATGCTGCTACTATAGGATACAAAGGAAGCTCCTTCTATACAATCATAAAGGATTTTGTGATCTAGGGTGGCGGTTTTGTT
AATGGTGATGGTTCTGGGGTTGCCTGTACTTAACATGGTCAATTTATAGCAGAAAAC

Alignment

ORF - retro_mmus_3709 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.61 %
• Parental protein coverage: 52.66 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAVANSSPVNPVVFFDVSIGGQEVGRMKIELFADVVPKTAENFRQFCTGEFRKDGVPIGYKGSTFHRVIK
          ..V.NS...NPV.F.DVSI..QEVG.MK.E.FA.V..KT.E.FR.FC..EFRKD...IGYKGS.F...IK
Retrocopy IVVENSRSLNPVFFSDVSIDSQEVGGMKTEMFANVMSKTEEKFRKFCS*EFRKDAATIGYKGSSFYTIIK

Parental  DFMIQGGDFVNGDGTGVASIYRGPFADEN
          DF.I.GG.FVNGDG.GVA....G.F..EN
Retrocopy DFVI*GGGFVNGDGSGVACT*HGQFIAEN

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	4.30 RPM
SRP007412_cerebellum	0.00 RPM	4.82 RPM
SRP007412_heart	0.00 RPM	3.14 RPM
SRP007412_kidney	0.00 RPM	5.41 RPM
SRP007412_liver	0.00 RPM	3.66 RPM
SRP007412_testis	0.00 RPM	10.02 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_3709 was not detected

EST

No EST(s) were mapped for retro_mmus_3709 retrocopy.

TSS

No TSS is located nearby retro_mmus_3709 retrocopy 5' end.

Lab

retro_mmus_3709 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3709 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Rattus norvegicus	retro_rnor_2784
Rattus norvegicus	retro_rnor_2911

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000003145	5 retrocopies	retro_cjac_129, retro_cjac_1886, retro_cjac_2205, retro_cjac_3120, retro_cjac_4110,
Macropus eugenii	ENSMEUG00000001691	1 retrocopy	retro_meug_1699,
Macaca mulatta	ENSMMUG00000013129	1 retrocopy	retro_mmul_1124,
Mustela putorius furo	ENSMPUG00000013966	2 retrocopies	retro_mputfur_285, retro_mputfur_542,
Mus musculus	ENSMUSG00000060288	7 retrocopies	retro_mmus_2563, retro_mmus_2873, retro_mmus_3195, retro_mmus_3709 , retro_mmus_749, retro_mmus_913, retro_mmus_977,
Otolemur garnettii	ENSOGAG00000014937	1 retrocopy	retro_ogar_2368,
Procavia capensis	ENSPCAG00000011139	1 retrocopy	retro_pcap_81,
Rattus norvegicus	ENSRNOG00000008489	1 retrocopy	retro_rnor_2911,