RetrogeneDB ID: retro_mmus_1570

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 17:37860806..37861577(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000092458
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Vps72
• Ensembl ID: ENSMUSG00000008958
• Aliases: Vps72, Tcfl1, YL-1
• Description: vacuolar protein sorting 72 (yeast) [Source:MGI Symbol;Acc:MGI:1202305]

Sequence

>retro_mmus_1570
AGTTTGGCTTGTGGCCGGGTCCCAGGGAAAACCACTGGGAACCTGCTTTCTGGGCTCCTGGAAGCAGAGGAGGAAGACGA
GTTCTACCAGACAACTAACGGGGCTTTCACCTAGGAATCTGGAGATGATGAGTATCAAGGAGACCAGTCTGATATGGAGG
ATGAGGTAGACTCTGACTTTGACATTGATGAAGGGGATGAACCATCTAGTGATGGAGAAGTGGAAGAGCCAAGAAGGAAG
CGCAGAGTCGTCACCTAAGCCTATAAGGAGCCTCTAAAGAGCTTGAGGCCTCGCAAGGTCAGCACCCCAGCAAGCAGCTC
CCAGAAGGCCAGAGAGAAGACGCTGCTGCCGCCGCTGGAGCTCCAGGACGACGGCTCTGACAGCCACAAGTCCATGTGTC
AGTCTACAGCTGAGCACACATGACAAATGTTCCTTCGGGTTCAAGAGAGGCAAGGACAGTCCCGGAGGCGGAAGGGTCCA
CAATGTGAGCGACCACTAACCCAGGAAGAGTTGCTCAGGGAGGCCAAGATCACTGAAGAGCTCAATTTACGTTCACTCGA
GACCTATGAAAGGCTGGAGGCTGACAAAAAGAAGCAGATTCACAAGAAGCGGAAGTACCCTGGGCCGATAATCACCTACC
ACTCAGTGACAGTGCAGCTTGTTGGGAAGCCTGGCCCCAAGGAGGAGAATGTGGACATGGAAGGCCTTGATTCTGCTCCT
ACAGCCTCTGCTCTGACTCTACTTGTTGGGACTGGGACTGGAGCTACCGCC

Alignment

ORF - retro_mmus_1570 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.94 %
• Parental protein coverage: 69.84 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SLAGGRAPRKTAGNRLSGLLEAEEEDEFYQTTYGGFTEESGDDEYQGDQSDTEDEVDSDFDIDEGDEPSS
          SLA.GR.P.KT.GN.LSGLLEAEEEDEFYQTT.G.FT.ESGDDEYQGDQSD.EDEVDSDFDIDEGDEPSS
Retrocopy SLACGRVPGKTTGNLLSGLLEAEEEDEFYQTTNGAFT*ESGDDEYQGDQSDMEDEVDSDFDIDEGDEPSS

Parental  DGEAEEPRRKRRVVTKAYKEPLKSLRPRKVSTPASSSQKAREEKTLLPLELQDDGSDSRKSMRQSTAEHT
          DGE.EEPRRKRRVVT.AYKEPLKSLRPRKVSTPASSSQKARE...L.PLELQDDGSDS.KSM.QSTAEHT
Retrocopy DGEVEEPRRKRRVVT*AYKEPLKSLRPRKVSTPASSSQKAREKTLLPPLELQDDGSDSHKSMCQSTAEHT

Parental  RQTFLRVQERQGQSRRRKGPHCERPLTQEELLREAKITEELNLRSLETYERLEADKKKQVHKKRKCPGPI
          .Q.FLRVQERQGQSRRRKGP.CERPLTQEELLREAKITEELNLRSLETYERLEADKKKQ.HKKRK.PGPI
Retrocopy *QMFLRVQERQGQSRRRKGPQCERPLTQEELLREAKITEELNLRSLETYERLEADKKKQIHKKRKYPGPI

Parental  ITYHSVTVPLVGEPGPKEENVDVEGLDPAPTASALAPHAGTGTGAAA
          ITYHSVTV.LVG.PGPKEENVD.EGLD.APTASAL....GTGTGA.A
Retrocopy ITYHSVTVQLVGKPGPKEENVDMEGLDSAPTASALTLLVGTGTGATA

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	17.50 RPM
SRP007412_cerebellum	0.04 RPM	27.14 RPM
SRP007412_heart	0.03 RPM	23.88 RPM
SRP007412_kidney	0.00 RPM	22.39 RPM
SRP007412_liver	0.00 RPM	13.87 RPM
SRP007412_testis	0.23 RPM	22.87 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_1570 was not detected

EST

No EST(s) were mapped for retro_mmus_1570 retrocopy.

TSS

No TSS is located nearby retro_mmus_1570 retrocopy 5' end.

Lab

retro_mmus_1570 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1570 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000000824	1 retrocopy	retro_amel_1768,
Canis familiaris	ENSCAFG00000012540	1 retrocopy	retro_cfam_807,
Equus caballus	ENSECAG00000017754	1 retrocopy	retro_ecab_13,
Echinops telfairi	ENSETEG00000004257	1 retrocopy	retro_etel_101,
Mustela putorius furo	ENSMPUG00000004027	1 retrocopy	retro_mputfur_1542,
Mus musculus	ENSMUSG00000008958	1 retrocopy	retro_mmus_1570 ,