RetrogeneDB ID: retro_mmus_3679

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: X:104346533..104348234(-)
• Located in intron of: ENSMUSG00000031333

Retrocopy information

• Ensembl ID: ENSMUSG00000083327
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Vcp
• Ensembl ID: ENSMUSG00000028452
• Aliases: Vcp, 3110001E05, CDC48, p97, p97/VCP
• Description: valosin containing protein [Source:MGI Symbol;Acc:MGI:99919]

Sequence

>retro_mmus_3679
ATGGCCTCTGGAGCCGATTCAAAAGGTGATGATTTATCAACAGCCATTCTCAAACAGAAGAACCGACCCAATCGGTTAAT
TGTTGATGAAGCCATCAATGAAGATAACAGCGTGGTGTCCTTGTCCCAGCCCAAGATGGATGAACTGCAGTTGTTCCGAG
GTGACACGGTGTTGCTAAAAGGAAAGAAAAGACGGGAAGCTGTATGCATTGTTCTTTCTGATGACACGTGTTCTGATGAG
AAGATTCGAATGAATAGAGTTGTTCGGAATAACCTCCGAGTTCGCCTAGGAGATGTCATCAGCATCCAGCCATGCCCTGA
TGTAAAGTATGGCAAACGTATCCACGTTCTACCCATCGATGACACAGTGGAAGGCATCACTGGCAATCTCTTTGAGGTAT
ACCTTAAGCCGTACTTCCTGGAAGCTTATCGGCCCATCCGTAAAGGAGATATTTTTCTTGTCCGGGGTGGGATGCGTGCT
GTGGAGTTCAAAGTTGTAGAGACAGATCCCAGCCCTTACTGTATTGTTGCTCCAGACACAGTGATCCACTGTGAGGGGGA
GCCAATCAAACGAGAGGATGAGGAGGAATCCTTGAATGAAGTAGGCTATGATGACATCGGTGGTTGCAGGAAGCAGCTAG
CTCAGATAAAGGAGATGGTGGAGCTGCCACTGAGACATCCTGCGCTCTTCAAGGCGATTGGTGTAAAGCCTCCTCGGGGA
ATCTTGTTGTATGGGCCTCCTGGGACAGGGAAGACCCTGATTGCTCGAGCTGTGGCAAATGAAACTGGAGCCTTCTTCTT
TCTGATCAATGGTCCTGAAATCATGAGCAAATTGGCTGGTGAGTCTGAGAGCAACCTTCGTAAAGCCTTTGAGGAAGCTG
AAAAGAATGCTCCTGCTATCATCTTCATCGATGAGCTTGATGCCATTGCACCCAAAAGAGAGAAAACTCATGGGGAAGTG
GAGCGTCGCATCGTGTCTCAGTTGTTGACCCTCATGGATGGCCTAAAGCAGAGAGCACATGTGATAGTTATGGCAGCAAC
CAATAGACCCAACAGCATTGACCCAGCCCTACGGCGATTTGGTCGCTTTGACAGAGAGGTAGATATTGGAATACCTGATG
CTACAGGACGTTTGGAGATTCTTCAGATCCATACCAAGAACATGAAACTGGCAGATGATGTGGACTTGGAACAGGTAGCC
AATGAGACTCATGGTCATGTTGGTGCTGATTTGGCAGCCCTATGTTCAGAGGCTGCTCTGCAGGCCATCCGGAAAAAAAT
GGACCTCATTGACCTAGAAGATGAGACCATTGATGCTGAGGTCATGAATTCCCTGGCAGTTACTATGGATGACTTCCGGT
GGGCTTTGAGTCAAAGCAACCCATCAGCACTTCGGGAAACTGTGGTAGAGGTGCCACAAGTAACCTGGGAAGATATTGGA
GGCCTGGAGGATGTCAAACGTGAGCTTCAGGAGTTGGTTCAGTACCCCGTGGAACATCCAGACAAATTCCTCAAATTTGG
CATGACTCCCTCCAAAGGTGTTCTTTTCTATGGACCTCCTGGCTGTGGGAAAACCTTACTGGCTAAAGCCATTGCTAATG
AATGCCAGGCCAACTTCATCTCCATCAAGGGTCCTGAGCTGCTTACCATGTGGTTTGGGGAATCTGAGGCCAATGTCCGG
GAAATTTTTGACAAGGCACGT

Alignment

ORF - retro_mmus_3679 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 100.0 %
• Parental protein coverage: 70.35 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MASGADSKGDDLSTAILKQKNRPNRLIVDEAINEDNSVVSLSQPKMDELQLFRGDTVLLKGKKRREAVCI
          MASGADSKGDDLSTAILKQKNRPNRLIVDEAINEDNSVVSLSQPKMDELQLFRGDTVLLKGKKRREAVCI
Retrocopy MASGADSKGDDLSTAILKQKNRPNRLIVDEAINEDNSVVSLSQPKMDELQLFRGDTVLLKGKKRREAVCI

Parental  VLSDDTCSDEKIRMNRVVRNNLRVRLGDVISIQPCPDVKYGKRIHVLPIDDTVEGITGNLFEVYLKPYFL
          VLSDDTCSDEKIRMNRVVRNNLRVRLGDVISIQPCPDVKYGKRIHVLPIDDTVEGITGNLFEVYLKPYFL
Retrocopy VLSDDTCSDEKIRMNRVVRNNLRVRLGDVISIQPCPDVKYGKRIHVLPIDDTVEGITGNLFEVYLKPYFL

Parental  EAYRPIRKGDIFLVRGGMRAVEFKVVETDPSPYCIVAPDTVIHCEGEPIKREDEEESLNEVGYDDIGGCR
          EAYRPIRKGDIFLVRGGMRAVEFKVVETDPSPYCIVAPDTVIHCEGEPIKREDEEESLNEVGYDDIGGCR
Retrocopy EAYRPIRKGDIFLVRGGMRAVEFKVVETDPSPYCIVAPDTVIHCEGEPIKREDEEESLNEVGYDDIGGCR

Parental  KQLAQIKEMVELPLRHPALFKAIGVKPPRGILLYGPPGTGKTLIARAVANETGAFFFLINGPEIMSKLAG
          KQLAQIKEMVELPLRHPALFKAIGVKPPRGILLYGPPGTGKTLIARAVANETGAFFFLINGPEIMSKLAG
Retrocopy KQLAQIKEMVELPLRHPALFKAIGVKPPRGILLYGPPGTGKTLIARAVANETGAFFFLINGPEIMSKLAG

Parental  ESESNLRKAFEEAEKNAPAIIFIDELDAIAPKREKTHGEVERRIVSQLLTLMDGLKQRAHVIVMAATNRP
          ESESNLRKAFEEAEKNAPAIIFIDELDAIAPKREKTHGEVERRIVSQLLTLMDGLKQRAHVIVMAATNRP
Retrocopy ESESNLRKAFEEAEKNAPAIIFIDELDAIAPKREKTHGEVERRIVSQLLTLMDGLKQRAHVIVMAATNRP

Parental  NSIDPALRRFGRFDREVDIGIPDATGRLEILQIHTKNMKLADDVDLEQVANETHGHVGADLAALCSEAAL
          NSIDPALRRFGRFDREVDIGIPDATGRLEILQIHTKNMKLADDVDLEQVANETHGHVGADLAALCSEAAL
Retrocopy NSIDPALRRFGRFDREVDIGIPDATGRLEILQIHTKNMKLADDVDLEQVANETHGHVGADLAALCSEAAL

Parental  QAIRKKMDLIDLEDETIDAEVMNSLAVTMDDFRWALSQSNPSALRETVVEVPQVTWEDIGGLEDVKRELQ
          QAIRKKMDLIDLEDETIDAEVMNSLAVTMDDFRWALSQSNPSALRETVVEVPQVTWEDIGGLEDVKRELQ
Retrocopy QAIRKKMDLIDLEDETIDAEVMNSLAVTMDDFRWALSQSNPSALRETVVEVPQVTWEDIGGLEDVKRELQ

Parental  ELVQYPVEHPDKFLKFGMTPSKGVLFYGPPGCGKTLLAKAIANECQANFISIKGPELLTMWFGESEANVR
          ELVQYPVEHPDKFLKFGMTPSKGVLFYGPPGCGKTLLAKAIANECQANFISIKGPELLTMWFGESEANVR
Retrocopy ELVQYPVEHPDKFLKFGMTPSKGVLFYGPPGCGKTLLAKAIANECQANFISIKGPELLTMWFGESEANVR

Parental  EIFDKAR
          EIFDKAR
Retrocopy EIFDKAR

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	3.27 RPM	76.93 RPM
SRP007412_cerebellum	9.47 RPM	55.75 RPM
SRP007412_heart	1.31 RPM	134.79 RPM
SRP007412_kidney	14.01 RPM	101.14 RPM
SRP007412_liver	8.00 RPM	89.60 RPM
SRP007412_testis	9.79 RPM	62.85 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_3679 was not detected

EST

No EST(s) were mapped for retro_mmus_3679 retrocopy.

TSS

TSS No.	TSS Name	TSS expression level (Expr) in TPM range:
		no expression	0 < Expr ≤ 1	1 < Expr ≤ 5	5 < Expr ≤ 10	Expr > 10
TSS #1	TSS_154717	386 libraries	43 libraries	224 libraries	265 libraries	154 libraries

The graphical summary, for retro_mmus_3679 TSS expression levels > 0 TPM .
TSS expression levels were studied across 1072 TSS-CAGE libraries, based on FANTOM5 data.
The expression values were visualized using beanplot. If you have any doubts, how to read it, read more in Kampstra P (2008)

Lab

retro_mmus_3679 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3679 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Mus musculus	ENSMUSG00000028452	1 retrocopy	retro_mmus_3679 ,