RetrogeneDB ID: retro_mmus_1774

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 18:46465367..46465790(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000046487
• Aliases: Mospd4, 2010013H21Rik
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Vapa
• Ensembl ID: ENSMUSG00000024091
• Aliases: Vapa, 33kDa, VAP33
• Description: vesicle-associated membrane protein, associated protein A [Source:MGI Symbol;Acc:MGI:1353561]

Sequence

>retro_mmus_1774
ATGGCGTCCACCTCCCGCGCCCCCGCGAAGCCCCAGCAGGTCCTAGTCCTCGACCCACCCACGGACCTCAAGTTCAAAGG
CCCCTTCACCGGGTTGCTCACGGCGCATCTTAAACTGCGCAACCCGTCGGCGAGGAAGGTGTGTTTCAAGGTGAAGAGCA
CCAGCCCTCGGCGCTACTGCGTGCGGCCCAACAACGGAGTCATCGACCCGGGTTGCACCGTGACCGTCGCTGCCACGATG
CAACCCTCCTGCTGCGGCCCCAGCAAGGAGGTCAAGCACAAGTTCATGGTGCAGACAGTGTTTGCTCCTCCGGACATTTC
GGATCTGGAAGCCGTGTGGAGGGAGGCACACCCTGGGGAACTAATGGATTCGAAACTGAGGTGTGTGTTTGAACCGCCGA
CAGAAAGTGACAAACTGGAAGAT

Alignment

ORF - retro_mmus_1774 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.21 %
• Parental protein coverage: 56.63 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MASASGAMAKHEQILVLDPPSDLKFKGPFTDVVTTNLKLQNPSDRKVCFKVKTTAPRRYCVRPNSGIIDP
          MAS.S.A.AK..Q.LVLDPP.DLKFKGPFT...T..LKL.NPS.RKVCFKVK.T.PRRYCVRPN.G.IDP
Retrocopy MASTSRAPAKPQQVLVLDPPTDLKFKGPFTGLLTAHLKLRNPSARKVCFKVKSTSPRRYCVRPNNGVIDP

Parental  GSIVTVSVMLQPFDYDPNEKSKHKFMVQTIFAPPNISDMEAVWKEAKPDELMDSKLRCVFEMPNENDKLN
          G..VTV....QP....P....KHKFMVQT.FAPP.ISD.EAVW.EA.P.ELMDSKLRCVFE.P.E.DKL.
Retrocopy GCTVTVAATMQPSCCGPSKEVKHKFMVQTVFAPPDISDLEAVWREAHPGELMDSKLRCVFEPPTESDKLE

Parental  D
          D
Retrocopy D

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	0.02 RPM	94.46 RPM
SRP007412_cerebellum	0.13 RPM	65.13 RPM
SRP007412_heart	0.03 RPM	36.45 RPM
SRP007412_kidney	0.06 RPM	51.94 RPM
SRP007412_liver	0.03 RPM	47.90 RPM
SRP007412_testis	56.30 RPM	59.92 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_1774 was not detected

EST

No EST(s) were mapped for retro_mmus_1774 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_59542	1039 libraries	26 libraries	1 library	2 libraries	4 libraries

The graphical summary, for retro_mmus_1774 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_1774 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1774 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Rattus norvegicus	retro_rnor_266

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000006042	2 retrocopies	retro_cpor_783, retro_cpor_931,
Myotis lucifugus	ENSMLUG00000008965	1 retrocopy	retro_mluc_542,
Monodelphis domestica	ENSMODG00000021442	1 retrocopy	retro_mdom_57,
Mus musculus	ENSMUSG00000024091	1 retrocopy	retro_mmus_1774 ,
Rattus norvegicus	ENSRNOG00000014765	1 retrocopy	retro_rnor_266,