RetrogeneDB ID: retro_mmus_1038

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 13:76696672..76697907(+)
• Located in intron of: ENSMUSG00000021596

Retrocopy information

• Ensembl ID: ENSMUSG00000090027
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Vps4a
• Ensembl ID: ENSMUSG00000031913
• Aliases: Vps4a, 4930589C15Rik, AI325971, AW553189
• Description: vacuolar protein sorting 4a (yeast) [Source:MGI Symbol;Acc:MGI:1890520]

Sequence

>retro_mmus_1038
GAGGACAAAGCCAAGAACTATGTGCATGCTGTGGCGTATTTCCTCTACGCAATCAAATATGAAGCACATAGTTACAAGGC
CAAGGAGAGCATTCAAGCAAAGTGCATGTAGTACCTAGAGAGAGCAGAGAAGCTGAAGGATTATTTACGAAACAAAGAGA
AATATGGTAAGAAGCCAGTCGAAGAGAATCAGAGTGAAAGCAAGGGCAGTGACAGTGACAGAAAAAGGGATAATCCAGAG
AAAAAGAAATTACAAGAACAATTGATGGGTGCTGTTGTGATGGAGAAGCCTAACACAAGATGGAATGATGTAGCTGGGCT
GGATGGGGCTAAAGAGGTTCTCTTTAAAACCTGTGATTTTGCCAATTAAATTCCCACACTTCTTCACAGGCAAGCACACT
CTTTGGTGAGATATACTGCTGTTTGGGTCCCCAGGCATAGGCAAGTCCTACCTGGCAAAAGCCATGGCAACAGAAGGCAA
CAATTCCACCTTCTTCTCTATGTCCTCCTTGAATCTGATGTATAAGTGGTTGGGGAAAAGCAAGAAGCTAGTCAAGAACC
TGCTTGAGCTGGCCAGGCAGAATAAGTCTTCCATCATCTTCATCGATAAGGTGGATTCCCTCTGCAGGTCATGGAATGAA
AATGAGAGTGAGACCACCTGTAGGATCAAAATAGAGTTCTTGGTCCAGATGCAAGGAGTGAGGCATCATAATGATGGGAC
TCTTGTTCTTGGTGCCACAAACATCCCTTGGGTATTGGATTCAGCCATCAGGAGGAGGTTTGAAAAGCGAATTTATATCC
CATTGCCAGAGGAAATGGCCTGTGCCCACATGTTTCCATTATATCTGGGAAGCACATCCCACAACCTCACAGATGCTAAC
ATTCATGAGCTAGCCCACAAGACAGAAGGCTACTCAGGAGCAGATATCAGCATCATTGTGAGGGACTCCCTCATGTAGCC
AGTCAGAAAAGTACAGTCAACAACACACTTCAAGAAGGTTTGTGGCCCTTCTCGAACCAATCCTAGTGTTATGATTGATG
ATCTTCTGACCCCATGTTCTCCAGGAGATCCAGGGGCCATAGAGATGACTGGATGGATGTCTCTGGTGATAAACTCTTAG
AGCCTGGGTTTGCATGTCGGACATGATCCAGTCTTTGGCCACTACCCGGCCTACAGTGAATGCAGACAACCTCCTGAATG
TAAAGAAATTCTCTGAGGACTTTGGACAGAAGAGT

Alignment

ORF - retro_mmus_1038 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.89 %
• Parental protein coverage: 94.28 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  EEALRLYQHAVEYFLHAIKYEAHSDKAKESIRAKCMQYLDRAEKLKDYLRNKEKHGKKPVKENQSEGKGS
          E.....Y.HAV.YFL.AIKYEAHS.KAKESI.AKCM.YL.RAEKLKDYLRNKEK.GKKPV.ENQSE.KGS
Retrocopy EDKAKNYVHAVAYFLYAIKYEAHSYKAKESIQAKCM*YLERAEKLKDYLRNKEKYGKKPVEENQSESKGS

Parental  DSDSEGDNPEKKKLQEQLMGAVVMEKPNIRWNDVAGLEGAKEALKEA-VILPIKFPHLFTGKRTPWRGIL
          DSD...DNPEKKKLQEQLMGAVVMEKPN.RWNDVAGL.GAKE.L....VILPIKFPH.FTGK.T.W..IL
Retrocopy DSDRKRDNPEKKKLQEQLMGAVVMEKPNTRWNDVAGLDGAKEVLFKT>VILPIKFPHFFTGKHTLW*DIL

Parental  LFGPPGTGKSYLAKAVATEANNSTFFSVSSSDLMSKWLGESEKLVKNLFELARQHKPSIIFIDEVDSLCG
          LFG.PG.GKSYLAKA.ATE.NNSTFFS.SS..LM.KWLG.S.KLVKNL.ELARQ.K.SIIFID.VDSLC.
Retrocopy LFGSPGIGKSYLAKAMATEGNNSTFFSMSSLNLMYKWLGKSKKLVKNLLELARQNKSSIIFIDKVDSLCR

Parental  SRNENESEAARRIKTEFLVQMQGVGNNNDGTLVLGATNIPWVLDSAIRRRFEKRIYIPLPEEAARAQMFR
          S.NENESE...RIK.EFLVQMQGV...NDGTLVLGATNIPWVLDSAIRRRFEKRIYIPLPEE.A.A.MF.
Retrocopy SWNENESETTCRIKIEFLVQMQGVRHHNDGTLVLGATNIPWVLDSAIRRRFEKRIYIPLPEEMACAHMFP

Parental  LHLGSTPHNLTDANIHELARKTEGYSGADISIIVRDSLMQPVRKVQSATHFKKVCGPSRTNPSVMIDDLL
          L.LGST.HNLTDANIHELA.KTEGYSGADISIIVRDSLM.PVRKVQS.THFKKVCGPSRTNPSVMIDDLL
Retrocopy LYLGSTSHNLTDANIHELAHKTEGYSGADISIIVRDSLM*PVRKVQSTTHFKKVCGPSRTNPSVMIDDLL

Parental  TPCSPGDPGAIEMT-WMDVPGDKLLEP-VVCMSDMLRSLATTRPTVNADDLLKVKKFSEDFGQES
          TPCSPGDPGAIEMT.WMDV.GDKLLEP..VCMSDM..SLATTRPTVNAD.LL.VKKFSEDFGQ.S
Retrocopy TPCSPGDPGAIEMT<WMDVSGDKLLEP<WVCMSDMIQSLATTRPTVNADNLLNVKKFSEDFGQKS

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	0.09 RPM	81.98 RPM
SRP007412_cerebellum	0.04 RPM	94.31 RPM
SRP007412_heart	0.00 RPM	59.93 RPM
SRP007412_kidney	0.00 RPM	61.98 RPM
SRP007412_liver	0.08 RPM	25.89 RPM
SRP007412_testis	0.09 RPM	181.35 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_1038 was not detected

EST

No EST(s) were mapped for retro_mmus_1038 retrocopy.

TSS

No TSS is located nearby retro_mmus_1038 retrocopy 5' end.

Lab

retro_mmus_1038 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1038 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 6 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Macropus eugenii	ENSMEUG00000007309	1 retrocopy	retro_meug_1360,
Myotis lucifugus	ENSMLUG00000006550	2 retrocopies	retro_mluc_2432, retro_mluc_2513,
Mus musculus	ENSMUSG00000009907	1 retrocopy	retro_mmus_1250,
Mus musculus	ENSMUSG00000031913	1 retrocopy	retro_mmus_1038 ,
Otolemur garnettii	ENSOGAG00000016975	1 retrocopy	retro_ogar_391,
Tarsius syrichta	ENSTSYG00000012535	1 retrocopy	retro_tsyr_1246,