RetrogeneDB ID: retro_mmus_407

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 1:5319870..5320333(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: Psma7
• Ensembl ID: ENSMUSG00000027566
• Aliases: Psma7, C6-I
• Description: proteasome (prosome, macropain) subunit, alpha type 7 [Source:MGI Symbol;Acc:MGI:1347070]

Sequence

>retro_mmus_407
ATCATTATCTTCTGGCCCTATGTCTACCTCTTCCAACTAGAGCATGTGCCGGGGTGATCAAGAAGGGTTGGTTTTTGAAG
AAGGTACAGTGTTGTTCTTGGTCTGGAAAACAATCAGTGACCAAGCTACAACATGAAAGAACAGTGCATAAGATCTGTAC
TTTGGGTGACAGTGTCTGTGTGGCCTATGCAGGCCATACTGCTGATGCAAGAATAGTTATCAATAGAGCCTTGGTGAGTG
CCAGAGCCACCAGCTGACTATGGAAAATCCAGTCTCCATGGAGTACAACACCTGCTAAATTGATAGTTTGAATCAGTGCT
ATACACAGAGCAATGAGTTATTGCCATTTGGCATCTTTGCTCTCATTGTGACTTTTTACTATGATGGCATCCCCAGACTC
TATAATACTGACCCCTTAGACACATACCATACCTAAAAAACCAATGCCACAGGCTAGGGTTCC

Alignment

ORF - retro_mmus_407 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.63 %
• Parental protein coverage: 64.11 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  ITVFSPDGHLFQVEYAQEAVKKGSTAVGVRGKDIVVLGVE-KKSVAKLQDERTVRKICALDDNVCMAFAG
          I..F.P...LFQ.....E.V...S..VG......VVLG.E.K.SV.KLQ.ERTV.KIC.L.D.VC.A.AG
Retrocopy IIIFWPYVYLFQL----EHVPG*SRRVGF*RRYSVVLGLE<KQSVTKLQHERTVHKICTLGDSVCVAYAG

Parental  LTADARIVINRARV-ECQSHRLTVEDPVTVEYITRYIASLKQRYTQSNGRRPFGISALIVGFDFDGTPRL
          .TADARIVINRA.V.ECQSH.LT.E.PV..EY.T..I.SL.Q.YTQSN...PFGI.ALIV.F..DG.PRL
Retrocopy HTADARIVINRALV<ECQSHQLTMENPVSMEYNTC*IDSLNQCYTQSNELLPFGIFALIVTFYYDGIPRL

Parental  YQTDPSGTYHAWKANAIGRGA
          Y.TDP..TYH..K.NA.G.G.
Retrocopy YNTDPLDTYHT*KTNATG*GS

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	52.43 RPM
SRP007412_cerebellum	0.00 RPM	64.31 RPM
SRP007412_heart	0.00 RPM	62.63 RPM
SRP007412_kidney	0.00 RPM	77.92 RPM
SRP007412_liver	0.00 RPM	76.55 RPM
SRP007412_testis	0.00 RPM	18.48 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_407 was not detected

EST

No EST(s) were mapped for retro_mmus_407 retrocopy.

TSS

No TSS is located nearby retro_mmus_407 retrocopy 5' end.

Lab

retro_mmus_407 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_407 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000014419	1 retrocopy	retro_cjac_426,
Felis catus	ENSFCAG00000003249	1 retrocopy	retro_fcat_1621,
Mus musculus	ENSMUSG00000027566	1 retrocopy	retro_mmus_407 ,
Rattus norvegicus	ENSRNOG00000008630	1 retrocopy	retro_rnor_2693,
Ictidomys tridecemlineatus	ENSSTOG00000012489	1 retrocopy	retro_itri_279,
Tupaia belangeri	ENSTBEG00000012281	2 retrocopies	retro_tbel_1048, retro_tbel_2392,
Drosophila melanogaster	FBgn0004066	1 retrocopy	retro_dmel_63,