RetrogeneDB ID: retro_mmus_3029

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 7:57899962..57900576(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Lias
• Ensembl ID: ENSMUSG00000029199
• Aliases: Lias, 2900022L22Rik, 4933425M12Rik, 7a5ex, C77512, mLip1
• Description: lipoic acid synthetase [Source:MGI Symbol;Acc:MGI:1934604]

Sequence

>retro_mmus_3029
TATTTACATAATGGATCAGACCTTCAAGATTTTGTATTTGGCAATCTATTGGACAAGAGTTCCTGGGATGAATATAAAGG
AAATTTAAAGCTTAGAAAGGAGAAAGGTTAAGACTAAAGATAGTGATACACATGAGCATAAATTACAGTAAACTGAAAAA
TATATTGCAGAATTTGAATCTCCAACCAGTGTGTCAAGAAGTCCAGTGCCTCAACATTGGAGAGTGTTGGAGAGGTGGAG
GATATGCCACAGACACAGCTATGATCATGTTGATGGGAGACACATATACAAAAGTTTGAACATTTTGTTCTGTTAAGACC
GAAAGAAATCCTCCTCCATTGGATGCCAGTGTGCCCTACAATATGTCCAGTGCAACTGCAGAGTGGGATCTGGATTACGT
TGGTCTGACATCTGACGATCGATATGATGTGCCCGACAGGAGAACTGAATGCATTGCCAAGACTGTGTCATGCTTGAAGG
AAAGGAATCCAAGAATCTTCATAGAATGCCTCACCCCTGACTTCTGAGGAAATTGGAGAGCAATTGAAAAGGTCATTCTT
TCAGGATTAGATGTGCGCACACATGCTGTAAATACAGTTCCAGAATTACAGAGG

Alignment

ORF - retro_mmus_3029 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.57 %
• Parental protein coverage: 56.03 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  FLHNGPDLQDFVSGDLADKSTWDEYKGNLKRQK-GERLRLPPWLKTKIPMGKNYNKLKNTLRNLSLHTVC
          .LHNG.DLQDFV.G.L.DKS.WDEYKGNLK..K.GERLR....LK..I.M..NY.KLKN.L.NL.L..VC
Retrocopy YLHNGSDLQDFVFGNLLDKSSWDEYKGNLKLRK<GERLR----LKIVIHMSINYSKLKNILQNLNLQPVC

Parental  EEARCPNIGECWGGGEYATATATIMLMGDTCTRGCRFCSVKTARNPPPLDANEPDNTAKAIAEWGLDYVV
          .E..C.NIGECW.GG.YAT.TA.IMLMGDT.T....FCSVKT.RNPPPLDA..P.N...A.AEW.LDYV.
Retrocopy QEVQCLNIGECWRGGGYATDTAMIMLMGDTYTKV*TFCSVKTERNPPPLDASVPYNMSSATAEWDLDYVG

Parental  LTSVDRDDVADGGAEHIAKTVSCLKERNPKILVECLTPDFRGDLRAVEKVALSGLDVYAHNVETVPELQR
          LTS.DR.DV.D...E.IAKTVSCLKERNP.I..ECLTPDF.G..RA.EKV.LSGLDV..H.V.TVPELQR
Retrocopy LTSDDRYDVPDRRTECIAKTVSCLKERNPRIFIECLTPDF*GNWRAIEKVILSGLDVRTHAVNTVPELQR

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	23.95 RPM
SRP007412_cerebellum	0.04 RPM	24.66 RPM
SRP007412_heart	0.00 RPM	31.85 RPM
SRP007412_kidney	0.00 RPM	35.09 RPM
SRP007412_liver	0.00 RPM	22.80 RPM
SRP007412_testis	0.00 RPM	47.52 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_3029 was not detected

EST

No EST(s) were mapped for retro_mmus_3029 retrocopy.

TSS

No TSS is located nearby retro_mmus_3029 retrocopy 5' end.

Lab

retro_mmus_3029 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3029 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000012946	2 retrocopies	retro_chof_1942, retro_chof_2555,
Dasypus novemcinctus	ENSDNOG00000007417	1 retrocopy	retro_dnov_266,
Myotis lucifugus	ENSMLUG00000004602	2 retrocopies	retro_mluc_1985, retro_mluc_347,
Mus musculus	ENSMUSG00000029199	1 retrocopy	retro_mmus_3029 ,
Tursiops truncatus	ENSTTRG00000014293	1 retrocopy	retro_ttru_1371,