RetrogeneDB ID: retro_mmus_687

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 11:3479386..3479697(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Ndufc2
• Ensembl ID: ENSMUSG00000030647
• Aliases: Ndufc2, 1810004I06Rik, 2010300P09Rik, G1, R75094
• Description: NADH dehydrogenase (ubiquinone) 1, subcomplex unknown, 2 [Source:MGI Symbol;Acc:MGI:1344370]

Sequence

>retro_mmus_687
CCTTAAAATTCCTGCCAGATGAGGCCCGGAGCCTGCCCACATCCAAACTGAATGACCTGTGGCTTCCTGAGCTACTCCAC
CTCCTGGCTGGACAGCATGCTTCAGAGGAGGCCTGTGATAAAAGCAGGTTTGCATCGCCACCTTCTGTGTCTTACTCCCT
TTTTCTTTGCTGAATGTTATTATTTTTTAAATGTCAAGACTATTTGTATGCTGTAAAGGACCATGACATATTTGTGTATA
TAAAATTACATCCAGAAGATTTTCCTGAAAAAGAGAAGACTTACGGTGAAATTCTTGAGGCATTCCATCCA

Alignment

ORF - retro_mmus_687 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.55 %
• Parental protein coverage: 86.67 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  PDEARSLPPPKLNDPRLVYMGLLGYCTGLMDNMLRMRPVMRAGLHRQLLFVTSFVFAG-YFYL-KRQNYL
          P.......P.....P.....G.L.Y.T...D.ML..RPV..AGLHR.LL..T.F.FA..Y..L.K.Q.YL
Retrocopy P*NSCQMRPGACPHPN*MTCGFLSYSTSWLDSMLQRRPVIKAGLHRHLLCLTPFFFAECYYFL<KCQDYL

Parental  YAVKDHDMFGYIKLHPEDFPEKEKKTYAEILEPFHP
          YAVKDHD.F.YIKLHPEDFPEKEK.TY.EILE.FHP
Retrocopy YAVKDHDIFVYIKLHPEDFPEKEK-TYGEILEAFHP

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	0.14 RPM	28.95 RPM
SRP007412_cerebellum	0.00 RPM	30.00 RPM
SRP007412_heart	0.00 RPM	72.60 RPM
SRP007412_kidney	0.02 RPM	55.32 RPM
SRP007412_liver	0.00 RPM	32.31 RPM
SRP007412_testis	0.05 RPM	9.79 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_687 was not detected

EST

No EST(s) were mapped for retro_mmus_687 retrocopy.

TSS

No TSS is located nearby retro_mmus_687 retrocopy 5' end.

Lab

retro_mmus_687 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_687 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Felis catus	ENSFCAG00000029444	1 retrocopy	retro_fcat_337,
Mus musculus	ENSMUSG00000030647	2 retrocopies	retro_mmus_2851, retro_mmus_687 ,
Oryctolagus cuniculus	ENSOCUG00000000958	1 retrocopy	retro_ocun_628,
Tursiops truncatus	ENSTTRG00000007154	1 retrocopy	retro_ttru_1263,