RetrogeneDB ID: retro_mmus_650

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 10:66740285..66740614(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Cbx5
• Ensembl ID: ENSMUSG00000009575
• Aliases: Cbx5, 2610029O15Rik, C75991, HP1, Hp1a, Hp1alpha
• Description: chromobox 5 [Source:MGI Symbol;Acc:MGI:109372]

Sequence

>retro_mmus_650
CCCAGGGAGAAGTCAGAAGGTAACAGGAGGAAATCCAATTTCTTGAACAATGCTGATGATATTAAGTGATGAAGAGAAGG
CTGTGAGGAGCTATAGTACTGCTCAGGGCTTTGAGGGCTTTTAGAACTTAGAAAGGATCGCTGGGGTAACAGATTCCCAT
GGTGACTTGAGTTCCTAACAAAACGGAATGGCACATGGGAGGCAGAGCTGGTTCTTGTAAAAGATGCTAATGTGAAATGT
CCACAAACTATGGGAGCATTTCTGAAGGGAGATAGCCATGGCACACGTATCCAAAGAATGGGGAAGACAAAGAAAAAGAT
AGTGCCAAG

Alignment

ORF - retro_mmus_650 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.52 %
• Parental protein coverage: 57.59 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  PREKSEGNKRKSSFSNSADDIK-SKKKREQSNDIARGFERGLEPEKIIGATDSCGDLM-FLMKWKDTDEA
          PREKSEGN.RKS.F.N.ADDIK....K...S...A.GFE.....E.I.G.TDS.GDL..FL.K...T.EA
Retrocopy PREKSEGNRRKSNFLNNADDIK>DEEKAVRSYSTAQGFEGF*NLERIAGVTDSHGDLS<FLTKRNGTWEA

Parental  DLVLAKEANVKCPQIVIAFY-EERLTWHAYPEDAENKEKESAK
          .LVL.K.ANVKCPQ...AF..E.R..WH.YP...E.KEK.SAK
Retrocopy ELVLVKDANVKCPQTMGAFL<EGR*PWHTYPKNGEDKEKDSAK

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	249.24 RPM
SRP007412_cerebellum	0.00 RPM	183.98 RPM
SRP007412_heart	0.03 RPM	98.87 RPM
SRP007412_kidney	0.04 RPM	135.25 RPM
SRP007412_liver	0.00 RPM	46.15 RPM
SRP007412_testis	0.55 RPM	84.85 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_650 was not detected

EST

No EST(s) were mapped for retro_mmus_650 retrocopy.

TSS

No TSS is located nearby retro_mmus_650 retrocopy 5' end.

Lab

retro_mmus_650 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_650 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Rattus norvegicus	retro_rnor_1727

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Echinops telfairi	ENSETEG00000001220	1 retrocopy	retro_etel_678,
Mus musculus	ENSMUSG00000009575	1 retrocopy	retro_mmus_650 ,
Mus musculus	ENSMUSG00000018666	1 retrocopy	retro_mmus_3108,
Mus musculus	ENSMUSG00000029836	1 retrocopy	retro_mmus_77,
Rattus norvegicus	ENSRNOG00000036841	1 retrocopy	retro_rnor_1727,