RetrogeneDB ID: retro_mmus_2296

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 3:121250355..121250737(-)
• Located in intron of: ENSMUSG00000028132

Retrocopy information

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

Parental gene information

• Parental gene symbol: Wibg
• Ensembl ID: ENSMUSG00000064030
• Aliases: Wibg, A030010B05Rik, Pym
• Description: within bgcn homolog (Drosophila) [Source:MGI Symbol;Acc:MGI:1925678]

Sequence

>retro_mmus_2296
ATGGAAACCCCCAGCACTCCTGAAGCCACCGGGACAGGCAAATACATTGTCTCAACACAGAGACCTGATGGGACTTGGTG
CAAGCAGCGGAGGGTCAAAGAAGGATACGTGCCCCAAGAGGAGGTCCCAGTCTATGAAAACAAGTATGTGAAGTTTTTCA
AGAGTAAACCAGAACTTCCCCCAGGGCTGAGCCCTGAGGCCACCACACCGGTCCCATCCAGACCTGAAGGTGGTGAAGCA
GGCCTCTCCAAGACAGCCAAATGCAACCTGAAGCAGAAGGAGAAGAGGAGGGAGGCAGCAGCAAGAGAAAGACACAGAGG
CCTTGAGCAGGACTCTTGATGAGGTGTCTCTGGGAGACAGCCCAGGCGCCCTACGCTCTCCA

Alignment

ORF - retro_mmus_2296 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.85 %
• Parental protein coverage: 64.04 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  METASTPEATGTGKYIASTQRPDGTWRKQRRVKEGYVPQEEVPVYENKYVKFFKSKPELPPGLSPEATTP
          MET.STPEATGTGKYI.STQRPDGTW.KQRRVKEGYVPQEEVPVYENKYVKFFKSKPELPPGLSPEATTP
Retrocopy METPSTPEATGTGKYIVSTQRPDGTWCKQRRVKEGYVPQEEVPVYENKYVKFFKSKPELPPGLSPEATTP

Parental  VTPSRPEGGETGLSKTAKRNLKRKEKRRQ-QQ-EKEAEALSRTLDKVSLGDTAQIPSALQGP
          V.PSRPEGGE.GLSKTAK.NLK.KEKRR..QQ.EK..EALSRTLD.VSLGD....P.AL..P
Retrocopy V-PSRPEGGEAGLSKTAKCNLKQKEKRRE>QQQEKDTEALSRTLDEVSLGDS---PGALRSP

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	0.05 RPM	9.46 RPM
SRP007412_cerebellum	0.13 RPM	9.42 RPM
SRP007412_heart	0.03 RPM	5.48 RPM
SRP007412_kidney	0.04 RPM	7.74 RPM
SRP007412_liver	0.14 RPM	8.71 RPM
SRP007412_testis	0.37 RPM	16.01 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_2296 was not detected

EST

No EST(s) were mapped for retro_mmus_2296 retrocopy.

TSS

No TSS is located nearby retro_mmus_2296 retrocopy 5' end.

Lab

retro_mmus_2296 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2296 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Echinops telfairi	ENSETEG00000004461	1 retrocopy	retro_etel_1561,
Mus musculus	ENSMUSG00000064030	1 retrocopy	retro_mmus_2296 ,