RetrogeneDB ID: retro_mmus_307

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 1:34985655..34985891(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Pfdn2
• Ensembl ID: ENSMUSG00000006412
• Aliases: None
• Description: prefoldin 2 [Source:MGI Symbol;Acc:MGI:1276111]

Sequence

>retro_mmus_307
GACTGAAGTGGTCCTGTGGGTAGGGCGGCAGGAGTGGCACTGGGAAGGGGGCAGGGTTGGCCGAATTGGTCAATGCTGGC
TTTAATCTCCTTCAGCAAGGACAGAGGGGCTTGGCATCCAAAGCAGCTGAGCTGGCGATGGAATTGAATGAACACAGCCT
AGTGATCAATACACTGAAGGAAGTGGATGAGATCCGCAAGAGCTACCGCATGGTTGGAGGTGTGCTGTCAGAGCGT

Alignment

ORF - retro_mmus_307 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.25 %
• Parental protein coverage: 51.3 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  DSSGRVGKSGG-SGAGKGAVSAEQVIAGFNRLRQEQRGLASKAAELEMELNEHSLVIDTLKEVDETRKCY
          D.SG.VG...G.SG.GKGA..AE.V.AGFN.L.Q.QRGLASKAAEL.MELNEHSLVI.TLKEVDE.RK.Y
Retrocopy D*SGPVGRAAG<SGTGKGAGLAELVNAGFNLLQQGQRGLASKAAELAMELNEHSLVINTLKEVDEIRKSY

Parental  RMVGGVLVER
          RMVGGVL.ER
Retrocopy RMVGGVLSER

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	58.83 RPM
SRP007412_cerebellum	0.00 RPM	88.23 RPM
SRP007412_heart	0.00 RPM	42.40 RPM
SRP007412_kidney	0.00 RPM	63.33 RPM
SRP007412_liver	0.00 RPM	46.42 RPM
SRP007412_testis	0.00 RPM	34.30 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_307 was not detected

EST

No EST(s) were mapped for retro_mmus_307 retrocopy.

TSS

No TSS is located nearby retro_mmus_307 retrocopy 5' end.

Lab

retro_mmus_307 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_307 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Dipodomys ordii	ENSDORG00000004588	1 retrocopy	retro_dord_362,
Myotis lucifugus	ENSMLUG00000004526	1 retrocopy	retro_mluc_1293,
Mus musculus	ENSMUSG00000006412	1 retrocopy	retro_mmus_307 ,
Tupaia belangeri	ENSTBEG00000015982	1 retrocopy	retro_tbel_2807,
Tursiops truncatus	ENSTTRG00000009181	1 retrocopy	retro_ttru_1756,