RetrogeneDB ID: retro_mmus_513

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 1:169595818..169596140(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Rnf125
• Ensembl ID: ENSMUSG00000033107
• Aliases: Rnf125, 4930553F04Rik
• Description: ring finger protein 125 [Source:MGI Symbol;Acc:MGI:1914914]

Sequence

>retro_mmus_513
ATGGAATGGGATCATCAGAACTGTGCTAAGTCCAGGGCTCTGGTTTGCCTCCGTGACACAAAGGTACACATAAGAACTTG
TGAGAAGTAAATGGACAAGTTTGGCCCATTGCAAGAACTTGGTGAAACAACAAGATGTGTATATCCATTTTATCAAAAAG
ACCTGGGTGAAGACAGCTTGCTGGATGGTTGTATTATCCACTACAGATCAGAAAGGCGGTTTCTTGTTCTGTTAGCTTTA
CCACTTAACACCTTACAAAAGTCTAAGTACCTTCAATGGCAGTTTCATTGGACATTTGCAAGTCAGTCACACATTGTTTT
TT

Alignment

ORF - retro_mmus_513 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.22 %
• Parental protein coverage: 77.14 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MKSEYQNCAECGTLVCLSDMRAHIRTCEKYIDKYGPLLELGDTTARCVCPFCQRELDEDCLLDHCIIHHR
          M....QNCA....LVCL.D...HIRTCEK..DK.GPL.ELG.TT.RCV.PF.Q..L.ED.LLD.CIIH.R
Retrocopy MEWDHQNCAKSRALVCLRDTKVHIRTCEK*MDKFGPLQELGETT-RCVYPFYQKDLGEDSLLDGCIIHYR

Parental  SERR-PVFCPLCHSRPDESPSTFNGSLIRHLQVSHTLFY
          SERR...FC.L.H..P..S.STFNGS.I.HLQVSHTLF.
Retrocopy SERR>FLFC*LYHLTPYKSLSTFNGSFIGHLQVSHTLFF

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	0.51 RPM
SRP007412_cerebellum	0.00 RPM	0.87 RPM
SRP007412_heart	0.00 RPM	2.55 RPM
SRP007412_kidney	0.00 RPM	1.04 RPM
SRP007412_liver	0.00 RPM	19.94 RPM
SRP007412_testis	0.00 RPM	13.45 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_513 was not detected

EST

No EST(s) were mapped for retro_mmus_513 retrocopy.

TSS

No TSS is located nearby retro_mmus_513 retrocopy 5' end.

Lab

retro_mmus_513 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_513 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Mus musculus	ENSMUSG00000024317	2 retrocopies	retro_mmus_3726, retro_mmus_494,
Mus musculus	ENSMUSG00000033107	2 retrocopies	retro_mmus_3069, retro_mmus_513 ,