RetrogeneDB ID: retro_mmus_492

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 1:139790077..139790304(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Cfhr3
• Ensembl ID: ENSMUSG00000090623
• Aliases: None
• Description: complement factor H-related 3 [Source:MGI Symbol;Acc:MGI:3647418]

Sequence

>retro_mmus_492
CAAGATGGACAATTACTTAATGAGACTTTATTTTGCTCCTCAGATAATTTCTGTGGGAATCCACACATGTGGCAAATGCT
ATTATAGTAACAAGGCCCCTGGCTAAATATCCATCTGGTGACAGATTACATTATGAATGTAATAAACATTTTGAACTATT
TGGGGATGTAGAAGACGTGTGTCAAAATGGGATTTGGACAGAACAACTGAAATGCAAACGGAGAACA

Alignment

ORF - retro_mmus_492 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 55.84 %
• Parental protein coverage: 55.15 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  QNGWSLQPSCIIITD-YCVNP-PHVPNATIVTMPMAKYPSGEKIHYECHKPFELFGKVEVMCQNGMWTEP
          Q.G..L........D..C.NP..HV.NA.IVT.P.AKYPSG...HYEC.K.FELFG.VE..CQNG.WTE.
Retrocopy QDGQLLNETLFCSSDNFCGNP<THVANAIIVTRPLAKYPSGDRLHYECNKHFELFGDVEDVCQNGIWTEQ

Parental  PRCKDPT
          ..CK..T
Retrocopy LKCKRRT

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	0.00 RPM
SRP007412_cerebellum	0.00 RPM	0.00 RPM
SRP007412_heart	0.00 RPM	0.00 RPM
SRP007412_kidney	0.00 RPM	0.00 RPM
SRP007412_liver	0.03 RPM	3.09 RPM
SRP007412_testis	0.00 RPM	2.38 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_492 was not detected

EST

No EST(s) were mapped for retro_mmus_492 retrocopy.

TSS

No TSS is located nearby retro_mmus_492 retrocopy 5' end.

Lab

retro_mmus_492 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_492 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
Mus musculus	ENSMUSG00000016481	1 retrocopy	retro_mmus_3214,
Mus musculus	ENSMUSG00000090623	1 retrocopy	retro_mmus_492 ,