RetrogeneDB ID: retro_mmus_3069

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 7:102647632..102648052(-)
• 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_3069
ATGAAGTCAGAATACCAGAACTGTGCTGAGTGCAGGACTCTGGTTTGCCTCAGTGACATGAGGGCGCACATAAGGACCTG
TGAGAAGTACATCGATAAATATGGCCCGCTGCAAGAACTTGGCGACACCACAGCAAGATGTGTATGTCCATTTTGTCAGC
GGGAACTGGATGAAGACTGCTTGCTGGATCATTGCATTATCCACCACAGATCAGAAAGGAGGCCCGTGTTCTGTCCGCTT
TGCCATTCACGACCTGATGTAAGCCCAAGTACCTTCAATGGCAGTTTAATTAGACATTTGCAAGTCAGTCACACTTTGTT
TTATGATGATTTCATAGATTTTGATATAATTGAGTAAGCCATTATTCGCAGAGTGCTAGACCGCTCACTTCTTGAATATG
TGAATCAGTCAAACACCACA

Alignment

ORF - retro_mmus_3069 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.14 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MKSEYQNCAECGTLVCLSDMRAHIRTCEKYIDKYGPLLELGDTTARCVCPFCQRELDEDCLLDHCIIHHR
          MKSEYQNCAEC.TLVCLSDMRAHIRTCEKYIDKYGPL.ELGDTTARCVCPFCQRELDEDCLLDHCIIHHR
Retrocopy MKSEYQNCAECRTLVCLSDMRAHIRTCEKYIDKYGPLQELGDTTARCVCPFCQRELDEDCLLDHCIIHHR

Parental  SERRPVFCPLCHSRPDESPSTFNGSLIRHLQVSHTLFYDDFIDFDIIEEAIIRRVLDRSLLEYVNQSNTT
          SERRPVFCPLCHSRPD.SPSTFNGSLIRHLQVSHTLFYDDFIDFDIIE.AIIRRVLDRSLLEYVNQSNTT
Retrocopy SERRPVFCPLCHSRPDVSPSTFNGSLIRHLQVSHTLFYDDFIDFDIIE*AIIRRVLDRSLLEYVNQSNTT

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	0.02 RPM	0.51 RPM
SRP007412_cerebellum	0.04 RPM	0.87 RPM
SRP007412_heart	0.00 RPM	2.55 RPM
SRP007412_kidney	0.08 RPM	1.04 RPM
SRP007412_liver	0.49 RPM	19.94 RPM
SRP007412_testis	1.51 RPM	13.45 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_3069 was not detected

EST

No EST(s) were mapped for retro_mmus_3069 retrocopy.

TSS

No TSS is located nearby retro_mmus_3069 retrocopy 5' end.

Lab

retro_mmus_3069 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3069 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,