RetrogeneDB ID: retro_mmus_522

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 10:3992370..3992814(+)
• Located in intron of: ENSMUSG00000040675

Retrocopy information

• Ensembl ID: ENSMUSG00000082247
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Rnf4
• Ensembl ID: ENSMUSG00000029110
• Aliases: Rnf4, AU018689, Gtrgeo8
• Description: ring finger protein 4 [Source:MGI Symbol;Acc:MGI:1201691]

Sequence

>retro_mmus_522
ATGAGGACAAGAAATCCTCAAAGAAAGCGGCGTGGTGCAGCCTTAAATTCCAGACAAACCCAGAAGCGAACTCGGGAAAC
AACTTCAACCCCTGAGGTTGCCTTGGAAACAGAACCCATAGAACTTATGGAAACTGTTGGAGATGAAATCGTGGACCTCG
CCTGTAAATCTTTAGAGCCCGTGGTTGTGGACCTGACTCACAATGACTCTGCTGTAATTGTTGAAGAAAGGAGAAATGGG
AGGAGGTTGCGCCAAGACCATGCTGACAGCTGTGTGGTGAGCAGTGATGATGAGGAGCTGTCTAGGGACAAAGACATGTA
CGTGACTACCCATACTCCTCGAAACACCAAGGATGATGGAGCTCCTGGACCCAGGCGCTCAGGTACCCTCAGGTGTCCGA
TCTGCATGGATGGATACTCTGAGATTGTGTAGAATGGGCGTCTC

Alignment

ORF - retro_mmus_522 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.84 %
• Parental protein coverage: 78.35 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSTRNPQRKRRGGTVNSRQTQKRTRETTSTPEVSLETEPIELVETVGDEIVDLTCESLEPVVVDLTHNDS
          M.TRNPQRKRRG...NSRQTQKRTRETTSTPEV.LETEPIEL.ETVGDEIVDL.C.SLEPVVVDLTHNDS
Retrocopy MRTRNPQRKRRGAALNSRQTQKRTRETTSTPEVALETEPIELMETVGDEIVDLACKSLEPVVVDLTHNDS

Parental  VVIVEERRRPRRNGRRLRQDHADSCVVSSDDEELSRDKDVYVTTHTPRSTKDDGATGPRPSGTVSCPICM
          .VIVEERR....NGRRLRQDHADSCVVSSDDEELSRDKD.YVTTHTPR.TKDDGA.GPR.SGT..CPICM
Retrocopy AVIVEERR----NGRRLRQDHADSCVVSSDDEELSRDKDMYVTTHTPRNTKDDGAPGPRRSGTLRCPICM

Parental  DGYSEIVQNGRL
          DGYSEIV.NGRL
Retrocopy DGYSEIV*NGRL

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	70.42 RPM
SRP007412_cerebellum	0.09 RPM	67.30 RPM
SRP007412_heart	0.09 RPM	31.66 RPM
SRP007412_kidney	0.04 RPM	60.73 RPM
SRP007412_liver	0.08 RPM	83.51 RPM
SRP007412_testis	0.32 RPM	166.49 RPM

ChIP-Seq

RNA Polymerase II actvity may be related with retro_mmus_522 in 1 libraries

ENCODE library ID	Target	ChIP-Seq Peak coordinates
ENCFF001YKA	POLR2A	10:3991155..3992403

EST

No EST(s) were mapped for retro_mmus_522 retrocopy.

TSS

No TSS is located nearby retro_mmus_522 retrocopy 5' end.

Lab

retro_mmus_522 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_522 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000014366	1 retrocopy	retro_amel_77,
Canis familiaris	ENSCAFG00000014856	1 retrocopy	retro_cfam_25,
Equus caballus	ENSECAG00000024877	1 retrocopy	retro_ecab_33,
Homo sapiens	ENSG00000063978	1 retrocopy	retro_hsap_319,
Gorilla gorilla	ENSGGOG00000015149	2 retrocopies	retro_ggor_1144, retro_ggor_345,
Loxodonta africana	ENSLAFG00000007382	1 retrocopy	retro_lafr_44,
Microcebus murinus	ENSMICG00000001767	1 retrocopy	retro_mmur_1265,
Mus musculus	ENSMUSG00000029110	1 retrocopy	retro_mmus_522 ,
Nomascus leucogenys	ENSNLEG00000000160	2 retrocopies	retro_nleu_1713, retro_nleu_37,
Oryctolagus cuniculus	ENSOCUG00000004998	2 retrocopies	retro_ocun_1566, retro_ocun_162,
Otolemur garnettii	ENSOGAG00000010776	1 retrocopy	retro_ogar_2121,
Pongo abelii	ENSPPYG00000025865	2 retrocopies	retro_pabe_1240, retro_pabe_36,
Pteropus vampyrus	ENSPVAG00000017017	1 retrocopy	retro_pvam_167,
Ictidomys tridecemlineatus	ENSSTOG00000011101	2 retrocopies	retro_itri_1108, retro_itri_171,
Tarsius syrichta	ENSTSYG00000011244	1 retrocopy	retro_tsyr_1606,