RetrogeneDB ID: retro_mmus_3659

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: X:89440184..89440577(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000082422
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Eif4h
• Ensembl ID: ENSMUSG00000040731
• Aliases: Eif4h, AU018978, D5Ertd355e, E430026L18Rik, Ef4h, Wbscr1, Wscr1, mKIAA0038
• Description: eukaryotic translation initiation factor 4H [Source:MGI Symbol;Acc:MGI:1341822]

Sequence

>retro_mmus_3659
GACAGGTCACTTTGTTTGGCAAAAGGCAGAAAACAAGATAAAGTTAGCTTCGGATTCAGGAGCAGAAGGGATAACAGAGG
AATGGGTGGCTCTCAAGAATCTAGCGGTGGACCGGATTCCCGGGATGACTTCAAATCTGACTCCATTGATGGATGACTTT
TTAGGGGGTGGTGGGCAGTGCAGTCACCCTGGGGATCGGCGAGCAGACTCTCCAATGGAGAGTCACTTTCAAGATGGTCC
TCCTCTGCTCGGTTCCAACATGGACTTCATAGAACTCACAGAATAGCACAAGAGAGCACAGCTGCAGCTTAAACCTCAGA
CAGTGGCAACACCCCTCAAACAAGTAGCCAGTCCCAACTTAGCCACTTTGGGGGATACAGGTCCAGAGAGGAG

Alignment

ORF - retro_mmus_3659 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.77 %
• Parental protein coverage: 54.03 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  DRSLRVDIAEGRKQDKGGFGFRKGGPDDRGMGGSRESRGGWDSRDDFNSGYRD-DFLGGRGG--SRPGDR
          DRSL....A.GRKQDK..FGFR....D.RGMGGS.ES.GG.DSRDDF.S...D.D...G.GG..S.PGDR
Retrocopy DRSLC--LAKGRKQDKVSFGFRSRR-DNRGMGGSQESSGGPDSRDDFKSDSID>DDFLGGGGQCSHPGDR

Parental  RAGPPMGSRFRDGPPLRGSNMDFREPTEEERAQRPRLQLKPRTVATPLNQVANPNSAI-FGGARPREE
          RA..PM.S.F.DGPPL.GSNMDF.E.TE.....R..LQLKP.TVATPL.QVA.PN.A..FGG.R.REE
Retrocopy RADSPMESHFQDGPPLLGSNMDFIELTE*HK--RAQLQLKPQTVATPLKQVASPNLAT<FGGYRSREE

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	258.44 RPM
SRP007412_cerebellum	0.00 RPM	213.11 RPM
SRP007412_heart	0.00 RPM	116.52 RPM
SRP007412_kidney	0.00 RPM	142.85 RPM
SRP007412_liver	0.00 RPM	114.64 RPM
SRP007412_testis	0.00 RPM	211.31 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_3659 was not detected

EST

No EST(s) were mapped for retro_mmus_3659 retrocopy.

TSS

No TSS is located nearby retro_mmus_3659 retrocopy 5' end.

Lab

retro_mmus_3659 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3659 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000002525	2 retrocopies	retro_chof_1279, retro_chof_1903,
Felis catus	ENSFCAG00000029386	1 retrocopy	retro_fcat_580,
Gorilla gorilla	ENSGGOG00000005284	1 retrocopy	retro_ggor_1598,
Macaca mulatta	ENSMMUG00000006205	2 retrocopies	retro_mmul_2634, retro_mmul_619,
Mus musculus	ENSMUSG00000040731	1 retrocopy	retro_mmus_3659 ,
Mus musculus	ENSMUSG00000058655	1 retrocopy	retro_mmus_3686,
Oryctolagus cuniculus	ENSOCUG00000017685	1 retrocopy	retro_ocun_1475,
Otolemur garnettii	ENSOGAG00000028051	1 retrocopy	retro_ogar_2796,
Pongo abelii	ENSPPYG00000017489	2 retrocopies	retro_pabe_1879, retro_pabe_1988,
Pan troglodytes	ENSPTRG00000019287	1 retrocopy	retro_ptro_1489,
Rattus norvegicus	ENSRNOG00000001454	1 retrocopy	retro_rnor_2924,
Tupaia belangeri	ENSTBEG00000009558	2 retrocopies	retro_tbel_1636, retro_tbel_2470,