RetrogeneDB ID: retro_mmus_825

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 11:92792876..92793279(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000081141
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Ykt6
• Ensembl ID: ENSMUSG00000002741
• Aliases: Ykt6, 0610042I15Rik, 1810013M05Rik, AW105923
• Description: YKT6 homolog (S. Cerevisiae) [Source:MGI Symbol;Acc:MGI:1927550]

Sequence

>retro_mmus_825
ATGAAGCTGTACAGCCTCAGTGTCCTCTACAAAGGTGAACCAAAAAGTGGTGCTGTTTAAAGCCATGTATGAAGTATCAT
CCTTCAGTTTCTTCCAGAGGTCCAATGTTCAGGAATTCATGACCTTTGCAAGTCAACTGATTGTAGAATGTTCAGAGAAA
GGCAGCAGATCTTCTGTCAGAGAACAAGTGTGCCTTTGCCATGTCTACGTCCAGAGCGACAGTCTGGCAGGTATGGTCAC
TGCTAACAGCGAATATCCTTTCAGAGTGGCCTTCACCTTGCTAGAGAAGGTACTAGGTGAATTCTCCAAGCAGGTCGATC
GAATGGACTGGCCAGTTGGATCTCCTGCTACAATCGGGTACATAGCCCTGTATGGTCTCCTTAGTAGATACCAGAACCCG
AGA

Alignment

ORF - retro_mmus_825 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.26 %
• Parental protein coverage: 67.68 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MKLYSLSVLYKGDPKA-VLLKAAYDVSSFSFFQRSSVQEFMTFTSQLIVERSGKGSRASVKEQEYLCHVY
          MKLYSLSVLYKG.PK..VL.KA.Y.VSSFSFFQRS.VQEFMTF.SQLIVE.S.KGSR.SV.EQ..LCHVY
Retrocopy MKLYSLSVLYKGEPKS>VLFKAMYEVSSFSFFQRSNVQEFMTFASQLIVECSEKGSRSSVREQVCLCHVY

Parental  VRSDSLAGVVIADSEYPSRVAFTLLEKVLDEFSKQVDRIDWPVGSPATIQYTGLDDHLSKYQNPR
          V.SDSLAG.V.A.SEYP.RVAFTLLEKVL.EFSKQVDR.DWPVGSPATI.Y..L...LS.YQNPR
Retrocopy VQSDSLAGMVTANSEYPFRVAFTLLEKVLGEFSKQVDRMDWPVGSPATIGYIALYGLLSRYQNPR

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	70.37 RPM
SRP007412_cerebellum	0.00 RPM	56.84 RPM
SRP007412_heart	0.00 RPM	73.37 RPM
SRP007412_kidney	0.02 RPM	83.64 RPM
SRP007412_liver	0.00 RPM	69.09 RPM
SRP007412_testis	0.00 RPM	52.19 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_825 was not detected

EST

No EST(s) were mapped for retro_mmus_825 retrocopy.

TSS

No TSS is located nearby retro_mmus_825 retrocopy 5' end.

Lab

retro_mmus_825 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_825 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 20 parental genes, and 23 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000017618	1 retrocopy	retro_amel_967,
Bos taurus	ENSBTAG00000000274	1 retrocopy	retro_btau_601,
Canis familiaris	ENSCAFG00000002903	1 retrocopy	retro_cfam_740,
Choloepus hoffmanni	ENSCHOG00000011207	1 retrocopy	retro_chof_657,
Callithrix jacchus	ENSCJAG00000008053	2 retrocopies	retro_cjac_2394, retro_cjac_2492,
Dasypus novemcinctus	ENSDNOG00000015173	1 retrocopy	retro_dnov_1364,
Dipodomys ordii	ENSDORG00000016393	1 retrocopy	retro_dord_621,
Erinaceus europaeus	ENSEEUG00000001247	1 retrocopy	retro_eeur_267,
Felis catus	ENSFCAG00000014362	1 retrocopy	retro_fcat_1327,
Homo sapiens	ENSG00000106636	1 retrocopy	retro_hsap_3687,
Gorilla gorilla	ENSGGOG00000027036	1 retrocopy	retro_ggor_2493,
Macropus eugenii	ENSMEUG00000014769	1 retrocopy	retro_meug_2068,
Mustela putorius furo	ENSMPUG00000018200	2 retrocopies	retro_mputfur_141, retro_mputfur_165,
Mus musculus	ENSMUSG00000002741	1 retrocopy	retro_mmus_825 ,
Nomascus leucogenys	ENSNLEG00000003689	1 retrocopy	retro_nleu_2275,
Oryctolagus cuniculus	ENSOCUG00000002981	1 retrocopy	retro_ocun_15,
Pongo abelii	ENSPPYG00000017595	1 retrocopy	retro_pabe_3022,
Pan troglodytes	ENSPTRG00000019141	1 retrocopy	retro_ptro_2500,
Sus scrofa	ENSSSCG00000016750	1 retrocopy	retro_sscr_1063,
Tursiops truncatus	ENSTTRG00000006052	2 retrocopies	retro_ttru_1320, retro_ttru_417,