RetrogeneDB ID: retro_sscr_1063

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 9:78771688..78772172(-)
• Located in intron of: ENSSSCG00000015310

Retrocopy information

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

Parental gene information

• Parental gene symbol: YKT6
• Ensembl ID: ENSSSCG00000016750
• Aliases: None
• Description: YKT6 v-SNARE homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:16959]

Sequence

>retro_sscr_1063
ATGAAGCCCTACGGCCTCAGCGTCCTTTACAAAGGCGATTCCAAGGCAGTGTTGCTCGAAGCCGCATACGATGTGTCCTC
CTTCATTTCTTCCAGAGGTCCAGTGTTTAGGAATTCATGACATTCACAAGTCAACTGATTGTGGAGAGCTCGGCAGAAGG
CAGCAAAGCTTCTGTCAAAGAACAAGAATATCTGTGCCACGTCTATGTGAGAAACGGCAGTCTTGCGGGAGTGGTCCTTG
CTGACAGTGAACACCCATCCTGGGTGGCTTTTACCTTGCTAGAGAAAGTACTAGACGAATTCTCCAAGCAGGTCGACAGG
ATATTTTGGCCAGTTGGATCTCCTGCTACCATCTAGCACACAGGCCTGGTGGTCACCTCAGTAGATACCAGAACCCCCAA
GAACCTGACACCATGAGTAAAGTGCAGGCTGAACTAGATGAGACCAAAATCATCCTGCACAACACCATGGAGTCTTTGTT
AGAG

Alignment

ORF - retro_sscr_1063 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.98 %
• Parental protein coverage: 81.82 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MKLYSLSVLYKGDPKVVLLKAAYDVSSF-SFFQRSSVQEFMTFTSQLIVERSAKGSRASVKEQEYLCHVY
          MK.Y.LSVLYKGD.K.VLL.AAYDVSSF..FFQRSSV.EFMTFTSQLIVE.SA.GS.ASVKEQEYLCHVY
Retrocopy MKPYGLSVLYKGDSKAVLLEAAYDVSSF<HFFQRSSV*EFMTFTSQLIVESSAEGSKASVKEQEYLCHVY

Parental  VRNDSLAGVVIADSEYPSRVAFTLLEKVLDEFSKQVDRIEWPVGSPATILYTGL-DGHLSRYQNPREADP
          VRN.SLAGVV.ADSE.PS.VAFTLLEKVLDEFSKQVDRI.WPVGSPATI..TGL..GHLSRYQNP.E.D.
Retrocopy VRNGSLAGVVLADSEHPSWVAFTLLEKVLDEFSKQVDRIFWPVGSPATI*HTGL<GGHLSRYQNPQEPDT

Parental  MSKVQAELDETKIILHNTMESLLE
          MSKVQAELDETKIILHNTMESLLE
Retrocopy MSKVQAELDETKIILHNTMESLLE

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
SRP014902_placenta	0.00 RPM	66.10 RPM
SRP014902_testis	0.28 RPM	34.94 RPM
SRP018288_heart	0.05 RPM	31.93 RPM
SRP018288_kidney	0.10 RPM	48.46 RPM
SRP018288_liver	0.00 RPM	26.39 RPM
SRP018288_lung	0.10 RPM	52.64 RPM
SRP018856_adipose	0.00 RPM	57.13 RPM
SRP035408_brain	0.00 RPM	39.92 RPM
SRP035408_liver	0.00 RPM	27.92 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_1063 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_1063 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_1063 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,