RetrogeneDB ID: retro_sscr_590

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 18:8053670..8054058(+)
• Located in intron of: ENSSSCG00000016487

Retrocopy information

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

Parental gene information

• Parental gene symbol: TPGS2
• Ensembl ID: ENSSSCG00000026953
• Aliases: None
• Description: tubulin polyglutamylase complex subunit 2 [Source:HGNC Symbol;Acc:24561]

Sequence

>retro_sscr_590
ATGATTTCTTCATGGGAACAAAAAAAGTAACTGCCTGCTGCGTGCAAATCTACAGAACTTTTACCTGATAACAGATGGCT
TCCATATGACATGGAGAGTGAAGCTGGTTGCACACACCATTCCTTTGAGCTGCATGGCAATTAACAGCATCTCAAAACTG
ACTCAACTCAGCCAGCCTTCCATGCACTCAACTCCTAATGCACCAACTCTGGCAGATCTGGAGGACGATACCCAAGAAGC
CAGTGAGAACCAGCCAGAGAAGCCTCGCTTTAATTCATGCAGTGTGATATTTGAGCTGGATCCTTGCAAAGGGAATGGGG
AGGCTTTTCTTGTCTACAAAAGAGGAAAACCAGCAGTCGCACAAGACTCTGAGGTCTGGTTCCTTGAC

Alignment

ORF - retro_sscr_590 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.69 %
• Parental protein coverage: 52.8 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MISSWEQK-NNCLLPEDLKNFYLMTNGFHMTWSVKLDEHTIPLGSMAINSISKLTQLNQSSMYSLPNAPT
          MISSWEQK..NCLL...L.NFYL.T.GFHMTW.VKL..HTIPL..MAINSISKLTQL.Q.SM.S.PNAPT
Retrocopy MISSWEQK>SNCLLRANLQNFYLITDGFHMTWRVKLVAHTIPLSCMAINSISKLTQLSQPSMHSTPNAPT

Parental  LADLEDDTQEGNWTGENQPEKPHFDSRSVIFELDPCNGNGKVCLVYKRGKPALAQDSEIWFLD
          LADLEDDTQE.....ENQPEKP.F.S.SVIFELDPC.GNG...LVYKRGKPA.AQDSE.WFLD
Retrocopy LADLEDDTQEAS---ENQPEKPRFNSCSVIFELDPCKGNGEAFLVYKRGKPAVAQDSEVWFLD

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	3.98 RPM
SRP014902_testis	0.14 RPM	18.67 RPM
SRP018288_heart	0.00 RPM	18.91 RPM
SRP018288_kidney	0.10 RPM	13.20 RPM
SRP018288_liver	0.48 RPM	3.68 RPM
SRP018288_lung	0.00 RPM	18.02 RPM
SRP018856_adipose	0.08 RPM	31.17 RPM
SRP035408_brain	0.06 RPM	55.90 RPM
SRP035408_liver	0.03 RPM	5.43 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_590 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_590 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_590 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000017766	3 retrocopies	retro_cfam_355, retro_cfam_457, retro_cfam_626,
Choloepus hoffmanni	ENSCHOG00000007960	1 retrocopy	retro_chof_1642,
Erinaceus europaeus	ENSEEUG00000005257	3 retrocopies	retro_eeur_208, retro_eeur_324, retro_eeur_516,
Myotis lucifugus	ENSMLUG00000001739	1 retrocopy	retro_mluc_1194,
Mustela putorius furo	ENSMPUG00000001097	2 retrocopies	retro_mputfur_1622, retro_mputfur_507,
Mus musculus	ENSMUSG00000024269	1 retrocopy	retro_mmus_2648,
Otolemur garnettii	ENSOGAG00000008218	1 retrocopy	retro_ogar_686,
Rattus norvegicus	ENSRNOG00000014957	1 retrocopy	retro_rnor_2961,
Sus scrofa	ENSSSCG00000026953	1 retrocopy	retro_sscr_590 ,
Tarsius syrichta	ENSTSYG00000005299	2 retrocopies	retro_tsyr_1161, retro_tsyr_512,
Tursiops truncatus	ENSTTRG00000007153	1 retrocopy	retro_ttru_1112,