RetrogeneDB ID: retro_sscr_595

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 18:24320798..24321065(+)
• Located in intron of: ENSSSCG00000016597

Retrocopy information

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

Parental gene information

• Parental gene symbol: TIMM9
• Ensembl ID: ENSSSCG00000027270
• Aliases: None
• Description: translocase of inner mitochondrial membrane 9 homolog (yeast) [Source:HGNC Symbol;Acc:11819]

Sequence

>retro_sscr_595
ATGGCTGCACAAATACCAGAATCTGATCAGATAAAATAGTATAAGGAATTTCTTGGAACCGACAATAAACTTACAGAAAC
CTGCTTTTTGGACTGTGTTAAAGACTTCACAACAAGAGAAGTAAAACCTGAAGAGAACACCTATTCAGAACATTGCTTGC
AGAAATGTTTAAAAACGACTCAGTGAATATCCATGAGATTTCAGAAATATCATATTCAGCAGAGTGAAGCCCTGGCTGCA
AAAGCAGGACTCCTTGGTTAACCACGA

Alignment

ORF - retro_sscr_595 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.64 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MATQIPESDQIKQFKEFLGTYNKLTETCFLDCVKDFTTREVKPEENTCSEHCLQKYLKMTQRISMRFQEY
          MA.QIPESDQIK..KEFLGT.NKLTETCFLDCVKDFTTREVKPEENT.SEHCLQK.LK.TQ.ISMRFQ.Y
Retrocopy MAAQIPESDQIK*YKEFLGTDNKLTETCFLDCVKDFTTREVKPEENTYSEHCLQKCLKTTQ*ISMRFQKY

Parental  HIQQNEALAAKAGLLGQPR
          HIQQ.EALAAKAGLLG.PR
Retrocopy HIQQSEALAAKAGLLG*PR

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	1.73 RPM
SRP014902_testis	0.00 RPM	7.92 RPM
SRP018288_heart	0.00 RPM	41.83 RPM
SRP018288_kidney	0.00 RPM	25.81 RPM
SRP018288_liver	0.00 RPM	22.87 RPM
SRP018288_lung	0.00 RPM	6.11 RPM
SRP018856_adipose	0.00 RPM	7.57 RPM
SRP035408_brain	0.00 RPM	13.72 RPM
SRP035408_liver	0.00 RPM	9.25 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_595 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_595 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_595 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 23 parental genes, and 54 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000002589	1 retrocopy	retro_amel_496,
Bos taurus	ENSBTAG00000010503	2 retrocopies	retro_btau_1154, retro_btau_1355,
Cavia porcellus	ENSCPOG00000020422	5 retrocopies	retro_cpor_1080, retro_cpor_1115, retro_cpor_484, retro_cpor_719, retro_cpor_881,
Dasypus novemcinctus	ENSDNOG00000014822	4 retrocopies	retro_dnov_1495, retro_dnov_177, retro_dnov_804, retro_dnov_820,
Dipodomys ordii	ENSDORG00000002185	2 retrocopies	retro_dord_343, retro_dord_729,
Equus caballus	ENSECAG00000017063	1 retrocopy	retro_ecab_161,
Echinops telfairi	ENSETEG00000014123	8 retrocopies	retro_etel_1494, retro_etel_1551, retro_etel_1603, retro_etel_1986, retro_etel_1994, retro_etel_2201, retro_etel_760, retro_etel_778,
Felis catus	ENSFCAG00000010833	2 retrocopies	retro_fcat_1296, retro_fcat_465,
Homo sapiens	ENSG00000100575	2 retrocopies	retro_hsap_1260, retro_hsap_692,
Loxodonta africana	ENSLAFG00000008658	1 retrocopy	retro_lafr_34,
Macropus eugenii	ENSMEUG00000003698	2 retrocopies	retro_meug_1499, retro_meug_314,
Microcebus murinus	ENSMICG00000011791	3 retrocopies	retro_mmur_1263, retro_mmur_680, retro_mmur_963,
Monodelphis domestica	ENSMODG00000007898	2 retrocopies	retro_mdom_1338, retro_mdom_920,
Nomascus leucogenys	ENSNLEG00000013292	2 retrocopies	retro_nleu_2098, retro_nleu_2226,
Otolemur garnettii	ENSOGAG00000002472	2 retrocopies	retro_ogar_359, retro_ogar_37,
Ochotona princeps	ENSOPRG00000002924	1 retrocopy	retro_opri_693,
Procavia capensis	ENSPCAG00000003568	1 retrocopy	retro_pcap_398,
Pongo abelii	ENSPPYG00000005859	2 retrocopies	retro_pabe_1049, retro_pabe_530,
Pan troglodytes	ENSPTRG00000006394	2 retrocopies	retro_ptro_3041, retro_ptro_496,
Sorex araneus	ENSSARG00000012165	1 retrocopy	retro_sara_235,
Sus scrofa	ENSSSCG00000027270	2 retrocopies	retro_sscr_595 , retro_sscr_596,
Tarsius syrichta	ENSTSYG00000000502	5 retrocopies	retro_tsyr_1026, retro_tsyr_104, retro_tsyr_1441, retro_tsyr_241, retro_tsyr_370,
Tursiops truncatus	ENSTTRG00000008743	1 retrocopy	retro_ttru_1011,