RetrogeneDB ID: retro_pcap_398

Retrocopy location

• Organism: Hyrax (Procavia capensis)
• Coordinates: scaffold_6765:40208..40471(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TIMM9
• Ensembl ID: ENSPCAG00000003568
• Aliases: None
• Description: translocase of inner mitochondrial membrane 9 homolog (yeast) [Source:HGNC Symbol;Acc:11819]

Sequence

>retro_pcap_398
ATGGCTGTACAAATACTAGAATGTGGTCAAATAAAACAATATGAGGTATTTCTTGGAATCTACAATAAACTTACAGAAAT
CTGCCTTTTGGATCGTGATAAGGACTTCACAATAAGAAAAGGAAAACCTGAAGAGACTACCTGTTCAGAATATTGCTTAC
AGAGATATTTAAAAATGATGCCAAGAATATCTGTGAGGTTTTAGGAATATTAGATTCAGCAGAAAGAAGCTCTGGCAGCC
AAAGCAGACTCTTTGGCCAGCCA

Alignment

ORF - retro_pcap_398 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.54 %
• Parental protein coverage: 98.88 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MASQIPESDQIKQFKEFLGTYNKLTETCFLDCVKDFTTREVKPEEXTCSEHCLQKYLKMTQSISMRFQEY
          MA.QI.E..QIKQ...FLG.YNKLTE.C.LD..KDFT.R..KPEE.TCSE.CLQ.YLKM...IS.RF.EY
Retrocopy MAVQILECGQIKQYEVFLGIYNKLTEICLLDRDKDFTIRKGKPEETTCSEYCLQRYLKMMPRISVRF*EY

Parental  HIQQNEALAAKAG-LLGQP
          .IQQ.EALAAKA..L.GQP
Retrocopy *IQQKEALAAKAD<LFGQP

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Procavia capensis was not studied using RNA-Seq expression data.

ChIP-Seq

Procavia capensis was not studied using ChIP-Seq data.

EST

Procavia capensis was not studied using EST data.

TSS

Procavia capensis was not studied using FANTOM5 data.

Lab

retro_pcap_398 was not experimentally validated.

Homology

Retrocopy orthology:

Procavia capensis does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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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,