RetrogeneDB ID: retro_pcap_125

Retrocopy location

• Organism: Hyrax (Procavia capensis)
• Coordinates: GeneScaffold_7593:71358..71583(+)
• Located in intron of: ENSPCAG00000016588

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPL31
• Ensembl ID: ENSPCAG00000004787
• Aliases: None
• Description: ribosomal protein L31 [Source:HGNC Symbol;Acc:10334]

Sequence

>retro_pcap_125
GAGTACACTGTCAACATTCACAAGCACACCCATGGAGTTGGCTTCCGGAAGCATGTCCTTGGGCAATCAATGAGATCTGG
CAATTTGTCATGAAGGAAATGGGAATGCAAGAAGTGTGCACTGACACCAGACTCAACAAAGCTGTTTGGGACAAAAAAAA
TAAGGAATGTTCCATACTATATCCATGTATAGTTATTTAGAAAATGTAATGAAGATCAAGATTCA

Alignment

ORF - retro_pcap_125 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.34 %
• Parental protein coverage: 60.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  EYTINIHKRIHGVGFKKRA-PRALKEIRKFAMKEMGTPDVRIDTRLNKAVW-AKGIRNVPYRIRVRLSRK
          EYT.NIHK..HGVGF.K...P.A..EI..F.MKEMG...V..DTRLNKAVW.....RNVPY.I.V.L.RK
Retrocopy EYTVNIHKHTHGVGFRKHV<PWAINEIWQFVMKEMGMQEVCTDTRLNKAVW>XXXXRNVPYYIHV*LFRK

Parental  RNEDEDS
          .NED.DS
Retrocopy CNEDQDS

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_125 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 12 parental genes, and 112 retrocopies.

Species	Parental gene accession	Retrocopies number
Dipodomys ordii	ENSDORG00000015728	3 retrocopies	retro_dord_164, retro_dord_515, retro_dord_770,
Felis catus	ENSFCAG00000026430	13 retrocopies	retro_fcat_1420, retro_fcat_148, retro_fcat_17, retro_fcat_190, retro_fcat_1957, retro_fcat_2003, retro_fcat_251, retro_fcat_46, retro_fcat_466, retro_fcat_658, retro_fcat_725, retro_fcat_803, retro_fcat_881,
Latimeria chalumnae	ENSLACG00000013603	1 retrocopy	retro_lcha_94,
Macropus eugenii	ENSMEUG00000000963	8 retrocopies	retro_meug_1083, retro_meug_1433, retro_meug_1731, retro_meug_1741, retro_meug_198, retro_meug_418, retro_meug_588, retro_meug_649,
Myotis lucifugus	ENSMLUG00000002507	21 retrocopies	retro_mluc_1072, retro_mluc_1135, retro_mluc_1239, retro_mluc_1301, retro_mluc_1406, retro_mluc_1470, retro_mluc_1666, retro_mluc_1678, retro_mluc_1896, retro_mluc_1913, retro_mluc_2028, retro_mluc_2124, retro_mluc_2126, retro_mluc_269, retro_mluc_303, retro_mluc_463, retro_mluc_767, retro_mluc_782, retro_mluc_914, retro_mluc_922, retro_mluc_997,
Otolemur garnettii	ENSOGAG00000014494	10 retrocopies	retro_ogar_103, retro_ogar_143, retro_ogar_150, retro_ogar_178, retro_ogar_181, retro_ogar_186, retro_ogar_262, retro_ogar_271, retro_ogar_29, retro_ogar_3,
Procavia capensis	ENSPCAG00000004787	10 retrocopies	retro_pcap_121, retro_pcap_125 , retro_pcap_152, retro_pcap_228, retro_pcap_230, retro_pcap_266, retro_pcap_33, retro_pcap_378, retro_pcap_401, retro_pcap_413,
Pongo abelii	ENSPPYG00000025870	4 retrocopies	retro_pabe_106, retro_pabe_1635, retro_pabe_168, retro_pabe_895,
Rattus norvegicus	ENSRNOG00000013508	8 retrocopies	retro_rnor_101, retro_rnor_152, retro_rnor_1809, retro_rnor_217, retro_rnor_22, retro_rnor_267, retro_rnor_277, retro_rnor_286,
Sus scrofa	ENSSSCG00000008170	4 retrocopies	retro_sscr_1072, retro_sscr_1073, retro_sscr_128, retro_sscr_263,
Sus scrofa	ENSSSCG00000025180	6 retrocopies	retro_sscr_20, retro_sscr_34, retro_sscr_469, retro_sscr_501, retro_sscr_713, retro_sscr_81,
Tursiops truncatus	ENSTTRG00000016447	24 retrocopies	retro_ttru_1054, retro_ttru_1072, retro_ttru_1102, retro_ttru_1470, retro_ttru_1717, retro_ttru_215, retro_ttru_230, retro_ttru_262, retro_ttru_281, retro_ttru_316, retro_ttru_40, retro_ttru_482, retro_ttru_507, retro_ttru_527, retro_ttru_67, retro_ttru_671, retro_ttru_690, retro_ttru_785, retro_ttru_80, retro_ttru_804, retro_ttru_842, retro_ttru_886, retro_ttru_896, retro_ttru_99,