RetrogeneDB ID: retro_pcap_148

Retrocopy location

• Organism: Hyrax (Procavia capensis)
• Coordinates: scaffold_113421:1701..2129(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ATP6V0C
• Ensembl ID: ENSPCAG00000015060
• Aliases: None
• Description: ATPase, H+ transporting, lysosomal 16kDa, V0 subunit c [Source:HGNC Symbol;Acc:855]

Sequence

>retro_pcap_148
GGCCCAAGTATACCTCTTTTTTTCACCATCATGAGTGCCTTGGCTGCCATCTTCTTCAGCACCCTGGGTGCTGCCTATGG
CATGGCCAAGAGCAGAAAGGGCATCACTGCCATGTTAGCCACTCAGTCAAATTGCATCATGAAGTCCATCTTCCTGGTTA
TAGCTGTCGTCATCACCATCTACAGCCTGGTAGTGGCTCTCTTTTTCGCCAACTCCGTGAATGACAATATGACCCTCTAC
AAGAGTTGCCTTCAGTGGGGTGTGGGCTTGAGCATGGGCTTGAGTGGACTGGCAGCCAGCTTTCACATTAGCATTGTGCA
GGATGCCAGTGTAGGGGCACTGCCCAGCAGCCCCAATTATCAGTGGGCATGCTCCTGATCTTCACATTTGCTGAGGTACT
CAGCCTCTGTGGTTTCATTGTTGCTCTC

Alignment

ORF - retro_pcap_148 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.76 %
• Parental protein coverage: 92.9 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GPEYASFFAVMGASAAMVFSALGAAYGTAKSGTGIAAMSVMRPEQIMKSIIPVVMAGIIAIYGLVVAVLI
          GP....FF..M.A.AA..FS.LGAAYG.AKS..GI.AM.......IMKSI...V.A..I.IY.LVVA...
Retrocopy GPSIPLFFTIMSALAAIFFSTLGAAYGMAKSRKGITAMLATQSNCIMKSIF-LVIAVVITIYSLVVALFF

Parental  ANSLNANITLYKSFLQLGAGLSVGLSGLAAGFAIGIVGDAGV-RGTAQQPRLFVGMILILIFAEVLGLYG
          ANS.N.N.TLYKS.LQ.G.GLS.GLSGLAA.F.I.IV.DA.V.RGTAQQP.L.VGM.LI..FAEVL.L.G
Retrocopy ANSVNDNMTLYKSCLQWGVGLSMGLSGLAASFHISIVQDASV<RGTAQQPQLSVGMLLIFTFAEVLSLCG

Parental  LIVAL
          .IVAL
Retrocopy FIVAL

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_148 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 15 parental genes, and 31 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000026428	1 retrocopy	retro_btau_1638,
Homo sapiens	ENSG00000185883	2 retrocopies	retro_hsap_1798, retro_hsap_3462,
Gorilla gorilla	ENSGGOG00000028600	2 retrocopies	retro_ggor_1323, retro_ggor_2335,
Macropus eugenii	ENSMEUG00000004597	2 retrocopies	retro_meug_1428, retro_meug_1837,
Myotis lucifugus	ENSMLUG00000026715	2 retrocopies	retro_mluc_2507, retro_mluc_294,
Monodelphis domestica	ENSMODG00000015439	5 retrocopies	retro_mdom_1669, retro_mdom_1739, retro_mdom_507, retro_mdom_84, retro_mdom_982,
Mus musculus	ENSMUSG00000024121	2 retrocopies	retro_mmus_2726, retro_mmus_2888,
Nomascus leucogenys	ENSNLEG00000009416	2 retrocopies	retro_nleu_1692, retro_nleu_2770,
Procavia capensis	ENSPCAG00000015060	1 retrocopy	retro_pcap_148 ,
Pan troglodytes	ENSPTRG00000007653	2 retrocopies	retro_ptro_1204, retro_ptro_2346,
Rattus norvegicus	ENSRNOG00000006542	1 retrocopy	retro_rnor_118,
Sarcophilus harrisii	ENSSHAG00000014251	1 retrocopy	retro_shar_194,
Ictidomys tridecemlineatus	ENSSTOG00000013420	3 retrocopies	retro_itri_119, retro_itri_387, retro_itri_691,
Drosophila melanogaster	FBgn0262736	3 retrocopies	retro_dmel_3, retro_dmel_38, retro_dmel_65,
Caenorhabditis elegans	R10E11.2	2 retrocopies	retro_cele_1, retro_cele_5,