RetrogeneDB ID: retro_pcap_269

Retrocopy location

• Organism: Hyrax (Procavia capensis)
• Coordinates: scaffold_244728:294..594(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: AAED1
• Ensembl ID: ENSPCAG00000003177
• Aliases: None
• Description: AhpC/TSA antioxidant enzyme domain containing 1 [Source:HGNC Symbol;Acc:16881]

Sequence

>retro_pcap_269
ATGGTGGCCCTGGTCACATGGCAGGTCAGCAGCAGCACTGCCCGGGCTCCTGTTCGACCAGCCCTGAGTGCTGGCAGCCA
CTGTCTACCCCTGTGTCTGAGCTGCCAGTGCTGGACCTCTCTGGGAAGCGGGGGCCATTCTGCACACTCCTCTGGCAGCC
CTGGGTCATTGTGGCCTTCGTGTGGCATTTCCTATGCTACATCTGCAAGGAATGTGTGGAAGATCTGGCCAAAGTGCCCA
GGAGTTTCCTAGAAGAAACCAGTGTTGCCCTTATAGTTGACCGGATAGCCATCCTACCAT

Alignment

ORF - retro_pcap_269 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.86 %
• Parental protein coverage: 54.64 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAAPVTQQVCGRAAPAPEE-SGPEPGQPLAAAVAELPVLDASGKRVAFGSLFRERQAIVVFVRHFLCYIC
          M.A.VT.QV....A.AP.....PE..QPL...V.ELPVLD.SGKR..F..L......IV.FV.HFLCYIC
Retrocopy MVALVTWQVSSSTARAPVR<TSPECWQPLSTPVSELPVLDLSGKRGPFCTLLWQPWVIVAFVWHFLCYIC

Parental  KEYVEDLAKIPKSFLDGANVTLIV-IGQSSYH
          KE.VEDLAK.P.SFL....V.LIV..G..SYH
Retrocopy KECVEDLAKVPRSFLEETSVALIV>TG*PSYH

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_269 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 10 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000006422	1 retrocopy	retro_chof_1792,
Choloepus hoffmanni	ENSCHOG00000007723	7 retrocopies	retro_chof_1026, retro_chof_1037, retro_chof_1808, retro_chof_2079, retro_chof_2149, retro_chof_2642, retro_chof_811,
Callithrix jacchus	ENSCJAG00000005509	1 retrocopy	retro_cjac_4168,
Dasypus novemcinctus	ENSDNOG00000024562	4 retrocopies	retro_dnov_1226, retro_dnov_1419, retro_dnov_1519, retro_dnov_1871,
Homo sapiens	ENSG00000158122	1 retrocopy	retro_hsap_4843,
Macaca mulatta	ENSMMUG00000008295	1 retrocopy	retro_mmul_2586,
Otolemur garnettii	ENSOGAG00000017058	1 retrocopy	retro_ogar_1866,
Procavia capensis	ENSPCAG00000003177	1 retrocopy	retro_pcap_269 ,
Pongo abelii	ENSPPYG00000019418	1 retrocopy	retro_pabe_3765,
Pan troglodytes	ENSPTRG00000021156	1 retrocopy	retro_ptro_3227,