RetrogeneDB ID: retro_pcap_327

Retrocopy location

• Organism: Hyrax (Procavia capensis)
• Coordinates: scaffold_38375:7629..7982(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MRPS7
• Ensembl ID: ENSPCAG00000015942
• Aliases: None
• Description: mitochondrial ribosomal protein S7 [Source:HGNC Symbol;Acc:14499]

Sequence

>retro_pcap_327
GAATTCGGTAAAACTCAGTTCGTTAGAGCTGCTGCTTCAAGCAAAACAAGCTCTGTGTCTGAAGACTCAGTGGTCAGTCA
GTTCACCAACATGGTAATAAGAGTAGGAAACAAAGTGTTCCTCGTGATACACACCCTGGAAACCAAAAAGTAATTTGAGT
AGTCCCATGTTGTTACTCAGAGGAACAGGCAACCATTGAATGCAATCCCTGTACCATCTTCCAGCAGGCTCTCAAAAACT
GGGAACCTGTGATTGGGCTGGTACCTGTTCTCAAGGGCAGCCTCTCCCCCCAGGTCTCTGGGCCCCTGTCTGACCCGCAT
TGCTGCTTCCCAGCAGTGAGGTGGGTGATAAGT

Alignment

ORF - retro_pcap_327 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.03 %
• Parental protein coverage: 50.83 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  ELRRTQLIKAAPATRTTSVFEDPVVSKFINMMMKGGNKVLARSLMIQTLETVKRKQFEKYHAAS-AEEQA
          E...TQ...AA....T.SV.ED.VVS.F.NM....GNKV....L.I.TLET...K.FE..H.....EEQA
Retrocopy EFGKTQFVRAAASSKTSSVSEDSVVSQFTNMVIRVGNKVF---LVIHTLET--KK*FE*SHVVT<SEEQA

Parental  TIERNPYTIFHQALKNCEPVIGLVPILKGGHFYQVPVPLADKRRRFLAMKWMIT
          TIE.NP.TIF.QALKN.EPVIGLVP.LKG....QV..PL.D....F.A..W.I.
Retrocopy TIECNPCTIFQQALKNWEPVIGLVPVLKGSLSPQVSGPLSDPHCCFPAVRWVIS

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_327 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 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000009287	1 retrocopy	retro_amel_1444,
Canis familiaris	ENSCAFG00000004752	5 retrocopies	retro_cfam_2020, retro_cfam_2197, retro_cfam_438, retro_cfam_443, retro_cfam_540,
Callithrix jacchus	ENSCJAG00000014458	2 retrocopies	retro_cjac_290, retro_cjac_3316,
Erinaceus europaeus	ENSEEUG00000015775	1 retrocopy	retro_eeur_212,
Felis catus	ENSFCAG00000028759	2 retrocopies	retro_fcat_2013, retro_fcat_424,
Loxodonta africana	ENSLAFG00000002873	1 retrocopy	retro_lafr_945,
Macropus eugenii	ENSMEUG00000012264	1 retrocopy	retro_meug_1826,
Mustela putorius furo	ENSMPUG00000013928	1 retrocopy	retro_mputfur_976,
Oryctolagus cuniculus	ENSOCUG00000017928	1 retrocopy	retro_ocun_609,
Procavia capensis	ENSPCAG00000015942	1 retrocopy	retro_pcap_327 ,
Pteropus vampyrus	ENSPVAG00000008433	3 retrocopies	retro_pvam_610, retro_pvam_615, retro_pvam_678,
Ictidomys tridecemlineatus	ENSSTOG00000015200	2 retrocopies	retro_itri_1805, retro_itri_461,