RetrogeneDB ID: retro_pcap_226

Retrocopy location

• Organism: Hyrax (Procavia capensis)
• Coordinates: scaffold_19045:12024..12331(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PFDN6
• Ensembl ID: ENSPCAG00000006019
• Aliases: None
• Description: prefoldin subunit 6 [Source:HGNC Symbol;Acc:4926]

Sequence

>retro_pcap_226
ATGGCTGAGCTGATCCAAAAGAAGCTACAAGGAAGAAGTGGAGAAATATCAACAGCTACAGAAAGACTTGAGTAAGTCCA
TGTCAGGGCGGCAGAAGCTTGAGGCCCAACTAACAGAAAATAATACCGTGAAGTAGGAACTGGCCCTACTTGATGGGTCC
AACGTGGTCTTTAAACTTCTGGGTCCTGTGCTGGTCAAACAGGAGCTGGGAGAGGCTCGGGCCACAGTGGGGAAGAGGCT
GGACTATGTAACAGCTGAAATTAAGTGATTCGAACCCCAGCTCCGGGACCTGGAGAAGCAGTCCGAG

Alignment

ORF - retro_pcap_226 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.2 %
• Parental protein coverage: 79.07 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAELIQKKLQG-EVEKYQQLQKDLSKSMSGRQKLEAQLTENNIVKEELALLDGSNVVFKLLGPVLVKQEL
          MAELIQKKLQG.EVEKYQQLQKDLSKSMSGRQKLEAQLTENN.VK.ELALLDGSNVVFKLLGPVLVKQEL
Retrocopy MAELIQKKLQG>EVEKYQQLQKDLSKSMSGRQKLEAQLTENNTVK*ELALLDGSNVVFKLLGPVLVKQEL

Parental  GEARATVGKRLDYITAEIKRYESQLRDLEKQSE
          GEARATVGKRLDY.TAEIK..E.QLRDLEKQSE
Retrocopy GEARATVGKRLDYVTAEIK*FEPQLRDLEKQSE

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_226 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 6 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000011211	2 retrocopies	retro_dnov_1317, retro_dnov_2064,
Loxodonta africana	ENSLAFG00000012967	1 retrocopy	retro_lafr_363,
Macropus eugenii	ENSMEUG00000016778	1 retrocopy	retro_meug_1930,
Otolemur garnettii	ENSOGAG00000028341	4 retrocopies	retro_ogar_1185, retro_ogar_2023, retro_ogar_3508, retro_ogar_85,
Ochotona princeps	ENSOPRG00000000983	1 retrocopy	retro_opri_12,
Procavia capensis	ENSPCAG00000006019	1 retrocopy	retro_pcap_226 ,