RetrogeneDB ID: retro_pcap_171

Retrocopy location

• Organism: Hyrax (Procavia capensis)
• Coordinates: scaffold_133035:472..880(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPCAG00000008313
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: H3F3A
• Ensembl ID: ENSPCAG00000004484
• Aliases: None
• Description: H3 histone, family 3A [Source:HGNC Symbol;Acc:4764]

Sequence

>retro_pcap_171
ATGGCTCGTACAAAGCAGACTGCCCGCAAATCAACCGGTGGTAAAGCGCCCAGGAAGCAACTGGCCACAAAAGCCGCTCG
CAAGAGTGCGCCCTCTACTGGAGGGGTGAAGAAACCTCATCGTTACAGGCCTGGTACTGTGGCACTCCGGGAAATCAGAC
GTTATCAGAAGTCGACTGAACTTCTGATTCGCAAACTTCCCTTCCAACGTCTGGTGCGAGAAGTTGCTCAGGACTTCAAG
ACAGATCTGCGTTTCCAGAGCGCAGCTATTGGTACTTTGTAGGAGGCAAGTGAGGCCTATCTGGTTGGCCTTTTTGAAGA
CACCAACCTGTGTGCTATCCATGCCAAACATGTAACAATTATGCCAAAAGACATCCAGCTAGCACGCCGCATACGTGGAG
AACGTGCT

Alignment

ORF - retro_pcap_171 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.06 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MARTKQTARKSTGGKAPRKQLATKAARKSAPSTGGVKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQR
          MARTKQTARKSTGGKAPRKQLATKAARKSAPSTGGVKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQR
Retrocopy MARTKQTARKSTGGKAPRKQLATKAARKSAPSTGGVKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQR

Parental  LVREIAQDFKTDLRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGERA
          LVRE.AQDFKTDLRFQSAAIG.L.EASEAYLVGLFEDTNLCAIHAK.VTIMPKDIQLARRIRGERA
Retrocopy LVREVAQDFKTDLRFQSAAIGTL*EASEAYLVGLFEDTNLCAIHAKHVTIMPKDIQLARRIRGERA

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_171 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 13 parental genes, and 50 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000024561	3 retrocopies	retro_btau_156, retro_btau_204, retro_btau_47,
Canis familiaris	ENSCAFG00000004916	2 retrocopies	retro_cfam_1117, retro_cfam_622,
Canis familiaris	ENSCAFG00000016119	4 retrocopies	retro_cfam_168, retro_cfam_1845, retro_cfam_650, retro_cfam_673,
Erinaceus europaeus	ENSEEUG00000013796	1 retrocopy	retro_eeur_2,
Felis catus	ENSFCAG00000003617	4 retrocopies	retro_fcat_1085, retro_fcat_1953, retro_fcat_592, retro_fcat_830,
Felis catus	ENSFCAG00000030424	5 retrocopies	retro_fcat_1251, retro_fcat_1532, retro_fcat_1533, retro_fcat_2011, retro_fcat_674,
Macaca mulatta	ENSMMUG00000031483	9 retrocopies	retro_mmul_108, retro_mmul_147, retro_mmul_201, retro_mmul_213, retro_mmul_215, retro_mmul_286, retro_mmul_337, retro_mmul_346, retro_mmul_7,
Nomascus leucogenys	ENSNLEG00000001577	2 retrocopies	retro_nleu_25, retro_nleu_35,
Otolemur garnettii	ENSOGAG00000025933	14 retrocopies	retro_ogar_1285, retro_ogar_1364, retro_ogar_1449, retro_ogar_1575, retro_ogar_1576, retro_ogar_2200, retro_ogar_2316, retro_ogar_2449, retro_ogar_2634, retro_ogar_3235, retro_ogar_42, retro_ogar_733, retro_ogar_937, retro_ogar_952,
Procavia capensis	ENSPCAG00000004484	2 retrocopies	retro_pcap_171 , retro_pcap_95,
Pongo abelii	ENSPPYG00000008636	1 retrocopy	retro_pabe_2662,
Pteropus vampyrus	ENSPVAG00000008459	2 retrocopies	retro_pvam_218, retro_pvam_52,
Sarcophilus harrisii	ENSSHAG00000005807	1 retrocopy	retro_shar_565,