RetrogeneDB ID: retro_pcap_302

Retrocopy location

• Organism: Hyrax (Procavia capensis)
• Coordinates: scaffold_289410:438..891(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PCGF5
• Ensembl ID: ENSPCAG00000007871
• Aliases: None
• Description: polycomb group ring finger 5 [Source:HGNC Symbol;Acc:28264]

Sequence

>retro_pcap_302
ATGGCTACCCAAAGGAAACACTTGGTGAAAGATTTCAATCCTTACATCACCTGCTATATTTGTAAAGGGTGTCTGATCAA
GCCAACTACGGTGACAGAACGCCTCCATACCTTCTGTAAGACATGTATTGTCCAGCACTTTGAAGATAGCAATGATTGTT
CAAGGTGTGGCAACCAAGTTCATGAGACAAATCCATTAGAAATGTTGAGGTTGGATAATACGTTAGAAGAAATTATATTT
AAGCTGGTTCCAGGACTACGGGAACAAGAAATTGAGCGTGAATCTGAATTTTGGAAGAAAAATAAGCCTCAAGAAAATGG
ACAAGATGACACTGCAAAAGTTGACAAACCTAAAGTAGATGAGGACGGTGATGAAAATCAAGATGATAAAGACTAGCAGA
GAAGTGACCCACAAATTGCTATATGTCTAGATTGTTTACGTAATAATGGACAA

Alignment

ORF - retro_pcap_302 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.69 %
• Parental protein coverage: 58.98 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MATQRKHLVKDFNPYITCYICKGYLIKPTTVTECLHTFCKTCIVQHFEDSNDCPRCGNQVHETNPLEMLR
          MATQRKHLVKDFNPYITCYICKG.LIKPTTVTE.LHTFCKTCIVQHFEDSNDC.RCGNQVHETNPLEMLR
Retrocopy MATQRKHLVKDFNPYITCYICKGCLIKPTTVTERLHTFCKTCIVQHFEDSNDCSRCGNQVHETNPLEMLR

Parental  LDNTLEEIIFKLVPGLREQEIERESEFWKKNKPQENGQDDTAKVDKPKVDEDGDENQDDKDYHRSDPQIA
          LDNTLEEIIFKLVPGLREQEIERESEFWKKNKPQENGQDDTAKVDKPKVDEDGDENQDDKD..RSDPQIA
Retrocopy LDNTLEEIIFKLVPGLREQEIERESEFWKKNKPQENGQDDTAKVDKPKVDEDGDENQDDKD*QRSDPQIA

Parental  ICLDCLRNNGQ
          ICLDCLRNNGQ
Retrocopy ICLDCLRNNGQ

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_302 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 4 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000011001	1 retrocopy	retro_cjac_2702,
Equus caballus	ENSECAG00000016162	1 retrocopy	retro_ecab_213,
Microcebus murinus	ENSMICG00000012035	5 retrocopies	retro_mmur_1358, retro_mmur_1499, retro_mmur_253, retro_mmur_858, retro_mmur_982,
Procavia capensis	ENSPCAG00000007871	1 retrocopy	retro_pcap_302 ,