RetrogeneDB ID: retro_pcap_87

Retrocopy location

• Organism: Hyrax (Procavia capensis)
• Coordinates: GeneScaffold_5185:23194..23410(+)
• Located in intron of: ENSPCAG00000008555

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSPCAG00000000834
• Aliases: None
• Description: None

Sequence

>retro_pcap_87
AAAGGGCTTCTCACTCTAGAGGTGAACAGCTGTGGTGCTGATGTGATCATGCTCACCTAGCCCATGATGAATGGCTCCTG
GAGTACCAAGCTGTTAGGTAAGGCAGCCTGAAACATGGTACCATGGGAAGATGCCACCTTGTGCTCAGAAGATAGTTTAA
GGGAAATGGCAATGATAACAACACATCTTCAAAATCATCAAGAAGCTATTTAGAAG

Alignment

ORF - retro_pcap_87 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.67 %
• Parental protein coverage: 81.82 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KGLLTEKVNTCGTDVIALTKQVLKGSRSSELLGQAARNMVLQEDAILHSEDSLRKMAIITTHLQYQQEAI
          KGLLT..VN.CG.DVI.LT.....GS.S..LLG.AA.NMV..EDA.L.SEDSLR.MA.ITTHLQ..QEAI
Retrocopy KGLLTLEVNSCGADVIMLT*PMMNGSWSTKLLGKAA*NMVPWEDATLCSEDSLREMAMITTHLQNHQEAI

Parental  QK
          .K
Retrocopy *K

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_87 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 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000021622	1 retrocopy	retro_cpor_829,
Loxodonta africana	ENSLAFG00000020646	4 retrocopies	retro_lafr_1177, retro_lafr_299, retro_lafr_608, retro_lafr_800,
Macropus eugenii	ENSMEUG00000013119	3 retrocopies	retro_meug_112, retro_meug_1350, retro_meug_231,
Procavia capensis	ENSPCAG00000000834	1 retrocopy	retro_pcap_87 ,