RetrogeneDB ID: retro_pcap_287

Retrocopy location

• Organism: Hyrax (Procavia capensis)
• Coordinates: scaffold_273154:307..502(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSPCAG00000000300
• Aliases: None
• Description: None

Sequence

>retro_pcap_287
AGAAAAGGGGAACAGGAGGCTGACAATGAGACAGACTAAGAAGGTAGATGAAGAAGAGGAGGAGGAAAACGTGATGGTGA
GGAAGAGGATGGACATCACGAGGAAACAACGGAGACAGCTACTGGCAAATGGGTAGCTGGAGATGATGAGGATGACGATG
CTGACAGCAAGAAGCAAATGGCCAATGAGGCCGAC

Alignment

ORF - retro_pcap_287 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 53.73 %
• Parental protein coverage: 50.39 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  QEADNEVDEEEEEGG-EEEEEEE-EGDGEEEDGDEDEEAEAATGKRAAEDDEDDDVDTKKQKTDEDD
          .....E.D.E....G..EEEEEE...DGEEEDG...E..E.ATGK..A.DDEDDD.D.KKQ...E.D
Retrocopy RKGEQEADNETD*EG>DEEEEEE<KRDGEEEDGHHEETTETATGKWVAGDDEDDDADSKKQMANEAD

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_287 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 3 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000006234	1 retrocopy	retro_chof_60,
Procavia capensis	ENSPCAG00000000300	1 retrocopy	retro_pcap_287 ,
Tursiops truncatus	ENSTTRG00000009156	2 retrocopies	retro_ttru_1596, retro_ttru_1609,