RetrogeneDB ID: retro_pcap_402

Retrocopy location

• Organism: Hyrax (Procavia capensis)
• Coordinates: scaffold_69625:8340..8690(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSPCAG00000003516
• Aliases: None
• Description: None

Sequence

>retro_pcap_402
TTGCTGCCCCCGGTAGGACCACAGGTGCTTTGTTTGACATCCAGGGCTTGCTCAGTCTCCTTCTCTCATGCTTCTCCCCT
CTTTGCTCCTCAGCGGTTGTCCCAAAGGCAGTGGTGAATTTGGAGCCCCCATGGATCAGGGTTCTCCAAGAGGACTTTGT
GACTCTGAAGTGCCATGGGGCCCACTCCCCTGAAAACAGCTCCACCCAGTGGTTCCGCAGAGGAACTCCTATTCCTACTC
AGGTCCAGCCCAGCTACAGCTTTAAGGCCACCGTCAATGACAGCGGGGAGTACAGGTGCCAGACTGGCCGGACCCGCCTC
AGCGACCCTGTGCAGCTGGATGTGTTTTCC

Alignment

ORF - retro_pcap_402 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.19 %
• Parental protein coverage: 55.83 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MLEDMYPGNLCLLQRLTVL-LLLACTDT--QAADLPKAVVSLEPPWIRVLQEDFVSLKCHGAHFPGNSST
          .L....P..LCL..R.....LLL.C.......A..PKAVV.LEPPWIRVLQEDFV.LKCHGAH.P.NSST
Retrocopy LLPPVGPQVLCLTSRACSV<LLLSCFSPLCSSAVVPKAVVNLEPPWIRVLQEDFVTLKCHGAHSPENSST

Parental  QWFHRGSPIPTQVQPTYSFKATVNDSGEYRCQTGRTQLSDPLQLDVFT
          QWF.RG.PIPTQVQP.YSFKATVNDSGEYRCQTGRT.LSDP.QLDVF.
Retrocopy QWFRRGTPIPTQVQPSYSFKATVNDSGEYRCQTGRTRLSDPVQLDVFS

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_402 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Procavia capensis	ENSPCAG00000003516	1 retrocopy	retro_pcap_402 ,