RetrogeneDB ID: retro_pcap_18

Retrocopy location

• Organism: Hyrax (Procavia capensis)
• Coordinates: scaffold_288156:415..811(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPCAG00000006502
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSPCAG00000004570
• Aliases: None
• Description: None

Sequence

>retro_pcap_18
TTCAGTAAGAAGGCGGCCAGCAGTGTCAGCTACGCTGCTGCTGCAGCCAGCAACTTCATGAAAGCAGTCTTCAGCTGGGA
CACGAACGAGGCCAAGCGGAGGGTATGCAAACTCTACTTTGCCTGGTACCGGGAGGTGCCGAACACTGTGCACTTATTCC
AGTTAGACATCACCGTGAAACAGGGGCGGGACAAAGTCCGAGAAATGTTCATGAAGAATGCCCATGTCACAGACCCCAGG
GTGGTTGATCTTCTGGTCATTAAGGGAAAGATGGAACTGGAGGAAATGATCCATGTGTGGAAGCAGCGGACACATGTTAT
GCGGTTCTTCCATGAAACAGAAGCACCCAGGCCAAAGGATTTCCTGTCTAAGTTCTATATTGGCCATGACCCATGA

Alignment

ORF - retro_pcap_18 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.1 %
• Parental protein coverage: 92.86 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  FLRELKASGACRGAAATSKVRAVLIQGRNQAKRRVCDLYSA-RQEMPNTVHLFQLDITVKQGRDKVREMF
          F......S.....AAA.....AV.....N.AKRRVC.LY.A...E.PNTVHLFQLDITVKQGRDKVREMF
Retrocopy FSKKAASSVSYAAAAASNFMKAVFSWDTNEAKRRVCKLYFAWYREVPNTVHLFQLDITVKQGRDKVREMF

Parental  MKNAHVTDPRVVDLLVIKGKMELEETIHVWKQRTHLMRFFHETEAPRPKDFLSKFYIGHDP
          MKNAHVTDPRVVDLLVIKGKMELEE.IHVWKQRTH.MRFFHETEAPRPKDFLSKFYIGHDP
Retrocopy MKNAHVTDPRVVDLLVIKGKMELEEMIHVWKQRTHVMRFFHETEAPRPKDFLSKFYIGHDP

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_18 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 9 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Ciona savignyi	ENSCSAVG00000001466	1 retrocopy	retro_csav_29,
Erinaceus europaeus	ENSEEUG00000004117	1 retrocopy	retro_eeur_664,
Monodelphis domestica	ENSMODG00000007030	1 retrocopy	retro_mdom_397,
Mus musculus	ENSMUSG00000022450	1 retrocopy	retro_mmus_2693,
Oryctolagus cuniculus	ENSOCUG00000015446	1 retrocopy	retro_ocun_1128,
Otolemur garnettii	ENSOGAG00000014762	2 retrocopies	retro_ogar_1656, retro_ogar_312,
Procavia capensis	ENSPCAG00000004570	1 retrocopy	retro_pcap_18 ,
Rattus norvegicus	ENSRNOG00000008569	1 retrocopy	retro_rnor_604,
Sorex araneus	ENSSARG00000003814	1 retrocopy	retro_sara_75,