RetrogeneDB ID: retro_pcap_26

Retrocopy location

• Organism: Hyrax (Procavia capensis)
• Coordinates: GeneScaffold_1081:136585..136868(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: C19orf53
• Ensembl ID: ENSPCAG00000014250
• Aliases: None
• Description: chromosome 19 open reading frame 53 [Source:HGNC Symbol;Acc:24991]

Sequence

>retro_pcap_26
ATGACGCAGGGGCAACACACATTCCAGCCGAAGAAGCCAGGGAAGAGCAAGGCAGCAGCGGCAGCTTCGGAGCGGAATCG
AGGCCCGAGGAAGGGTGGCTGTATCATCGCCCCCAGGAAGGCGCGCGTGGTGCAGCAACAAAAGCTGAAGGAGAATCTGG
AGATTGGGCTCCGGAAGAAGATAGAACATGATGTGGGTTTTGAAAGCCAGCGCTGCTATGCCCAAGAACCTATCACTGCT
GAAGTCCACAGGCAAGAAGGGGATGGCCTCCGTCAAGACACCG

Alignment

ORF - retro_pcap_26 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.46 %
• Parental protein coverage: 98.96 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAQGQRKFQPKKPGKTKAAAAASERNRGPRKGGRIIAPKKARVVQQQKLKKNLEIGIRKKIEHDV-VLKA
          M.QGQ..FQPKKPGK.KAAAAASERNRGPRKGG.IIAP.KARVVQQQKLK.NLEIG.RKKIEHDV.VLKA
Retrocopy MTQGQHTFQPKKPGKSKAAAAASERNRGPRKGGCIIAPRKARVVQQQKLKENLEIGLRKKIEHDV>VLKA

Parental  STAMPKNLSLLKSAGKKKGMASAKTP
          S.AMPKNLSLLKS.G.KKGMAS.KTP
Retrocopy SAAMPKNLSLLKSTG-KKGMASVKTP

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_26 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.

---

Parental genes homology:

Parental genes homology involve 11 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000002525	1 retrocopy	retro_btau_35,
Callithrix jacchus	ENSCJAG00000004427	3 retrocopies	retro_cjac_1003, retro_cjac_2634, retro_cjac_291,
Homo sapiens	ENSG00000104979	1 retrocopy	retro_hsap_628,
Gorilla gorilla	ENSGGOG00000027024	1 retrocopy	retro_ggor_550,
Monodelphis domestica	ENSMODG00000011876	2 retrocopies	retro_mdom_1436, retro_mdom_926,
Nomascus leucogenys	ENSNLEG00000013141	1 retrocopy	retro_nleu_452,
Otolemur garnettii	ENSOGAG00000007185	1 retrocopy	retro_ogar_640,
Procavia capensis	ENSPCAG00000014250	1 retrocopy	retro_pcap_26 ,
Pan troglodytes	ENSPTRG00000010565	1 retrocopy	retro_ptro_457,
Pteropus vampyrus	ENSPVAG00000006321	1 retrocopy	retro_pvam_1140,
Tursiops truncatus	ENSTTRG00000010354	1 retrocopy	retro_ttru_317,