RetrogeneDB ID: retro_pcap_1

Retrocopy location

• Organism: Hyrax (Procavia capensis)
• Coordinates: GeneScaffold_7657:13787..14405(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPCAG00000018827
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: RDH12
• Ensembl ID: ENSPCAG00000009359
• Aliases: None
• Description: retinol dehydrogenase 12 (all-trans/9-cis/11-cis) [Source:HGNC Symbol;Acc:19977]

Sequence

>retro_pcap_1
GAGGAACCAAGGCTGGATGTCTTGATCAATAATGCAGGAGTCTTCCAGTGCCCTTACATGAAGACTGAAGATGGATTTGA
GATGCAGTTTGGAGTGAACCATCTCGGGCACTTTCTACTCACCAATCTTCTTCTTGGACTCCTCAAGAGTTCAGCTCCCA
GCAGGATTGTGGTAGTATCTTCCAGACTTTATAAATATGGAGACATTAACTTTGAAGACCTAAACTGTGAACAAAGCTAT
AATAAAGGTTTTTGTTATAGTCGGAGCAAATTAGCTAACATTCTTTTCACCAGAGAGCTAGCCCGCCGCTTAGAAGGCAC
AAACGTCACTGTAAATGTGCTACATCCTGGTATTGTACGAACGAATCTTGGGAGGCACATAAATATTCCACTGCTGGTCA
AACCACTATTCAATTTGCTGTCATGGGCTTTTTTCAAAACGCCGTTGGAAGGTGCCCAGACATCTGTTTATTTAGCCTCG
TCACCTGAAGTAGAGGGCGTGTCAGGAAAGTACTTTGGGGATTGTAAAGAGGAAGCACTATTGCCCAAAGCTCTGGATGA
GTCTGTTGCAAGAAAACTCTGGGATATTAGTGAAGTGATGGTTGGCATATTAAAATAG

Alignment

ORF - retro_pcap_1 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.05 %
• Parental protein coverage: 55.23 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EEKQLHILINNAGVMMCPYSKTADGFETHLGVNHLGHFLLTYLLLERLKESAPARVVNLSSVVHHAGKIH
          EE..L..LINNAGV..CPY.KT.DGFE...GVNHLGHFLLT.LLL..LK.SAP.R.V..SS.....G.I.
Retrocopy EEPRLDVLINNAGVFQCPYMKTEDGFEMQFGVNHLGHFLLTNLLLGLLKSSAPSRIVVVSSRLYKYGDIN

Parental  FHDLQGEKRYSRCFAYCHSKLANVLFTRQLAKKLQGTGVTTYVVHPGIVRSELVRHSSLLCLLWRLFSPL
          F.DL..E..Y...F.Y..SKLAN.LFTR.LA..L.GT.VT..V.HPGIVR..L.RH.....L...LF..L
Retrocopy FEDLNCEQSYNKGFCYSRSKLANILFTRELARRLEGTNVTVNVLHPGIVRTNLGRHINIPLLVKPLFNLL

Parental  ----VKSAREGAQTSTH
          .....K...EGAQTS..
Retrocopy SWAFFKTPLEGAQTSVY

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_1 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 13 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000008036	1 retrocopy	retro_amel_673,
Canis familiaris	ENSCAFG00000016446	1 retrocopy	retro_cfam_2068,
Equus caballus	ENSECAG00000015001	1 retrocopy	retro_ecab_1059,
Felis catus	ENSFCAG00000014092	1 retrocopy	retro_fcat_1910,
Loxodonta africana	ENSLAFG00000022637	1 retrocopy	retro_lafr_847,
Macropus eugenii	ENSMEUG00000001473	1 retrocopy	retro_meug_41,
Meleagris gallopavo	ENSMGAG00000011960	1 retrocopy	retro_mgal_16,
Microcebus murinus	ENSMICG00000010855	1 retrocopy	retro_mmur_432,
Ornithorhynchus anatinus	ENSOANG00000015759	1 retrocopy	retro_oana_89,
Procavia capensis	ENSPCAG00000009359	1 retrocopy	retro_pcap_1 ,
Pelodiscus sinensis	ENSPSIG00000010721	1 retrocopy	retro_psin_24,
Sarcophilus harrisii	ENSSHAG00000012445	1 retrocopy	retro_shar_41,
Drosophila melanogaster	FBgn0033203	1 retrocopy	retro_dmel_79,