RetrogeneDB ID: retro_pcap_281

Retrocopy location

• Organism: Hyrax (Procavia capensis)
• Coordinates: scaffold_259473:200..611(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FAM213A
• Ensembl ID: ENSPCAG00000009696
• Aliases: None
• Description: family with sequence similarity 213, member A [Source:HGNC Symbol;Acc:28651]

Sequence

>retro_pcap_281
GAAGCTGTAGACTGTTCTCCCTGAAGCCTAAGTTGGGTTAGCTGGGCATCCCCCTCTACGCAGTGGTGAAGGAGCTGGTC
AGGACTAAAGTGAAGGACTTTAGCCATATCTCAAAGGAGAAATCTTCCTAGGTAAAAAGAAGTTCTATGGTCCTCAAAGG
CGCAAGATGATATTTATGGGATTTGCCCATCTGGATGTCTGGTGCAACTTCTTTTAGGGCTAGAACGGAGGCTTCTCTTG
AAACCTAGAAGGCAAGTCTTTATCCTTGGAGGAGTTTTTGTGGTGGGGTCAGGAAGACAGGGCATTCTCCTTAGGCACCA
AGAGAAAGAATTTGGAGACAAAGTAAACCTGGTTTCTGTTTTGGAAGCTGCTAGGAAGATCAAACCGCAGACCCTGGCCT
GAGAGGGAAAA

Alignment

ORF - retro_pcap_281 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.58 %
• Parental protein coverage: 60.7 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  EAADLS-SLKPKLDELGVPLYAVVKELVRTEVKDFQ-PYFKGEIFLDKKKKFYGPQRRKMMFMGFVRLGV
          EA.D.S.SLKPKL..LG.PLYAVVKELVRT.VKDF..PY.KGEIFL.KKK.FYGPQRRKM.FMGF..L.V
Retrocopy EAVDCS<SLKPKLG*LGIPLYAVVKELVRTKVKDFS<PYLKGEIFLGKKK-FYGPQRRKMIFMGFAHLDV

Parental  WCNFFRAWNGGFSGNLEGEG-FILGGVFVVGSGKQGILLEHREKEFGDKVNLASVLEAARKIKPQTLASE
          WCNFF...NGGFS.NLEG...FILGGVFVVGSG.QGILL.H.EKEFGDKVNL.SVLEAARKIKPQTLA.E
Retrocopy WCNFF*G*NGGFS*NLEGKS<FILGGVFVVGSGRQGILLRHQEKEFGDKVNLVSVLEAARKIKPQTLA*E

Parental  DK
          .K
Retrocopy GK

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_281 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 30 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000000813	1 retrocopy	retro_chof_878,
Callithrix jacchus	ENSCJAG00000003657	1 retrocopy	retro_cjac_3312,
Dasypus novemcinctus	ENSDNOG00000001981	3 retrocopies	retro_dnov_1843, retro_dnov_1901, retro_dnov_868,
Homo sapiens	ENSG00000122378	2 retrocopies	retro_hsap_1135, retro_hsap_4076,
Gorilla gorilla	ENSGGOG00000013246	2 retrocopies	retro_ggor_2733, retro_ggor_886,
Microcebus murinus	ENSMICG00000007485	2 retrocopies	retro_mmur_1346, retro_mmur_1481,
Macaca mulatta	ENSMMUG00000021773	3 retrocopies	retro_mmul_2351, retro_mmul_2409, retro_mmul_881,
Mus musculus	ENSMUSG00000021792	1 retrocopy	retro_mmus_2227,
Otolemur garnettii	ENSOGAG00000013638	7 retrocopies	retro_ogar_2126, retro_ogar_2435, retro_ogar_2562, retro_ogar_3327, retro_ogar_420, retro_ogar_580, retro_ogar_784,
Procavia capensis	ENSPCAG00000009696	1 retrocopy	retro_pcap_281 ,
Pongo abelii	ENSPPYG00000025862	4 retrocopies	retro_pabe_3345, retro_pabe_643, retro_pabe_738, retro_pabe_944,
Pan troglodytes	ENSPTRG00000002685	2 retrocopies	retro_ptro_2763, retro_ptro_774,
Rattus norvegicus	ENSRNOG00000011140	1 retrocopy	retro_rnor_1517,