RetrogeneDB ID: retro_pcap_240

Retrocopy location

• Organism: Hyrax (Procavia capensis)
• Coordinates: scaffold_206330:1..258(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CHP1
• Ensembl ID: ENSPCAG00000005419
• Aliases: None
• Description: calcineurin-like EF-hand protein 1 [Source:HGNC Symbol;Acc:17433]

Sequence

>retro_pcap_240
AACAGATCAGAATCACTCAACGGCCAAAGCAACAAACTGCTTTTTGCTTTTTGACCATATTATTTGGGTAAAGACAAGAG
CTCCTGAGACGAGCTGTTACAGTGCTACCCAGGATGACTGAACTGACTGTCTTACATGAGCACCTGGGGAGCACTGCAGA
CAGGTCCATCCAGGAGGATGATGGAGATGGGGCCAGCATCCTATCAGCCACAGAATTTCTTAAGGTTTTGGAAAAGGTGG
ACTTAAAAGCAGCTATG

Alignment

ORF - retro_pcap_240 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.95 %
• Parental protein coverage: 50.58 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  NGPEPLNSRSNKLHFAFRLYDLDKDDKISRDELLQ-VLRMMVGVNISDEQLGSIADRTIQEADQDGDSAI
          N..E.LN..SNKL.FAF..Y.L.KD.K.S.DELLQ.VL..M.......E.LGS.ADR.IQE.D.DG.S..
Retrocopy NRSESLNGQSNKLLFAF*PYYLGKD-KSS*DELLQ<VLPRMTELTVLHEHLGSTADRSIQEDDGDGASIL

Parental  SFTEFVKVLEKVDVEQKM
          S.TEF.KVLEKVD....M
Retrocopy SATEFLKVLEKVDLKAAM

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_240 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 20 parental genes, and 36 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000027173	1 retrocopy	retro_btau_1785,
Canis familiaris	ENSCAFG00000009525	1 retrocopy	retro_cfam_2136,
Callithrix jacchus	ENSCJAG00000020761	1 retrocopy	retro_cjac_2396,
Cavia porcellus	ENSCPOG00000010577	2 retrocopies	retro_cpor_1224, retro_cpor_726,
Equus caballus	ENSECAG00000019751	1 retrocopy	retro_ecab_1099,
Felis catus	ENSFCAG00000006346	1 retrocopy	retro_fcat_1964,
Homo sapiens	ENSG00000187446	2 retrocopies	retro_hsap_3334, retro_hsap_3541,
Gorilla gorilla	ENSGGOG00000007312	2 retrocopies	retro_ggor_1293, retro_ggor_2392,
Loxodonta africana	ENSLAFG00000014743	3 retrocopies	retro_lafr_221, retro_lafr_795, retro_lafr_838,
Macaca mulatta	ENSMMUG00000017092	2 retrocopies	retro_mmul_1809, retro_mmul_2088,
Mus musculus	ENSMUSG00000014077	4 retrocopies	retro_mmus_1458, retro_mmus_2094, retro_mmus_3133, retro_mmus_3469,
Nomascus leucogenys	ENSNLEG00000003465	4 retrocopies	retro_nleu_1678, retro_nleu_2269, retro_nleu_2608, retro_nleu_2609,
Oryctolagus cuniculus	ENSOCUG00000013832	1 retrocopy	retro_ocun_68,
Otolemur garnettii	ENSOGAG00000013099	2 retrocopies	retro_ogar_2442, retro_ogar_628,
Procavia capensis	ENSPCAG00000005419	1 retrocopy	retro_pcap_240 ,
Pongo abelii	ENSPPYG00000006370	2 retrocopies	retro_pabe_2749, retro_pabe_2925,
Pan troglodytes	ENSPTRG00000006942	2 retrocopies	retro_ptro_2144, retro_ptro_2407,
Pteropus vampyrus	ENSPVAG00000003150	1 retrocopy	retro_pvam_1207,
Rattus norvegicus	ENSRNOG00000004742	2 retrocopies	retro_rnor_2034, retro_rnor_2223,
Ictidomys tridecemlineatus	ENSSTOG00000014503	1 retrocopy	retro_itri_227,