RetrogeneDB ID: retro_pcap_37

Retrocopy location

• Organism: Hyrax (Procavia capensis)
• Coordinates: GeneScaffold_1733:13992..14338(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSPCAG00000008816
• Aliases: None
• Description: None

Sequence

>retro_pcap_37
CCATCCACTGCTCTGCCCTCCCAACATCTGTCCAATGCCTCATCTGCCTTCGGCATATAGGAGAATTTCTCCCTGCAAGC
CAGGTACACCTTCCCTTAGTGAAACCAGACCTGCCTGGTGCAATACAGGTGGAGGCTTGAAGATAGCAAGAAATTTGATT
CCCGCAGGGACAAAAACAAGCCCTTTAATTTTATGCTAAGCAAGCAGCGGGTGATCCAAGACTAGGAAAAGGGGTTGCCC
AGATGAATTCGAATCAAACAGCCCAATGGACTTTTCTCAAGACTATGCTTATGGTACCACAGGGTACTCAGACATCATCC
CACCAATTGCCACTCTTGTCCTTAAT

Alignment

ORF - retro_pcap_37 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 50.85 %
• Parental protein coverage: 79.31 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  PPVAPPAASVAAAAMGVQV-ETISPGDGRTFPKRGQTCVVHYTGMLEDGKKFDSSRDRNKPFKFMLGKQE
          P..A.P......A.......E..S.....TFP...QTC.V.Y...LED.KKFDS.RD.NKPF.FML.KQ.
Retrocopy PSTALPSQHLSNASSAFGI*ENFSLQARYTFP**NQTCLVQYRWRLEDSKKFDSRRDKNKPFNFMLSKQR

Parental  VIRGWE-EGVAQMSVGQRAKLT-ISPDYAYGATGHPGIIPPNATLVFD
          VI...E..GVAQM...Q.A..T..S.DYAYG.TG...IIPP.ATLV..
Retrocopy VIQD*E<KGVAQMNSNQTAQWT<FSQDYAYGTTGYSDIIPPIATLVLN

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_37 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 14 parental genes, and 39 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000008303	4 retrocopies	retro_btau_1220, retro_btau_1265, retro_btau_128, retro_btau_1760,
Ciona savignyi	ENSCSAVG00000006859	1 retrocopy	retro_csav_11,
Dasypus novemcinctus	ENSDNOG00000005868	16 retrocopies	retro_dnov_1289, retro_dnov_1577, retro_dnov_1666, retro_dnov_2236, retro_dnov_228, retro_dnov_2404, retro_dnov_2418, retro_dnov_2544, retro_dnov_2589, retro_dnov_263, retro_dnov_584, retro_dnov_621, retro_dnov_670, retro_dnov_684, retro_dnov_707, retro_dnov_937,
Homo sapiens	ENSG00000088832	1 retrocopy	retro_hsap_1198,
Gorilla gorilla	ENSGGOG00000001729	3 retrocopies	retro_ggor_1494, retro_ggor_2344, retro_ggor_933,
Macaca mulatta	ENSMMUG00000015996	1 retrocopy	retro_mmul_10,
Monodelphis domestica	ENSMODG00000019554	2 retrocopies	retro_mdom_151, retro_mdom_733,
Mus musculus	ENSMUSG00000032966	1 retrocopy	retro_mmus_1293,
Procavia capensis	ENSPCAG00000008816	2 retrocopies	retro_pcap_289, retro_pcap_37 ,
Procavia capensis	ENSPCAG00000011316	2 retrocopies	retro_pcap_454, retro_pcap_78,
Rattus norvegicus	ENSRNOG00000008822	1 retrocopy	retro_rnor_453,
Sus scrofa	ENSSSCG00000007188	1 retrocopy	retro_sscr_98,
Tursiops truncatus	ENSTTRG00000003547	3 retrocopies	retro_ttru_1227, retro_ttru_802, retro_ttru_904,
Vicugna pacos	ENSVPAG00000011511	1 retrocopy	retro_vpac_171,