RetrogeneDB ID: retro_pcap_247

Retrocopy location

• Organism: Hyrax (Procavia capensis)
• Coordinates: scaffold_2101:18628..19196(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PPA1
• Ensembl ID: ENSPCAG00000006788
• Aliases: None
• Description: pyrophosphatase (inorganic) 1 [Source:HGNC Symbol;Acc:9226]

Sequence

>retro_pcap_247
TTTACCAGCCAGAGCCATTCTGTGCCCTTTACTTCTCCGTAACCCAGTGTTCCTCACAAATGAAAAGGACAACAGGTCTC
TCCGTCCACATGATATTCCAATTTATGCAGATAAGGTTGCGTTCCACATGGTAGTTGAAGTAATACAACAGTCTGATACA
AAAAAATGGAGATTGCTACAAAGGACCCTTCAAACCCAAATTAAACAAGATGTGAAAGATAGACAACACTGTTACGTCAC
ATTCCATCACAAAGGATACATCTGGAACTGTGGTGCCCTCCCTCAGACCTGGGAAGACCTAGGACAACAGTAACAGGCAC
ACTGGCTGTTGTGGCAACAGTAACTCAATTGAGAAACATGAAATTGGAAGCAAGGAAAAGTCAAGAGGTAAAATAATCAA
TGTGAAAGTTTGGGTCAGACTGGCTATGATTTATGAAGGGGACAACAACTAGAAAGGCACTGCTGTTAATGTGAAAGACC
CTGACACAGCCAATTATAATGATATTAAAGATGTTAGACACTGAAGCCTGGGTATCTAGAAGCTCCTGTGGACTGTTTTA
GACGATTC

Alignment

ORF - retro_pcap_247 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.14 %
• Parental protein coverage: 65.74 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  FSSEERGAPFT-LEYRVFLKNKK-GQYISPF-HDIPIYADKDVFHMVVEVPRWSNA-KMEIATKDPLNPI
          F.S.....PFT.L...VFL.N.K.GQ..SP..HDIPIYADK..FHMVVEV...S...K...........I
Retrocopy FTSQSHSVPFT>LRNPVFLTNEK<GQQVSPS>HDIPIYADKVAFHMVVEVIQQSDTKKWRLLQRTLQTQI

Parental  KQDVKKGKLRYVANLFPYKGYIWNYGAIPQTWEDPG-HSDRHTGCCGDNDPIDVCDIGSKVCARGEIINV
          KQDVK.....YV...F..KGYIWN.GA.PQTWED.G..S.RHTGCCG....I....IGSK...RG.IINV
Retrocopy KQDVKDRQHCYVT--FHHKGYIWNCGALPQTWEDLG>NSNRHTGCCGNSNSIEKHEIGSKEKSRGKIINV

Parental  KVLGILAMIDEGETDWKVIAINVDDPDAANYNDIDDVKR-LKPGYLEATVDWFRRY
          KV...LAMI.EG....K..A.NV.DPD.ANYNDI.DV...LKPGYLEA.VD.FRR.
Retrocopy KVWVRLAMIYEGDNN*KGTAVNVKDPDTANYNDIKDVRH<LKPGYLEAPVDCFRRF

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_247 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 15 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000014033	1 retrocopy	retro_cfam_1040,
Cavia porcellus	ENSCPOG00000014023	1 retrocopy	retro_cpor_615,
Dasypus novemcinctus	ENSDNOG00000014861	1 retrocopy	retro_dnov_1310,
Equus caballus	ENSECAG00000018686	1 retrocopy	retro_ecab_691,
Homo sapiens	ENSG00000180817	2 retrocopies	retro_hsap_2756, retro_hsap_3267,
Loxodonta africana	ENSLAFG00000004048	1 retrocopy	retro_lafr_990,
Myotis lucifugus	ENSMLUG00000017790	1 retrocopy	retro_mluc_2469,
Macaca mulatta	ENSMMUG00000006397	1 retrocopy	retro_mmul_1540,
Nomascus leucogenys	ENSNLEG00000016098	1 retrocopy	retro_nleu_7,
Oryctolagus cuniculus	ENSOCUG00000016001	2 retrocopies	retro_ocun_1373, retro_ocun_883,
Procavia capensis	ENSPCAG00000006788	1 retrocopy	retro_pcap_247 ,
Pongo abelii	ENSPPYG00000029405	1 retrocopy	retro_pabe_37,
Pan troglodytes	ENSPTRG00000002585	2 retrocopies	retro_ptro_1864, retro_ptro_2210,
Tupaia belangeri	ENSTBEG00000008947	3 retrocopies	retro_tbel_3560, retro_tbel_3561, retro_tbel_848,
Tarsius syrichta	ENSTSYG00000005511	1 retrocopy	retro_tsyr_1856,