RetrogeneDB ID: retro_pcap_329

Retrocopy location

• Organism: Hyrax (Procavia capensis)
• Coordinates: scaffold_38450:731..1148(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PSMB1
• Ensembl ID: ENSPCAG00000000344
• Aliases: None
• Description: proteasome (prosome, macropain) subunit, beta type, 1 [Source:HGNC Symbol;Acc:9537]

Sequence

>retro_pcap_329
ATGTACAAGCACTCCAACAACAAGGCCATGATGATTGGGGCCATCGCCACTATGCTGTCCCCATCCTCTACTCAAGGCAC
TTCTTCACCTACTATGTCTACAACATCATCAGTGGGCTCGATGAGGAAGGAAAAGGGGCAGTGTACAGTTTCGACCCTGT
GGGGTCCTACCAGAGAGATTCCTTCAAACCTGGGACTCAGCCAGTGCAATGCTACAGCCGCTGCTTGACAGCCAGGTTGG
ATTAAAGAACACGCAGAATGTGGAGCATGTACTGCTGTCTCTGGACAGGGCCCTGCACCTGGTGTGGGATGTCTTCATTT
CCACTGCTGAACGAGACGTGTACACTGGCGATGCACTAAGGATCTGCATTGTCATCCGGGAGGCATCAGTGAGGAGATTG
TGACCCTATGGAGGGAC

Alignment

ORF - retro_pcap_329 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.62 %
• Parental protein coverage: 68.97 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MYKHSNNKAMTTGAIAAMLST-ILYSRRFFPYYVYNIIGGLDEEGKGAVYSFDPVGSYQRDSFKAG-GSA
          MYKHSNNKAM..GAIA.MLS..ILYSR.FF.YYVYNII.GLDEEGKGAVYSFDPVGSYQRDSFK.G..SA
Retrocopy MYKHSNNKAMMIGAIATMLSP<ILYSRHFFTYYVYNIISGLDEEGKGAVYSFDPVGSYQRDSFKPG<DSA

Parental  SAMLQPLLDNQVGFKNMQNVEHVPLSLDRALHLVRDVFISAAERDVYTGDALRICIVTRE-GIREETVTL
          SAMLQPLLD.QVG.KN.QNVEHV.LSLDRALHLV.DVFIS.AERDVYTGDALRICIV.RE.GI.EE.VTL
Retrocopy SAMLQPLLDSQVGLKNTQNVEHVLLSLDRALHLVWDVFISTAERDVYTGDALRICIVIRE<GISEEIVTL

Parental  RRD
          .RD
Retrocopy WRD

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_329 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 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000017047	1 retrocopy	retro_amel_1066,
Canis familiaris	ENSCAFG00000004116	1 retrocopy	retro_cfam_2108,
Callithrix jacchus	ENSCJAG00000020644	1 retrocopy	retro_cjac_632,
Dasypus novemcinctus	ENSDNOG00000019502	1 retrocopy	retro_dnov_2087,
Felis catus	ENSFCAG00000031269	1 retrocopy	retro_fcat_911,
Gorilla gorilla	ENSGGOG00000022128	1 retrocopy	retro_ggor_1661,
Microcebus murinus	ENSMICG00000007469	1 retrocopy	retro_mmur_173,
Macaca mulatta	ENSMMUG00000019919	1 retrocopy	retro_mmul_1135,
Mustela putorius furo	ENSMPUG00000007150	1 retrocopy	retro_mputfur_1196,
Mus musculus	ENSMUSG00000014769	2 retrocopies	retro_mmus_1784, retro_mmus_3664,
Oryctolagus cuniculus	ENSOCUG00000007973	2 retrocopies	retro_ocun_1029, retro_ocun_620,
Procavia capensis	ENSPCAG00000000344	1 retrocopy	retro_pcap_329 ,
Pongo abelii	ENSPPYG00000017191	1 retrocopy	retro_pabe_130,
Vicugna pacos	ENSVPAG00000006517	1 retrocopy	retro_vpac_521,