RetrogeneDB ID: retro_pcap_21

Retrocopy location

• Organism: Hyrax (Procavia capensis)
• Coordinates: GeneScaffold_1251:70807..71518(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPCAG00000006486
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: PSMB8
• Ensembl ID: ENSPCAG00000016741
• Aliases: None
• Description: proteasome (prosome, macropain) subunit, beta type, 8 [Source:HGNC Symbol;Acc:9545]

Sequence

>retro_pcap_21
ATGGCTCTGCAGGATGTGTGCAAGTGGCAAGCCCCTGATGCCCGAGGACCGTCACCTCACCTGCCTCAGGCTGGTGGCTG
GGCCGTGCCACGGGGCTGCGATCCTCAAACCTTCCTCCGGATCCATGGTCCCAAGCTGGCTCATGGCACCACCACCTTGG
CCTTCCGCTTCTGTCACGGAGTCATTGCTGCAGCTGACACGCGCTCCTCCTGTGGCAACTACGTGGCTTGTCCGGCCTCA
TGCAAAGTTATCCCGGTGCACCGGCACCTCCTGGGCACCACCTCTGGCACTTCCGCTGACTGCGCCACGTGGTACCGAGT
GCTGCGGCGGGAGATGCGGCTGCGGGAACTGAGGGAGGGTCAGCTGCCCAGTGTGGCTAGTGCAGCCAAACTCTTGTCAG
CCATGATGTCCCGCTACCGGGGGCTGGATCTCTGTGTGGCCACTGCCCTGTGTGGTTGGGACCACTCAGGCCCTGCTCTC
TTCTACGTGTACAGCGACGGCACTCGCCTGCAGGGGGATATCTTCTCAGTGGGCTCTGGATCTCCCTATGCCTATGGCGT
GTTGGACCGGAACTACCGCTATGACATGACCACCCAGGAAGCCTATGATCTGGCTCGCCGAGCAGTGGCCCATGCCACCC
GCCGTGATGCCTATTCAGGGGGTTCTGTGGACCTATTCCATGTGCGGGAGAGTGGATGGGAGTATGTGTCT

Alignment

ORF - retro_pcap_21 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.14 %
• Parental protein coverage: 68.48 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EMAHGTTTLAFKFQHGVIVAVDSRASAGNYIATIRVNKVIEINPYLLGTMSGCAADCQYWERLLAKECRL
          ..AHGTTTLAF.F.HGVI.A.D.R.S.GNY.A.....KVI.....LLGT.SG..ADC..W.R.L..E.RL
Retrocopy KLAHGTTTLAFRFCHGVIAAADTRSSCGNYVACPASCKVIPVHRHLLGTTSGTSADCATWYRVLRREMRL

Parental  YYLRNGERISVSAASKLLSNMMCQYRGMGLSMGSMICGWDKKGPGLYYVDHNGTRLSGDMFSTGSGNSYA
          ..LR.G...SV..A.KLLS.MM..YRG..L......CGWD..GP.L.YV...GTRL.GD.FS.GSG..YA
Retrocopy RELREGQLPSVASAAKLLSAMMSRYRGLDLCVATALCGWDHSGPALFYVYSDGTRLQGDIFSVGSGSPYA

Parental  YGVMDSGYRPDLTPEEAYDLGRRAIVHATHRDSYSGGVVNMYHMKEDGW
          YGV.D..YR.D.T..EAYDL.RRA..HAT.RD.YSGG.V...H..E.GW
Retrocopy YGVLDRNYRYDMTTQEAYDLARRAVAHATRRDAYSGGSVDLFHVRESGW

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_21 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 16 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000002026	1 retrocopy	retro_amel_27,
Bos taurus	ENSBTAG00000003039	1 retrocopy	retro_btau_11,
Canis familiaris	ENSCAFG00000000829	1 retrocopy	retro_cfam_75,
Equus caballus	ENSECAG00000018887	1 retrocopy	retro_ecab_18,
Felis catus	ENSFCAG00000023131	1 retrocopy	retro_fcat_30,
Loxodonta africana	ENSLAFG00000003213	1 retrocopy	retro_lafr_65,
Microcebus murinus	ENSMICG00000015254	1 retrocopy	retro_mmur_33,
Myotis lucifugus	ENSMLUG00000013876	1 retrocopy	retro_mluc_285,
Monodelphis domestica	ENSMODG00000014366	1 retrocopy	retro_mdom_179,
Otolemur garnettii	ENSOGAG00000013830	1 retrocopy	retro_ogar_256,
Procavia capensis	ENSPCAG00000016741	1 retrocopy	retro_pcap_21 ,
Pan troglodytes	ENSPTRG00000018022	2 retrocopies	retro_ptro_1102, retro_ptro_97,
Pteropus vampyrus	ENSPVAG00000002800	1 retrocopy	retro_pvam_20,
Sus scrofa	ENSSSCG00000026951	1 retrocopy	retro_sscr_90,
Tupaia belangeri	ENSTBEG00000007794	1 retrocopy	retro_tbel_2055,
Tarsius syrichta	ENSTSYG00000007730	1 retrocopy	retro_tsyr_1639,