RetrogeneDB ID: retro_pcap_385

Retrocopy location

• Organism: Hyrax (Procavia capensis)
• Coordinates: scaffold_62956:16168..16442(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MGST3
• Ensembl ID: ENSPCAG00000015774
• Aliases: None
• Description: microsomal glutathione S-transferase 3 [Source:HGNC Symbol;Acc:7064]

Sequence

>retro_pcap_385
GTGACTGTCCTCTCTAAGGAATATGGCTTCATGGTTCCAACTGGTGCCGCCAGCTTCATAAGGATAACTCATTTAGCCAT
CCATGTTGCCAAAGCCAGCGAGAAACACAACGCGGAGCATCCTGTCATGAGTTCCATGGACCCAGAAAATGGGCACTTCT
TCAGCTGCACTCAGTGAGCCCACAGAAGATGTTGGAAGTATGTTCTCCCTCTGATTTTTTCTAACTGTAGGAGGTGTTTA
TCACCTGTGTATAGTTTCTGGTTTGGGGGTGGCT

Alignment

ORF - retro_pcap_385 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.45 %
• Parental protein coverage: 59.48 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MTVLSKEYGFVLLTGAASFIMVTHLAVNVS-ARKRYKVEYPTMYSTDPEHGHLFNCIQRAH-QNTLEVYP
          .TVLSKEYGF...TGAASFI..THLA..V..A......E.P.M.S.DPE.GH.F.C.Q.AH.Q..LEV..
Retrocopy VTVLSKEYGFMVPTGAASFIRITHLAIHVAKASEKHNAEHPVMSSMDPENGHFFSCTQ*AH<QKMLEVCS

Parental  P-FLFFLAIGGVYHPRTASGLGLA
          P...FFL..GGVYH....SGLG.A
Retrocopy P<L*FFLTVGGVYHLCIVSGLGVA

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_385 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 10 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006658	1 retrocopy	retro_amel_1210,
Canis familiaris	ENSCAFG00000013353	1 retrocopy	retro_cfam_35,
Choloepus hoffmanni	ENSCHOG00000012723	2 retrocopies	retro_chof_1872, retro_chof_356,
Echinops telfairi	ENSETEG00000003507	3 retrocopies	retro_etel_1328, retro_etel_1527, retro_etel_1544,
Mustela putorius furo	ENSMPUG00000003817	1 retrocopy	retro_mputfur_1251,
Mus musculus	ENSMUSG00000026688	1 retrocopy	retro_mmus_2709,
Oryctolagus cuniculus	ENSOCUG00000010376	1 retrocopy	retro_ocun_270,
Procavia capensis	ENSPCAG00000015774	2 retrocopies	retro_pcap_385 , retro_pcap_393,
Rattus norvegicus	ENSRNOG00000004245	1 retrocopy	retro_rnor_195,
Tupaia belangeri	ENSTBEG00000005299	2 retrocopies	retro_tbel_2989, retro_tbel_752,