RetrogeneDB ID: retro_pcap_242

Retrocopy location

• Organism: Hyrax (Procavia capensis)
• Coordinates: scaffold_20739:22009..22407(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MYL6B
• Ensembl ID: ENSPCAG00000005927
• Aliases: None
• Description: myosin, light chain 6B, alkali, smooth muscle and non-muscle [Source:HGNC Symbol;Acc:29823]

Sequence

>retro_pcap_242
CAGCTGTTTGATCCAATGGGTGATGGCAACATCGTGTACAGCCAGGATGGGACTTGATGAGGGCCCTGGGCCAGAACTGC
ACTAGTGCAAAAGTGCTGAAGGTCCTGGGGAACCCAAAAAGTGGTGAGATGAATGTGAAGGTGCTGAATTTGAGCACTTC
CTGCCCTTTCTGCACACTGTGGCCAAGAACAAGGACCAGGGCACCTATCAGGACTGTGTCAAAGGCCTTCAGGTGTTTGA
CAAAAAAGGGAATGGCCCCATCATGGACACTGAAATCAGCATGTTCTTGTCACACCAGGTGTGAAGACAACAGAGGAAGA
AGTTGAGATGCTGGTGGCTGGGCACAAGACAGCAGTGGTCATATCAGCTGTGAGAAGCTCATCCATATGGTGCTGAAT

Alignment

ORF - retro_pcap_242 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 55.07 %
• Parental protein coverage: 64.56 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  ELFDRVGDGKILYGQCG-DVMRA-GQNPTNAEVLKVLGNPKSDEL-KSRRVDFETFLPMLQAVAKNRDQG
          .LFD..GDG.I.Y.Q.G.D.MRA.GQN.T.A.VLKVLGNPKS.E........FE.FLP.L..VAKN.DQG
Retrocopy QLFDPMGDGNIVYSQDG<DLMRALGQNCTSAKVLKVLGNPKSGEM<ECEGAEFEHFLPFLHTVAKNKDQG

Parental  NYQDYLEGLRVFDKEGNGKVMGAEL-RHVLTTLGERLTEEEVESILAGH-EDINGCINYEAFLKHILS
          .YQD...GL.VFDK.GNG..M..E...HVL.T.G...TEEEVE...AGH..D..G.I..E......L.
Retrocopy TYQDCVKGLQVFDKKGNGPIMDTEI<QHVLVTPGVKTTEEEVEMLVAGH<QDSSGHISCEKLIHMVLN

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_242 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 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000000110	1 retrocopy	retro_cfam_1894,
Callithrix jacchus	ENSCJAG00000011620	3 retrocopies	retro_cjac_113, retro_cjac_2566, retro_cjac_2848,
Dasypus novemcinctus	ENSDNOG00000007592	1 retrocopy	retro_dnov_2073,
Homo sapiens	ENSG00000196465	1 retrocopy	retro_hsap_2383,
Gorilla gorilla	ENSGGOG00000003277	2 retrocopies	retro_ggor_1808, retro_ggor_2233,
Loxodonta africana	ENSLAFG00000012658	1 retrocopy	retro_lafr_734,
Macaca mulatta	ENSMMUG00000005214	1 retrocopy	retro_mmul_962,
Nomascus leucogenys	ENSNLEG00000026948	1 retrocopy	retro_nleu_369,
Oryctolagus cuniculus	ENSOCUG00000017368	1 retrocopy	retro_ocun_374,
Otolemur garnettii	ENSOGAG00000001521	3 retrocopies	retro_ogar_1918, retro_ogar_3179, retro_ogar_680,
Procavia capensis	ENSPCAG00000005927	2 retrocopies	retro_pcap_223, retro_pcap_242 ,
Pongo abelii	ENSPPYG00000004646	1 retrocopy	retro_pabe_2150,
Pan troglodytes	ENSPTRG00000023043	2 retrocopies	retro_ptro_1741, retro_ptro_2579,
Rattus norvegicus	ENSRNOG00000028837	2 retrocopies	retro_rnor_1432, retro_rnor_216,