RetrogeneDB ID: retro_ocun_374

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 1:71575752..71576202(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MYL6B
• Ensembl ID: ENSOCUG00000017368
• Aliases: None
• Description: myosin, light chain 6B, alkali, smooth muscle and non-muscle [Source:HGNC Symbol;Acc:29823]

Sequence

>retro_ocun_374
AGGCCCTGAGAAAACCCTATGGATCACTGCAAAACAGCACCTGAGTTTAACAAGGACAAGATGGCAAAGTTCAAGGAGGC
CTTCCAGCTATCTGACCCAGTGAGTTATGACAAGATCCTATAAAGCTGGTGTCAAAAGGTGATGAAGGCCCTGTATCAGA
ACCACAACAAATCCAAGGAGCTCAAGATCCTGGAGGACACCAGGAGTGATGAGCTGAAATCCCAGAGTATGGATTCTGTG
ACTTGCCTGTCTATGCACTAAGCAGTGGCCAAGAATCAAGACTAAGGACCACATGATGGCTACCTACAGGAGTTTTAGGT
GTTTGACAAGGAGAGGAACAGCAAAGTCATAGAAGCAGAGCTCAGACACAGCCTTACCACCCCAAGAGATGACGAGGAGG
TGGTGAAAACTGCTCTAACAGGATGTGAGGACAGCAATGGCTCTATCAAC

Alignment

ORF - retro_ocun_374 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 53.29 %
• Parental protein coverage: 72.04 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KPQEPPVDLSKVVIEFNKDQLEEFKEAFELFDRVGDGKILYSQCGDVMRALGQNPTNAEVLKVLGNPKSD
          .P.E.P.D..K...EFNKD....FKEAF.L.D.V...KIL.S.C..VM.AL.QN......LK.L....SD
Retrocopy RP*ENPMDHCKTAPEFNKDKMAKFKEAFQLSDPVSYDKIL*SWCQKVMKALYQNHNKSKELKILEDTRSD

Parental  ELKSRRVDFETFLPMLQAVAKNRDQGSYDDYLEGLRVFDKEGNGKVMGAELRHVLTTLGEKMTEEEVETV
          ELKS...D..T.L.M..AVAKN.D.G..D.YL....VFDKE.N.KV..AELRH.LTT......EE.V.T.
Retrocopy ELKSQSMDSVTCLSMH*AVAKNQD*GPHDGYLQEF*VFDKERNSKVIEAELRHSLTT--PRDDEEVVKTA

Parental  LAGHEDSNGCIN
          L.G.EDSNG.IN
Retrocopy LTGCEDSNGSIN

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP017611_brain	0.06 RPM	77.43 RPM
SRP017611_kidney	0.20 RPM	7.20 RPM
SRP017611_liver	0.00 RPM	3.24 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_374 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_374 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_374 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 23 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 ,
Oryctolagus cuniculus	ENSOCUG00000017371	1 retrocopy	retro_ocun_1300,
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,