RetrogeneDB ID: retro_dnov_2073

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_45786:7538..7889(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MYL6B
• Ensembl ID: ENSDNOG00000007592
• Aliases: None
• Description: myosin, light chain 6B, alkali, smooth muscle and non-muscle [Source:HGNC Symbol;Acc:29823]

Sequence

>retro_dnov_2073
CCTATAGAGCAGAGCAGTCAATATTATGACTTCCATAAGGACCTGACCACAGAGTTCAAGGAGGCCTTCCAGCTGTTTGA
CCAAGCGGGTCATGGCGAGATCCTCTAGAGCCAGTATGGGGATATGACAAGCCCCTGGGCCCGAAGCCCCTCGATGCCAA
GGTGCTCACGTCCTGGGGAACCTCAAGAGTGATGAGATGAGCGTGAAGGTGCTGGACTTCGGCACTTCCTGCCATGCTAC
AGACTGGCTAAGACCGAGGACCAGGGCACCTAGGAGGACAACGGGGAAGGTCTTTGAGTGTTTAACAAGGAAGGGAATTG
CATCGTTACAGGCACAGAAATCCAACGAGTC

Alignment

ORF - retro_dnov_2073 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 52.46 %
• Parental protein coverage: 67.61 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  PIDLSKVVIEFNKDQLEEFKEAFELFDRVGDGKILYSQCGDVM-RALGQNPTNAEVL-KVLGNPKSDELK
          PI..S.....F.KD...EFKEAF.LFD..G.G.IL.SQ.GD.....LG..P..A.VL..VLGN.KSDE..
Retrocopy PIEQSSQYYDFHKDLTTEFKEAFQLFDQAGHGEIL*SQYGDMT<KPLGPKPLDAKVL<HVLGNLKSDEMS

Parental  SRRVDFET-FLPMLQAVAKNRDQGTYEDYLEGLRVFDKEGNGKVMGAELRHV
          ....DF.T.FLP.....AK..DQGT.ED..EGL.VF.KEGN..V.G.E...V
Retrocopy VKVLDFGT<FLPCYR-LAKTEDQGT*EDNGEGL*VFNKEGNCIVTGTEIQRV

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
SRP012922_ascending_colon	0.00 RPM	2.92 RPM
SRP012922_cerebellum	0.00 RPM	23.78 RPM
SRP012922_heart	0.00 RPM	6.26 RPM
SRP012922_kidney	0.00 RPM	7.12 RPM
SRP012922_liver	0.00 RPM	2.94 RPM
SRP012922_lung	0.00 RPM	5.19 RPM
SRP012922_quadricep_muscle	0.00 RPM	498.48 RPM
SRP012922_spleen	0.00 RPM	4.12 RPM

ChIP-Seq

Dasypus novemcinctus was not studied using ChIP-Seq data.

EST

Dasypus novemcinctus was not studied using EST data.

TSS

Dasypus novemcinctus was not studied using FANTOM5 data.

Lab

retro_dnov_2073 was not experimentally validated.

Homology

Retrocopy orthology:

Dasypus novemcinctus 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,