RetrogeneDB ID: retro_mmul_2619

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: X:95628836..95629199(-)
• Located in intron of: ENSMMUG00000020862

Retrocopy information

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

Parental gene information

• Parental gene symbol: NDUFB5
• Ensembl ID: ENSMMUG00000009746
• Aliases: None
• Description: NADH dehydrogenase [Source:RefSeq peptide;Acc:NP_001253462]

Sequence

>retro_mmul_2619
TTTTTGAATTTATTGAAATTCTACATTTTGTTTACAGGGATTCCAGTGGCAATTGGCGACACTCTAGTGAATGTGTTCAT
TGGTGAAACTGAACTAGTAGAAATTCCAGAAGGCTATATCCCAGAACAATGGGAATATTATAAGCATCCTATATTGAGAT
GGATTGTCCATATTTTCTATGATGATCCTGAAAATAATTACAAAAGAACAATGGCTATCCTTCAGACTGAAACTGAAAAG
GCTGAACTGCAGATAAAGGAGCTGGAAGTACGAAGATTAATCTAGAAGAGAAGAGATGGACCCTGGTATCAATATCTGAC
CACTGATAGGGCAACTATGGATCATTCTCCAAAAGCAACTCCC

Alignment

ORF - retro_mmul_2619 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.25 %
• Parental protein coverage: 64.02 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  FLKLLRFYIALTGIPVVIIITLVNVFIGEAELAEIPEGYIPEHWEYYKHPISRWIARNFYDSPEKIYEKS
          FL.LL.FYI..TGIPV.I..TLVNVFIGE.EL.EIPEGYIPE.WEYYKHPI.RWI...FYD.PE..Y...
Retrocopy FLNLLKFYILFTGIPVAIGDTLVNVFIGETELVEIPEGYIPEQWEYYKHPILRWIVHIFYDDPENNYKRT

Parental  MAVLQIEAEKAELRLKELEVRRLMRMRGDGPWYYYETIDKELIDHSPKATP
          MA.LQ.E.EKAEL..KELEVRRL...R.DGPWY.Y.T.D....DHSPKATP
Retrocopy MAILQTETEKAELQIKELEVRRLI*KRRDGPWYQYLTTDRATMDHSPKATP

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
SRP007412_brain	0.00 RPM	40.56 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	39.51 RPM
SRP007412_cerebellum	0.00 RPM	36.87 RPM
SRP007412_heart	0.00 RPM	89.62 RPM
SRP007412_kidney	0.00 RPM	67.84 RPM
SRP007412_liver	0.00 RPM	14.25 RPM
SRP007412_testis	0.04 RPM	32.19 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_2619 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_2619 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_2619 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000002684	1 retrocopy	retro_chof_1511,
Equus caballus	ENSECAG00000000682	1 retrocopy	retro_ecab_235,
Echinops telfairi	ENSETEG00000019363	1 retrocopy	retro_etel_1110,
Homo sapiens	ENSG00000136521	2 retrocopies	retro_hsap_3127, retro_hsap_4879,
Macropus eugenii	ENSMEUG00000014166	1 retrocopy	retro_meug_1852,
Myotis lucifugus	ENSMLUG00000000999	1 retrocopy	retro_mluc_2181,
Macaca mulatta	ENSMMUG00000009746	1 retrocopy	retro_mmul_2619 ,
Monodelphis domestica	ENSMODG00000021300	1 retrocopy	retro_mdom_1105,
Nomascus leucogenys	ENSNLEG00000005842	2 retrocopies	retro_nleu_2247, retro_nleu_2558,
Pongo abelii	ENSPPYG00000014493	2 retrocopies	retro_pabe_3018, retro_pabe_3796,
Pan troglodytes	ENSPTRG00000015649	1 retrocopy	retro_ptro_3252,
Pteropus vampyrus	ENSPVAG00000004286	1 retrocopy	retro_pvam_81,
Sorex araneus	ENSSARG00000006918	1 retrocopy	retro_sara_200,
Sus scrofa	ENSSSCG00000011764	1 retrocopy	retro_sscr_193,
Ictidomys tridecemlineatus	ENSSTOG00000010557	1 retrocopy	retro_itri_1810,
Tursiops truncatus	ENSTTRG00000008910	3 retrocopies	retro_ttru_1445, retro_ttru_1719, retro_ttru_1755,