RetrogeneDB ID: retro_pabe_3018

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 6:154733381..154733705(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NDUFB5
• Ensembl ID: ENSPPYG00000014493
• Aliases: None
• Description: NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 5, 16kDa [Source:HGNC Symbol;Acc:7700]

Sequence

>retro_pabe_3018
GCTCCTGTTCCACACAGTGGAGACCATGGGAAAAGGCTATTTGTCATCAAATTCTATGACAGGCATTTTTTGAAGTTATT
GAGATTCTACATTGCATTAACTGGGATTCCAGTAGCAATTTTCATAACTCTGGTGAATGTATTCATTGGTCAAGCTGAAC
TAGCAGAAATTCCAGAAGGCTATATCCCAGAACACTGGGAATATTATAAGCATCTCATATTGAGAAATTATGGGATTGCC
CATAATTTCTATGATAGTCCTGAAAAGACGTATGAAAGAACAATGGCCATCCTTCAGATTGAAGCTGAAAAGGCTGAATT
ACGG

Alignment

ORF - retro_pabe_3018 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.68 %
• Parental protein coverage: 74.15 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  APVRHSGAHGKRLFFIRPSRFYDRRFLKLLRFYIALTGIPVAIFITLVNVFIGQAELAEIPEGYIPEHWE
          APV.HSG.HGKRLF.I....FYDR.FLKLLRFYIALTGIPVAIFITLVNVFIGQAELAEIPEGYIPEHWE
Retrocopy APVPHSGDHGKRLFVIK---FYDRHFLKLLRFYIALTGIPVAIFITLVNVFIGQAELAEIPEGYIPEHWE

Parental  YYKHPISR--WIARNFYDSPEKIYERTMAVLQIEAETAELR
          YYKH.I.R...IA.NFYDSPEK.YERTMA.LQIEAE.AELR
Retrocopy YYKHLILRNYGIAHNFYDSPEKTYERTMAILQIEAEKAELR

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_prefrontal_cortex	0.44 RPM	11.06 RPM
SRP007412_cerebellum	0.12 RPM	10.46 RPM
SRP007412_heart	1.08 RPM	25.29 RPM
SRP007412_kidney	0.50 RPM	17.60 RPM
SRP007412_liver	0.67 RPM	11.69 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3018 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3018 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3018 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,