RetrogeneDB ID: retro_ptro_3252

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: X:97210702..97211213(-)
• Located in intron of: ENSPTRG00000022082

Retrocopy information

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

Parental gene information

• Parental gene symbol: NDUFB5
• Ensembl ID: ENSPTRG00000015649
• Aliases: None
• Description: Pan troglodytes NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 5, 16kDa (NDUFB5), nuclear gene encoding mitochondrial protein, mRNA. [Source:RefSeq mRNA;Acc:NM_001071806]

Sequence

>retro_ptro_3252
CTGTCTGGCCAGTGCCTTGACACTCGACTGGGATTCAGGGGCTTCCTCACCCGTGGCTTTGTTAAAGCTGTCACTCCTGT
TTAACACAGTGGAGATCATAGGAAAAAGACTATTTATCATGAAACCTTCTGGATTCTACAATGGGTGTTTTTTTAATTTA
TTGAAATTCTACATTTTGTTTATAGGGATTCCAGTGGCAATTGGAGAAACTCTAGTGAATGTATTCATTGGTGAAACTGA
ACTAGTAGGAATTCCAGAAGGCTATATCCCAGAAAAATGGGCATATTATAAGCATCCTATATTGAGATGGATTGTCCATA
CTTTCTATGATGATCCTGAAAATAATTACGAAAGAACAATGGCTATCCTTCAGACTGAAACTGAAAAGGCTGAACTGCAG
ATAAAGGAGCTGGAAGTACGAAGATTAATGTGGAAGAGAAGAGATGGACCCTGGTATCAATATGTGACCATTGATAGGGC
AATTATGGATCATTCTCCAAAAGCAACTCCC

Alignment

ORF - retro_ptro_3252 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.01 %
• Parental protein coverage: 89.95 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LSGRPLGTRLGFGGFLTRGFPKAAAPVRHSGDH-GKRLFVIRPSRFYDRRFLKLLRFYIALTGIPVAIFI
          LSG..L.TRLGF.GFLTRGF.KA..PV.HSGDH.GKRLF...PS.FY...F..LL.FYI...GIPVAI..
Retrocopy LSGQCLDTRLGFRGFLTRGFVKAVTPV*HSGDH>GKRLFIMKPSGFYNGCFFNLLKFYILFIGIPVAIGE

Parental  TLVNVFIGQAELAEIPEGYVPEHWEYYKHPISRWIARNFYDSPEKIYERTMAVLQIEAEKAELRVKELEV
          TLVNVFIG..EL..IPEGY.PE.W.YYKHPI.RWI...FYD.PE..YERTMA.LQ.E.EKAEL..KELEV
Retrocopy TLVNVFIGETELVGIPEGYIPEKWAYYKHPILRWIVHTFYDDPENNYERTMAILQTETEKAELQIKELEV

Parental  RKLMHVRGDGPWYYYETIDKELIDHSPKATP
          R.LM..R.DGPWY.Y.TID....DHSPKATP
Retrocopy RRLMWKRRDGPWYQYVTIDRAIMDHSPKATP

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	0.00 RPM	26.51 RPM
SRP007412_cerebellum	0.00 RPM	7.99 RPM
SRP007412_heart	0.00 RPM	51.41 RPM
SRP007412_kidney	0.00 RPM	36.80 RPM
SRP007412_liver	0.00 RPM	14.11 RPM
SRP007412_testis	0.00 RPM	28.66 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_3252 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_3252 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_3252 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4879
Pongo abelii	retro_pabe_3796

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 20 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,
Tursiops truncatus	ENSTTRG00000008910	3 retrocopies	retro_ttru_1445, retro_ttru_1719, retro_ttru_1755,