RetrogeneDB ID: retro_ptro_2406

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 6:159673031..159673306(+)
• Located in intron of: ENSPTRG00000018738

Retrocopy information

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

Parental gene information

• Parental gene symbol: HSPE1
• Ensembl ID: ENSPTRG00000012774
• Aliases: None
• Description: None

Sequence

>retro_ptro_2406
CAGGCACTTGGAAAGTTTCTTTCACTCTGAGTTTTGGTTGAAAGGAAAGCACCCAAAACTATAGCCAAAGGAGTCGTCAT
ACTTCCAGAAAAATCTCAAAAGTATTGCAAGCAACAGTAGTAGCTATTGGATCAGACCTTAAAGGTGGGGGTGGAAAGAT
TTAACCAGTTAGCTCAGTGAAAGTTAAAGTTTTCCCAGAATATGGAGGCAGCAAAGTAGTTCTAGACAAAGGTCATTTCT
TATTTAGAGGTGGTGCCATTCTTGGAAAGTGTGTA

Alignment

ORF - retro_ptro_2406 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58. %
• Parental protein coverage: 96.08 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  QAFRKFLPLFDRVLVERSAAETVTKGGIML-PEKSQGKVLQATVVAVGSGSKGKGGEIQPV-SVKVGDKV
          QA..KFL.L...VLVER.A..T..K.G..........KVLQATVVA.GS..KG.GG.I.PV.SVKV....
Retrocopy QALGKFLSL*--VLVERKAPKTIAK-GVVI<TSRKISKVLQATVVAIGSDLKGGGGKI*PVSSVKV---K

Parental  LLPEYGGTKVVLDDKDYFLFRDGDILGKYV
          ..PEYGG.KVVL.DK..FLFR.G.ILGK.V
Retrocopy VFPEYGGSKVVL-DKGHFLFRGGAILGKCV

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	0.09 RPM	33.00 RPM
SRP007412_cerebellum	0.18 RPM	43.05 RPM
SRP007412_heart	0.06 RPM	125.59 RPM
SRP007412_kidney	0.16 RPM	129.40 RPM
SRP007412_liver	0.07 RPM	156.86 RPM
SRP007412_testis	0.00 RPM	45.63 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2406 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2406 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2406 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3540

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 53 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000013246	27 retrocopies	retro_dnov_1088, retro_dnov_1117, retro_dnov_1214, retro_dnov_1375, retro_dnov_1391, retro_dnov_1405, retro_dnov_1412, retro_dnov_1428, retro_dnov_1445, retro_dnov_1546, retro_dnov_1647, retro_dnov_1652, retro_dnov_1686, retro_dnov_1821, retro_dnov_2176, retro_dnov_2291, retro_dnov_2413, retro_dnov_2569, retro_dnov_2625, retro_dnov_2652, retro_dnov_418, retro_dnov_481, retro_dnov_483, retro_dnov_490, retro_dnov_524, retro_dnov_554, retro_dnov_966,
Macaca mulatta	ENSMMUG00000010491	1 retrocopy	retro_mmul_344,
Pongo abelii	ENSPPYG00000025876	1 retrocopy	retro_pabe_179,
Pan troglodytes	ENSPTRG00000012774	17 retrocopies	retro_ptro_1033, retro_ptro_1117, retro_ptro_1152, retro_ptro_1591, retro_ptro_1752, retro_ptro_1907, retro_ptro_1908, retro_ptro_2343, retro_ptro_2406 , retro_ptro_2485, retro_ptro_2847, retro_ptro_287, retro_ptro_374, retro_ptro_667, retro_ptro_726, retro_ptro_786, retro_ptro_926,
Sus scrofa	ENSSSCG00000016078	7 retrocopies	retro_sscr_103, retro_sscr_1059, retro_sscr_106, retro_sscr_1088, retro_sscr_294, retro_sscr_298, retro_sscr_401,