RetrogeneDB ID: retro_ptro_2007

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 4:105509725..105510693(+)
• Located in intron of: ENSPTRG00000016327

Retrocopy information

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

Parental gene information

• Parental gene symbol: ACTR3B
• Ensembl ID: ENSPTRG00000019897
• Aliases: None
• Description: None

Sequence

>retro_ptro_2007
TATTCTGAGCTTGGCTATGCAGGCAACACTGAGCCATAGTTTACTATTCTTTCTTGCATTTCTATCAGAGAGTCAGCAAA
GGTAGTTGACAAAGCCCAAAGGAGAATGTTGAGGGGAGTTGATGACCTTGACTTTTTCATACAGGATGAAGCCATTGATA
AATCTATGTATGCTACAAAGTGGTCAATATGACATGGAATCACTGAAGACTGGGATATTATGGAAAGGTTCATGGAGCAA
GTGGTTTTTAAATATCTTTGAGCAGAATCTGAGGACCATTATTTTTTAATGACAGAACTTCCACTGAATACACTAGAAAA
TACAGAGCATTTTTGCAGAAATTATGTTTGAATTATTTAATGTACCAGGATTCTACATTGCAGTTCAGGAGGTACTGGCC
TTGGCAGTATCTTGGACATCTCAACAAGTGGGTGAATGTATGTTAATGAGTATAGTCATTGACAAAGGAGATGGAGTCAC
CCATGTTCTCCCAGTTGTAGAAGGTTATGTAATTGGGAGCTGCATCAATCACATCCTGATTGTAGGTGATACTGTGTATT
TCATTCAACAGCTGCTAAGGGAGAGGGAGGTAGGAATCCCTCTTGAGCAGTCACTGGAGACCACAAAAGCCATTAAGGAG
AAATACTGTTACATTTGCCCTGATACAGTCAAGGAATTTGCTAAGCATGATGTGGATTCCTGGAAGTGGATCAAACAATA
CACAGGTATCAATGTGATCAACCAGGAGAAGTTCATAATAGATGTTGGTTACAAAAGGTTCCTGCAACCTGAAATATTTT
TTTACCCAGAGTTTGCCAACCCAGACTTTATGGAATCCATCTTGAATGTTGTTGATGAATACAAAACTGTCCCATTGATG
TGTATGGTCCACTGTATAAGAATGTTGTTCTTTCAAGGGGTTTGACCATATTCGGGGATTTGAACCTCAACTACAGAGAG
ATTTGAAG

Alignment

ORF - retro_ptro_2007 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.05 %
• Parental protein coverage: 77.75 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  YTKLGYAGNTEPQFIIPSCIAIRESAKVVDQAQRRVLRGVDDLDFFIGDEAIDKPTYATKWPIRHGIIED
          Y..LGYAGNTEP.F.I.SCI.IRESAKVVD.AQRR.LRGVDDLDFFI.DEAIDK..YATKW.I.HGI.ED
Retrocopy YSELGYAGNTEP*FTILSCISIRESAKVVDKAQRRMLRGVDDLDFFIQDEAIDKSMYATKWSI*HGITED

Parental  WDLMERFMEQVVFKYLRAEPEDHYFLMTEPPLNTPENREYL-AEIMFESFNVPGLYIAVQAVLALAASWT
          WD.MERFMEQVVFKYL.AE.EDHYFLMTE.PLNT.EN.E...AEIMFE.FNVPG.YIAVQ.VLALA.SWT
Retrocopy WDIMERFMEQVVFKYL*AESEDHYFLMTELPLNTLENTEHF>AEIMFELFNVPGFYIAVQEVLALAVSWT

Parental  SRQVGERTLTGIVIDSGDGVTHVIPVAEGYVIGSCIKHIPIAGRDITYFIQQLLREREVGIPPEQSLETA
          S.QVGE..L..IVID.GDGVTHV.PV.EGYVIGSCI.HI.I.G.D..YFIQQLLREREVGIP.EQSLET.
Retrocopy SQQVGECMLMSIVIDKGDGVTHVLPVVEGYVIGSCINHILIVG-DTVYFIQQLLREREVGIPLEQSLETT

Parental  KAIKEKYCYICPDIVKEFAKYDVDPRKWIKQYTGINAINQKKFVIDVGYERFLGPEIFFHPEFANPDFME
          KAIKEKYCYICPD.VKEFAK.DVD..KWIKQYTGIN.INQ.KF.IDVGY.RFL.PEIFF.PEFANPDFME
Retrocopy KAIKEKYCYICPDTVKEFAKHDVDSWKWIKQYTGINVINQEKFIIDVGYKRFLQPEIFFYPEFANPDFME

Parental  SISDVVDEVIQNCPI-DVRRPLYKNVVLSGGSTMF-RDFGRRLQRDLK
          SI..VVDE.....P..DV..PLYKNVVLS.G.T.F.R.F...LQRDLK
Retrocopy SILNVVDE-YKTVPL<DVYGPLYKNVVLSRGLTIF<RGFEPQLQRDLK

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	52.96 RPM
SRP007412_cerebellum	0.00 RPM	23.66 RPM
SRP007412_heart	0.00 RPM	5.74 RPM
SRP007412_kidney	0.00 RPM	11.04 RPM
SRP007412_liver	0.00 RPM	11.03 RPM
SRP007412_testis	0.00 RPM	20.66 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2007 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2007 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2007 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2966
Pongo abelii	retro_pabe_2460

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 31 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000007730	5 retrocopies	retro_chof_1134, retro_chof_1204, retro_chof_1899, retro_chof_208, retro_chof_2171,
Dasypus novemcinctus	ENSDNOG00000019288	2 retrocopies	retro_dnov_1143, retro_dnov_2539,
Homo sapiens	ENSG00000133627	7 retrocopies	retro_hsap_1676, retro_hsap_2126, retro_hsap_2540, retro_hsap_2966, retro_hsap_4334, retro_hsap_4921, retro_hsap_561,
Macropus eugenii	ENSMEUG00000004885	5 retrocopies	retro_meug_1340, retro_meug_1477, retro_meug_2105, retro_meug_330, retro_meug_899,
Nomascus leucogenys	ENSNLEG00000015688	1 retrocopy	retro_nleu_733,
Pongo abelii	ENSPPYG00000018206	1 retrocopy	retro_pabe_2460,
Pan troglodytes	ENSPTRG00000012388	2 retrocopies	retro_ptro_3118, retro_ptro_955,
Pan troglodytes	ENSPTRG00000019897	8 retrocopies	retro_ptro_1137, retro_ptro_1479, retro_ptro_2007 , retro_ptro_2952, retro_ptro_2961, retro_ptro_3052, retro_ptro_3281, retro_ptro_420,