RetrogeneDB ID: retro_ptro_1479

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 22:15349980..15350948(+)
• Located in intron of: None

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_1479
TATTCCGAGCTTGGCTATACAGGCAACACTGAGCCATAGTTTACTATTCTTTCTTGCATTTCTATCAGAGAGTCAGCAAA
GGTAGTTGACAAAGCCCAAGGGAGAATGTTGAGGGGAGTTGATGACCTTGACTTTTTCATACAGGATGAAGCCATTGATA
AATCTATGTATGCTACAAAGTGGCCAATATGACATGGAATCACTGAAGACTGGGATATTATGGAAAGGTTCATGGAGCAA
GTGGTTTTTAAATATCTTTGAGCAGAATCTGAGGGCCATTATTTTTTAATGACAGAACTTCCACTGAATACACTAGAAAA
TACAGAGCATTTTTGCAGAAATTATGTTTGAATTATTTAATGTACCAGGATTCTACATTGCAGTTCAGGAGGTACTAGCC
TTGGAAGTATCTTGGACATCTCAACAAGTGGGTGAATATATGTTAATGAGTATAGTCATTGACAAAGGAGATGGAGTCAC
CCTTGTTCTCCCAGTTGTAGAAGGTTATGTAATTGGGAGCTGCATCAATCACATCCTGATTGTAGGTGATACTGTGTATT
TCATTCAACAGCTGCTAAGGGAGAGGGAGGTAGGAATCCCTCTTGAGCAGTCACTGGAGACCACAAAAGCCATTAAGGAG
AAATACTGTTACATTTGCCCTGATATAGTCAAGGAATTTGCTAAGTATGATGTGGATCCCTGGAAGTGGATCAAACAGTA
CACAGGTATCAATGTGATCAACCAGGAGAAGTTCATAATAGACGTTGGTTACAAAAGTTTCCTGCAACCTGAAATATTTT
TTTACCCAGAGTTTGCCAACCCAGACTTTATGGAATCCATCTTGAATGTTGTTGATGAATACAAAACTGTCCCATTGATG
CGCATTGTCCACTGTATAAGAATGTTGTTCTTTCAAGGGGTTTGACCATATTCAGGGATTTGAATCTCAACTACAGAGAG
ATTTGAAG

Alignment

ORF - retro_ptro_1479 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.44 %
• Parental protein coverage: 77.75 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  YTKLGYAGNTEPQFIIPSCIAIRESAKVVDQAQRRVLRGVDDLDFFIGDEAIDKPTYATKWPIRHGIIED
          Y..LGY.GNTEP.F.I.SCI.IRESAKVVD.AQ.R.LRGVDDLDFFI.DEAIDK..YATKWPI.HGI.ED
Retrocopy YSELGYTGNTEP*FTILSCISIRESAKVVDKAQGRMLRGVDDLDFFIQDEAIDKSMYATKWPI*HGITED

Parental  WDLMERFMEQVVFKYLRAEPEDHYFLMTEPPLNTPENREYL-AEIMFESFNVPGLYIAVQAVLALAASWT
          WD.MERFMEQVVFKYL.AE.E.HYFLMTE.PLNT.EN.E...AEIMFE.FNVPG.YIAVQ.VLAL..SWT
Retrocopy WDIMERFMEQVVFKYL*AESEGHYFLMTELPLNTLENTEHF>AEIMFELFNVPGFYIAVQEVLALEVSWT

Parental  SRQVGERTLTGIVIDSGDGVTHVIPVAEGYVIGSCIKHIPIAGRDITYFIQQLLREREVGIPPEQSLETA
          S.QVGE..L..IVID.GDGVT.V.PV.EGYVIGSCI.HI.I.G.D..YFIQQLLREREVGIP.EQSLET.
Retrocopy SQQVGEYMLMSIVIDKGDGVTLVLPVVEGYVIGSCINHILIVG-DTVYFIQQLLREREVGIPLEQSLETT

Parental  KAIKEKYCYICPDIVKEFAKYDVDPRKWIKQYTGINAINQKKFVIDVGYERFLGPEIFFHPEFANPDFME
          KAIKEKYCYICPDIVKEFAKYDVDP.KWIKQYTGIN.INQ.KF.IDVGY..FL.PEIFF.PEFANPDFME
Retrocopy KAIKEKYCYICPDIVKEFAKYDVDPWKWIKQYTGINVINQEKFIIDVGYKSFLQPEIFFYPEFANPDFME

Parental  SISDVVDEVIQNCPI-DVRRPLYKNVVLSGGSTMFRD-FGRRLQRDLK
          SI..VVDE.....P..D...PLYKNVVLS.G.T.FRD.F...LQRDLK
Retrocopy SILNVVDE-YKTVPL<DAHCPLYKNVVLSRGLTIFRD<FESQLQRDLK

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_1479 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1479 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1479 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2540

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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,