RetrogeneDB ID: retro_ptro_3281

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: Y:244834..245639(+)
• 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_3281
TATTCCAAGCTTGGCTATGCAGGCAACACTGAGCCATAGTTTACTATTCTTTCATGCATTTCTATCAGAGAGTCAGCACA
GGCAGTTGACAAAGCCCAAGGGAGAATGTTGAGGGGAGTTGATGAGCTTGACTTTTTCATGCAGGATGAAGCCATTGATA
AATCTATGTATGCTACAAAGTGGTCAATATGACATGGAATCACTGAAGACTGGGATATTATGGAAAGGTTCATGGAGCAA
GTAGTTTTTTAATATCTTTGAGCAGAATCTGAGGACGATTATTTTTTAATGACAACTTCCACTGAATACACTAGAAAATA
CAGAATATTTTTTCAGAAATTATGTTTGAATTATTTAATATACCAGGATTCTACATTGCAGTTCAGGAGGTACTAGCCTT
GGAAGTATCTTGGACATCTCAACAAGTGGGTGAATATATGTTAATGAGTATAGTCATTGACAAGGGAGATGAAGTCACCC
TTATTCTCCCAGTTGAAGAAGGTCATATAATTGTTAACTGCATCAATCACATCCTGATTGTAGGTGATACTATGTATTTC
ATTAAACAACTGCTAAGGGAGAGGCAGGTAGGAATCCCTCTTGAGCAGTCACTGGAGACCACAAAGCCATTAAGGAGAAA
TACTGTTACATTTGCCCTGATATAATCAAGGAATTTGCTAAGTATGATGTGGATCCCTGGAAGTGGATCAAACAGTACAC
AGGTATCAATGTGATCAACCAGGAGAAGTTCATAATAGACGTTGGTTACAAAAGATTCCTACAACCTGAAATATTTTTTT
ACCCA

Alignment

ORF - retro_ptro_3281 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.06 %
• Parental protein coverage: 64.59 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  YTKLGYAGNTEPQFIIPSCIAIRESAKVVDQAQRRVLRGVDDLDFFIGDEAIDKPTYATKWPIRHGIIED
          Y.KLGYAGNTEP.F.I.SCI.IRESA..VD.AQ.R.LRGVD.LDFF..DEAIDK..YATKW.I.HGI.ED
Retrocopy YSKLGYAGNTEP*FTILSCISIRESAQAVDKAQGRMLRGVDELDFFMQDEAIDKSMYATKWSI*HGITED

Parental  WDLMERFMEQVVFKYLRAEPEDHYFLMTEPPLNTPENREY-LAEIMFESFNVPGLYIAVQAVLALAASWT
          WD.MERFMEQVVF.YL.AE.ED.YFLMT.....T...R.....EIMFE.FN.PG.YIAVQ.VLAL..SWT
Retrocopy WDIMERFMEQVVF*YL*AESEDDYFLMTTSTEYTRKYRIF<FSEIMFELFNIPGFYIAVQEVLALEVSWT

Parental  SRQVGERTLTGIVIDSGDGVTHVIPVAEGYVIGSCIKHIPIAGRDITYFIQQLLREREVGIPPEQSLETA
          S.QVGE..L..IVID.GD.VT...PV.EG..I..CI.HI.I.G.D..YFI.QLLRER.VGIP.EQSLET.
Retrocopy SQQVGEYMLMSIVIDKGDEVTLILPVEEGHIIVNCINHILIVG-DTMYFIKQLLRERQVGIPLEQSLETT

Parental  -KAIKEKYCYICPDIVKEFAKYDVDPRKWIKQYTGINAINQKKFVIDVGYERFLGPEIFFHP
          .KAIKEKYCYICPDI.KEFAKYDVDP.KWIKQYTGIN.INQ.KF.IDVGY.RFL.PEIFF.P
Retrocopy <KAIKEKYCYICPDIIKEFAKYDVDPWKWIKQYTGINVINQEKFIIDVGYKRFLQPEIFFYP

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_3281 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_3281 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_3281 has 0 orthologous retrocopies within eutheria group .

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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,