RetrogeneDB ID: retro_pabe_2460

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 4:107423537..107424502(+)
• Located in intron of: ENSPPYG00000014969

Retrocopy information

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

Parental gene information

• Parental gene symbol: ACTR3B
• Ensembl ID: ENSPPYG00000018206
• Aliases: None
• Description: ARP3 actin-related protein 3 homolog B (yeast) [Source:HGNC Symbol;Acc:17256]

Sequence

>retro_pabe_2460
TATTCTGAGCTTGGCCATGCAGGCAACACTGAGCCATAGTTTACTATTCTTTCATGCATTTCTATCAGAGAGTCAGCAAA
GGTAGTTGACAAAGCCCAAAGGAGAATGTTGAGGGGAGTTGATGACCTTGACTTTTTCATACAGGATGAAGCCATTGAGA
AATCTATGTATGCTTCAAAGTGGTCAATATGACATGGAATCACTGAAGACTGGGATATTATGGAAAGGTTCATGGAGCAA
GTGGTTTTTAAATATCTTTGAGCAGAATCTGAGGACCATTATTTTTTAATGACAGAACTTCCACTGAATACACTAGAAAA
TACAGAGCATTTTTGCAGAAATTATGTTTGAATTATTTAATGTACCAGGATTCTACATTGCAATTCAGGAGGTACTGGCC
TTGGCAGTATCTTGGACATCTCAACAAGTGAGTGAATGTATGTTAATGAGTATAGTCATTGACAAAGGAGATGGAGTCAC
CCATGTTCTCCCAGTTGTAGGTTATGTAATTGGGAGCTGCATCAATCACATCCTGATTGTAGGTGATACTGTGTATTTCA
TTCAACAGCTGCTAAGGGAGAGGGAGGTAGGAATCCCTCTTGAGCAGTCACTGGAGACCACAAAAGCCATTAAGGAGAAA
TACTGTTACATTTGCCCGGATATAGTCAAGGAATTTGCTAAGTACGATGTGAATTCCTGGAAGTGGATCAAACAATACAC
AGGTATCAATGTGATCAACCAGGAGAAGTTCATAATAGATGTTGGTTACAAAAGGTTCCCGCAACTTGAAATATTTTTTT
ACCCAGAGTTTGCCAACCCAGACTTTATGGAATCCATCTTGAATGTTGTTGATGAATACAAAACTGTCCCATTGATGTGC
ATCGTCCACTGTATAAGACTGTTGTTCTTTCAAGGGGTTTGACCATATTCGGGGATTTGAACCTCAACTACAGAGAGATT
TGAAG

Alignment

ORF - retro_pabe_2460 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.91 %
• Parental protein coverage: 77.75 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  YTKLGYAGNTEPQFIIPSCIAIRESAKVVDQAQRRVLRGVDDLDFFIGDEAIDKPTYATKWPIRHGIIED
          Y..LG.AGNTEP.F.I.SCI.IRESAKVVD.AQRR.LRGVDDLDFFI.DEAI.K..YA.KW.I.HGI.ED
Retrocopy YSELGHAGNTEP*FTILSCISIRESAKVVDKAQRRMLRGVDDLDFFIQDEAIEKSMYASKWSI*HGITED

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

Parental  SRQVGERTLTGIVIDSGDGVTHVIPVAEGYVIGSCIKHIPIAGRDITYFIQQLLREREVGIPPEQSLETA
          S.QV.E..L..IVID.GDGVTHV.PV..GYVIGSCI.HI.I.G.D..YFIQQLLREREVGIP.EQSLET.
Retrocopy SQQVSECMLMSIVIDKGDGVTHVLPVV-GYVIGSCINHILIVG-DTVYFIQQLLREREVGIPLEQSLETT

Parental  KAIKEKYCYICPDIVKEFAKYDVDPRKWIKQYTGINAINQKKFVIDVGYERFLGPEIFFHPEFANPDFME
          KAIKEKYCYICPDIVKEFAKYDV...KWIKQYTGIN.INQ.KF.IDVGY.RF...EIFF.PEFANPDFME
Retrocopy KAIKEKYCYICPDIVKEFAKYDVNSWKWIKQYTGINVINQEKFIIDVGYKRFPQLEIFFYPEFANPDFME

Parental  SISDVVDEVIQNCPI-DVRRPLYKNVVLSGGSTMF-RDFGRRLQRDLK
          SI..VVDE.....P..DV.RPLYK.VVLS.G.T.F.R.F...LQRDLK
Retrocopy SILNVVDE-YKTVPL<DVHRPLYKTVVLSRGLTIF<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	78.02 RPM
SRP007412_cerebellum	0.00 RPM	28.58 RPM
SRP007412_heart	0.00 RPM	9.90 RPM
SRP007412_kidney	0.03 RPM	11.30 RPM
SRP007412_liver	0.00 RPM	8.75 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2460 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2460 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2460 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2966
Pan troglodytes	retro_ptro_2007

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 30 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	ENSPPYG00000012798	1 retrocopy	retro_pabe_3647,
Pongo abelii	ENSPPYG00000018206	1 retrocopy	retro_pabe_2460 ,
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,