RetrogeneDB ID: retro_pabe_1047

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 13:41260547..41261115(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RAC3
• Ensembl ID: ENSPPYG00000008763
• Aliases: None
• Description: ras-related C3 botulinum toxin substrate 3 (rho family, small GTP binding protein Rac3) [Source:HGNC Symbol;Acc:9803]

Sequence

>retro_pabe_1047
GTGCAAGCCATCAAGTGTGTGGTGGTTGGAGATGGAGCTATAAGTAAAACTTGCCTACTAATCAGTGTTACACCCAATGC
ATTTCCCAGTGCATTATCACTATTGTCTTTGACAATTATTCTGCTGCCAATGTTAAGGTAGATGGAAAGCCAGTGAAGCT
GGGTTTATGGGATACATCTGGACAAGAAGATTATGACAGATTATGCCCCCATTCTATCTGTAAACAGACATATTTTTAAT
ATGCTTCTCTCTTGTGAGTCTTGCATCATTTGAAAATGTCTGTGCAGAGTGGCATCCTGAAATGCAGCACCATTTTCCCA
ACACTCCCATCATTCTTGTGGGAAGTAAACTTGATCTTAGTGTTGTTAAAGACACAACTGAGAAACTGAAGGAGAAGAAG
CTGACTCCCATCACCTATCTGCAGTTTTTAGCCAGGAATAAGGCGATTGGCGCTTTAAAATACCTGAAGTGCTTGGCTCT
CACATAGCGAGGGTTCAAAACAGTGTTTGACGAAGCTATCTGAGCAGTTCTCTGCCCACCTCCTGTGAAGAAGAGGAAGA
GAAAATGC

Alignment

ORF - retro_pabe_1047 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.35 %
• Parental protein coverage: 98.44 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  IQAIKCVVVGDGAVGKTCLLISYTTNAFPGEY-IPTVFDNYSA-NVMVDGKPVNLGLWDTAGQEDYDRLR
          .QAIKCVVVGDGA..KTCLLIS.T.NAFP....I..VFDNYSA.NV.VDGKPV.LGLWDT.GQEDYDRL.
Retrocopy VQAIKCVVVGDGAISKTCLLISVTPNAFPSAL<ITIVFDNYSAANVKVDGKPVKLGLWDTSGQEDYDRLC

Parental  PLS-YPQTDVFLICFSLVSPASFENVRAKWYPEVRHHCPQTPILLVGTKLDLRDDKDTIERLRDKKLAPI
          P.S.Y..TD.FLICFSLVS.ASFENV.A.W.PE..HH.P.TPI.LVG.KLDL...KDT.E.L..KKL.PI
Retrocopy PHS<YL*TDIFLICFSLVSLASFENVCAEWHPEMQHHFPNTPIILVGSKLDLSVVKDTTEKLKEKKLTPI

Parental  TYPQGLAMAREIGSVKYLECSALTQRGLKTVFDEAIRAVLCPPPVKKPGKKC
          TY.Q.LA....IG..KYL.C.ALT.RG.KTVFDEAI.AVLCPPPVKK...KC
Retrocopy TYLQFLARNKAIGALKYLKCLALT*RGFKTVFDEAI*AVLCPPPVKKRKRKC

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	13.16 RPM
SRP007412_cerebellum	0.00 RPM	8.51 RPM
SRP007412_heart	0.00 RPM	0.24 RPM
SRP007412_kidney	0.00 RPM	7.06 RPM
SRP007412_liver	0.00 RPM	1.38 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1047 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1047 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1047 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1256
Pan troglodytes	retro_ptro_3044

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 27 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000017364	1 retrocopy	retro_amel_1104,
Callithrix jacchus	ENSCJAG00000018194	1 retrocopy	retro_cjac_2687,
Cavia porcellus	ENSCPOG00000013861	1 retrocopy	retro_cpor_18,
Echinops telfairi	ENSETEG00000012902	3 retrocopies	retro_etel_1565, retro_etel_1645, retro_etel_42,
Macropus eugenii	ENSMEUG00000006196	1 retrocopy	retro_meug_201,
Otolemur garnettii	ENSOGAG00000012467	1 retrocopy	retro_ogar_2140,
Procavia capensis	ENSPCAG00000009949	1 retrocopy	retro_pcap_16,
Pongo abelii	ENSPPYG00000001755	6 retrocopies	retro_pabe_2240, retro_pabe_2461, retro_pabe_2801, retro_pabe_3215, retro_pabe_3239, retro_pabe_3295,
Pongo abelii	ENSPPYG00000008763	2 retrocopies	retro_pabe_1047 , retro_pabe_2546,
Pongo abelii	ENSPPYG00000011791	3 retrocopies	retro_pabe_1591, retro_pabe_21, retro_pabe_3818,
Pongo abelii	ENSPPYG00000012439	2 retrocopies	retro_pabe_1107, retro_pabe_2195,
Tupaia belangeri	ENSTBEG00000007272	4 retrocopies	retro_tbel_1796, retro_tbel_2564, retro_tbel_4296, retro_tbel_9,
Takifugu rubripes	ENSTRUG00000016201	1 retrocopy	retro_trub_15,