RetrogeneDB ID: retro_pabe_2546

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 4:111936045..111936610(-)
• 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_2546
ATGCAGGCCATCAAGGGTGTGGTGGTGGGAGACGGAGCTGTAGGTGAAATTTGCCTACTGATCAGTTACGCAACCAATGC
ATTTCCTGGAGAATATATCCCTACTGTCTTTGACAATTATTCTGCCAATGTTTTGGTAGATGGAAAACCGGTGAATCTGG
GCTTATGGGATACAGTTGCTCAAGAAGATTATGACAGATTATGCCGCCTATCCTATCCGCAAACAGATATGTTCTTAATT
TGCTTTTCCCTTGTGAGTCCTGCATCATTTGAAAGTGTCAGTGCAAAGTGGTATCCTGAGGTGCGGCACCACTGTCCCAA
CACTCCCATCATCCTATTGGGAACTAAACTTGAACTTAGGGATGATAAAGACACGATCGAGAAACTGAAGGAGAAGAAGC
TGACTCCCATCACCTATCTGCAGGGTCTAGCCATGGCTAAGGAGATTGGTGCTGTAAAATACCTGAAGTGCTCGGCACTC
ACACAGCAAGTCCTCAACAGTGTTTGACAAAGAGATCTAAGCAGTCCTCTGCCCACCTCCCTTGAAGAAGAGGAAGAGAA
AATGC

Alignment

ORF - retro_pabe_2546 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.84 %
• Parental protein coverage: 98.44 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  IQAIKCVVVGDGAVGKTCLLISYTTNAFPGEYIPTVFDNYSANVMVDGKPVNLGLWDTAGQEDYDRLRPL
          .QAIK.VVVGDGAVG..CLLISY.TNAFPGEYIPTVFDNYSANV.VDGKPVNLGLWDT..QEDYDRL..L
Retrocopy MQAIKGVVVGDGAVGEICLLISYATNAFPGEYIPTVFDNYSANVLVDGKPVNLGLWDTVAQEDYDRLCRL

Parental  SYPQTDVFLICFSLVSPASFENVRAKWYPEVRHHCPQTPILLVGTKLDLRDDKDTIERLRDKKLAPITYP
          SYPQTD.FLICFSLVSPASFE.V.AKWYPEVRHHCP.TPI.L.GTKL.LRDDKDTIE.L..KKL.PITY.
Retrocopy SYPQTDMFLICFSLVSPASFESVSAKWYPEVRHHCPNTPIILLGTKLELRDDKDTIEKLKEKKLTPITYL

Parental  QGLAMAREIGSVKYLECSALTQRGLKTVFDEAIRAVL-CPPPVKKPGKKC
          QGLAMA.EIG.VKYL.CSALTQ..L..V........L..PP..KK...KC
Retrocopy QGLAMAKEIGAVKYLKCSALTQQVLNSV*QRDLSSPL>PPP-LKKRKRKC

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	0.11 RPM	13.16 RPM
SRP007412_cerebellum	0.00 RPM	8.51 RPM
SRP007412_heart	0.03 RPM	0.24 RPM
SRP007412_kidney	0.10 RPM	7.06 RPM
SRP007412_liver	0.09 RPM	1.38 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2546 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2546 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2546 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3072
Gorilla gorilla	retro_ggor_2110
Macaca mulatta	retro_mmul_1964

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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,