RetrogeneDB ID: retro_ptro_1288

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 18:20385853..20386280(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RAC1
• Ensembl ID: ENSPTRG00000018910
• Aliases: None
• Description: Pan troglodytes ras-related C3 botulinum toxin substrate 1 (rho family, small GTP binding protein Rac1) (RAC1), mRNA. [Source:RefSeq mRNA;Acc:NM_001246381]

Sequence

>retro_ptro_1288
GACAGATTTGTAGATAAAACTTACCTACTGTTCAGTTACACACCAGTGCACTTCTTGGAGAAGAGATCCCCATTGTCTTT
GACAACTATTCTGCCAGTGTTACGGTGGATGGAAAAACCAGTGAATTTGGACTCAAGGGATACAACTGGATGGCAGAATA
TGATGGATTACACTTCCTGTCCTATCTGCAAACAGATGAATTCTTTATTTGCTTTTCCTTTGTGAGTCCTGCATCATTTG
AAAATACCTGTGCAAAGTGGTATCCTGATATTCACCACCATGTTCCAACATGCCCATCATCCTAGTGGGAACTAAGTGTG
ATCTTAGGGATGATAAAGCCATGATTAGGAAACTGAAGGAGAAGCAGCTGACTCCCATCACCTATCCATAGGGTTGAGCT
ACAGCTAAAGAGATCAGTGCCCTAAAA

Alignment

ORF - retro_ptro_1288 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.03 %
• Parental protein coverage: 74.48 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  DGAVGKTCLLISYT-TNAFPGEYIPTVFDNYSANVMVDGK-PVNLGLWDTAGQE-DYDRLRPLSYPQTDV
          D..V.KT.LL.SYT.T.A..GE.IP.VFDNYSA.V.VDGK.PVNL...DT.G....YD.L..LSY.QTD.
Retrocopy DRFVDKTYLLFSYT<TSALLGEEIPIVFDNYSASVTVDGK>PVNLDSRDTTGWQ<EYDGLHFLSYLQTDE

Parental  FLICFSLVSPASFENVRAKWYPEVRHH-CPNTPIILVGTKLDLRDDKDTIEKLKEKKLTPITYPQGLAMA
          F.ICFS.VSPASFEN..AKWYP...HH.C.N.PIILVGTK.DLRDDK..I.KLKEK.LTPITYP.G.A.A
Retrocopy FFICFSFVSPASFENTCAKWYPDIHHH<CSNMPIILVGTKCDLRDDKAMIRKLKEKQLTPITYP*G*ATA

Parental  KEIGAVK
          KEI.A.K
Retrocopy KEISALK

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	185.02 RPM
SRP007412_cerebellum	0.00 RPM	247.07 RPM
SRP007412_heart	0.00 RPM	136.81 RPM
SRP007412_kidney	0.00 RPM	172.24 RPM
SRP007412_liver	0.00 RPM	129.69 RPM
SRP007412_testis	0.00 RPM	92.63 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1288 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1288 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1288 has 5 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1925
Gorilla gorilla	retro_ggor_1403
Pongo abelii	retro_pabe_1591
Macaca mulatta	retro_mmul_1346
Callithrix jacchus	retro_cjac_1158

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Parental genes homology:

Parental genes homology involve 17 parental genes, and 39 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000009233	2 retrocopies	retro_btau_1601, retro_btau_332,
Canis familiaris	ENSCAFG00000015716	1 retrocopy	retro_cfam_496,
Felis catus	ENSFCAG00000011361	2 retrocopies	retro_fcat_1632, retro_fcat_717,
Homo sapiens	ENSG00000136238	6 retrocopies	retro_hsap_1256, retro_hsap_1925, retro_hsap_28, retro_hsap_3036, retro_hsap_3072, retro_hsap_4910,
Gorilla gorilla	ENSGGOG00000026733	2 retrocopies	retro_ggor_2110, retro_ggor_217,
Loxodonta africana	ENSLAFG00000012844	1 retrocopy	retro_lafr_818,
Myotis lucifugus	ENSMLUG00000009701	1 retrocopy	retro_mluc_1059,
Macaca mulatta	ENSMMUG00000021075	4 retrocopies	retro_mmul_1310, retro_mmul_1964, retro_mmul_2642, retro_mmul_721,
Mus musculus	ENSMUSG00000001847	2 retrocopies	retro_mmus_1372, retro_mmus_234,
Oryctolagus cuniculus	ENSOCUG00000009956	1 retrocopy	retro_ocun_305,
Pan troglodytes	ENSPTRG00000006424	4 retrocopies	retro_ptro_1643, retro_ptro_2091, retro_ptro_2971, retro_ptro_910,
Pan troglodytes	ENSPTRG00000018910	4 retrocopies	retro_ptro_1288 , retro_ptro_3044, retro_ptro_3274, retro_ptro_36,
Rattus norvegicus	ENSRNOG00000001068	1 retrocopy	retro_rnor_230,
Ictidomys tridecemlineatus	ENSSTOG00000006784	1 retrocopy	retro_itri_1503,
Tupaia belangeri	ENSTBEG00000007272	4 retrocopies	retro_tbel_1796, retro_tbel_2564, retro_tbel_4296, retro_tbel_9,
Tarsius syrichta	ENSTSYG00000001618	2 retrocopies	retro_tsyr_2027, retro_tsyr_2068,
Xenopus tropicalis	ENSXETG00000027593	1 retrocopy	retro_xtro_1,