RetrogeneDB ID: retro_ptro_3044

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: GL392075.1:2351996..2352573(-)
• 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_3044
GTGCAAGCCATCAAGTGTGTGGTGGTTGGAGATGGAGCTACAAGTAAAACTTGCCTACTAATCAGTGTTACACCCAATGC
ATTTCCCAATGCATTATCACTATTGTCTTTGACAATTATTCTGCTGCCAATGTTAAGGTAGATGGAAAGCCAGTGAATCT
GGGCTTATGGGATACATCTGGACAAGAAGATTATGACAGATTATGCCCCCATTCTATCTGTAAACAGACATATTTTTAAT
ATGCTTCTCCCTTGTGAGTCTTGCATCATTTGAAAATGTCTGTGCAGAGTGGCATCCTGAAATGCAGCACCATTTTCCCA
ACACTCCCATCATTCTTGTGGGAAGTAAACTTGATCTTAATGTTGTTAAAGACACGATTGAGAAACTGAAGGAGAAGAAG
CTGACTCCCATCACCTATCTGCAGTTTTTAGCCAGGAATAAGGAGATTGGCGCTTTAAAATACCTGAAGTGCTTGGCTCT
CACATAGCGAGGGTTCAAAACGGTGTTTGACAAAGCTATCTGAGCAGTTCTCTGCCCACCTCCTGTGAAGAAGAGGAAGA
GAAGATGCCTGCTGTTG

Alignment

ORF - retro_ptro_3044 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.95 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MQAIKCVVVGDGAVGKTCLLISYTTNAFPGEY-IPTVFDNYSA-NVMVDGKPVNLGLWDTAGQEDYDRLR
          .QAIKCVVVGDGA..KTCLLIS.T.NAFP....I..VFDNYSA.NV.VDGKPVNLGLWDT.GQEDYDRL.
Retrocopy VQAIKCVVVGDGATSKTCLLISVTPNAFPNAL<ITIVFDNYSAANVKVDGKPVNLGLWDTSGQEDYDRLC

Parental  PLS-YPQTDVFLICFSLVSPASFENVRAKWYPEVRHHCPNTPIILVGTKLDLRDDKDTIEKLKEKKLTPI
          P.S.Y..TD.FLICFSLVS.ASFENV.A.W.PE..HH.PNTPIILVG.KLDL...KDTIEKLKEKKLTPI
Retrocopy PHS<YL*TDIFLICFSLVSLASFENVCAEWHPEMQHHFPNTPIILVGSKLDLNVVKDTIEKLKEKKLTPI

Parental  TYPQGLAMAKEIGAVKYLECSALTQRGLKTVFDEAIRAVLCPPPVKKRKRKCLLL
          TY.Q.LA..KEIGA.KYL.C.ALT.RG.KTVFD.AI.AVLCPPPVKKRKR.CLLL
Retrocopy TYLQFLARNKEIGALKYLKCLALT*RGFKTVFDKAI*AVLCPPPVKKRKRRCLLL

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	0.04 RPM	247.07 RPM
SRP007412_heart	0.03 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_3044 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_3044 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_3044 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1256
Pongo abelii	retro_pabe_1047

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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,