RetrogeneDB ID: retro_ptro_534

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 11:21118393..21119096(+)
• Located in intron of: ENSPTRG00000003441

Retrocopy information

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

Parental gene information

• Parental gene symbol: IDH3G
• Ensembl ID: ENSPTRG00000024398
• Aliases: None
• Description: isocitrate dehydrogenase 3 (NAD+) gamma [Source:HGNC Symbol;Acc:5386]

Sequence

>retro_ptro_534
GAGATCCCCCTGAGAAGCTTCTCTTTTTCTCACACAATTCCTCCATCAGCGAAGTGTGGTGGGCAGCACACAGTGACTAT
GATTCCTGGAGATGGCACTGGGGCTGAACTTATGCTGCCTGTCAAGATTATGTTCAGACATGTATGTGTGCCTGTGGACT
TTGAGGGAATGTCAGTGACCTCCACCTCTGCCTCACATGAAGAGGAAATTCATAATGCCATCATGGCAGTTCATTGAAAC
CGTGTGGCTTTGAAGAGTAGCATTAAAACTGACGACACCCTGCCACCATCATACAAATCCTTCAACAACATGTTGCATAC
CACCCTAGATCTCTATGCCAATGTCATTCATTTAAAAAATTTGCCAAACTTGCAGACCTGGCACAAGGACTTAGACATCC
TAGTTGTTTGGGAAAACACAGAGGGTGAGTATAGCAATCTGGAGCATGACAGTGTGAAAGGAGTGACAGAGAGCCTAAAG
ATCATGACTAAGGCCAAGTCTTTGCGCACTGCTGAATATGCCTTCTGGCTGGCCCAGAAGATGGGATGCAAAAAGGTGAT
GGCTGTGCACAAGGTCAACATCACGAAACTGGGAGATGGTCTCTTCCTCCAGTGCTGTGGGGGAGGTGGCATCCTGCTAT
CCTCAGCTCACCTTAGAAGACATGATTGTGGAGAATGAATGCCACAATGCAGTGAGTATCCCA

Alignment

ORF - retro_ptro_534 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.81 %
• Parental protein coverage: 81.69 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  EVPSRNIFAVSTCPPSAKYGGRHTVTMIPGDGIGPELMLHVKSVFRHACVPVDFEEVHVSSNA--DEEDI
          E.P.R......T.PPSAK.GG.HTVTMIPGDG.G.ELML.VK..FRH.CVPVDFE...V.S.....EE.I
Retrocopy EIPLRSFSFSHTIPPSAKCGGQHTVTMIPGDGTGAELMLPVKIMFRHVCVPVDFEGMSVTSTSASHEEEI

Parental  RNAIMAIRRNRVALKGNIETNHNLPPSHKSRNNILRTSLDLYANVIHCKSLPGVVTRHKDIDILIVRENT
          .NAIMA...NRVALK..I.T...LPPS.KS.NN.L.T.LDLYANVIH.K.LP...T.HKD.DIL.V.ENT
Retrocopy HNAIMAVH*NRVALKSSIKTDDTLPPSYKSFNNMLHTTLDLYANVIHLKNLPNLQTWHKDLDILVVWENT

Parental  EGEYSSLEHESVAGVVESLKIITKAKSLRIAEYAFKLAQESGRKKVTAVHKANIMKLGDGLFLQCC-REV
          EGEYS.LEH.SV.GV.ESLKI.TKAKSLR.AEYAF.LAQ..G.KKV.AVHK.NI.KLGDGLFLQCC..EV
Retrocopy EGEYSNLEHDSVKGVTESLKIMTKAKSLRTAEYAFWLAQKMGCKKVMAVHKVNITKLGDGLFLQCC>GEV

Parental  AARYPQITFENMIVDNTTMQLVSRP
          A..YPQ.T.E.MIV.N.....VS.P
Retrocopy ASCYPQLTLEDMIVENECHNAVSIP

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	0.02 RPM	38.91 RPM
SRP007412_cerebellum	0.04 RPM	42.52 RPM
SRP007412_heart	0.00 RPM	26.93 RPM
SRP007412_kidney	0.00 RPM	80.36 RPM
SRP007412_liver	0.00 RPM	26.71 RPM
SRP007412_testis	3.16 RPM	4.74 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_534 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_534 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_534 has 7 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_759
Mus musculus	retro_mmus_134
Oryctolagus cuniculus	retro_ocun_80
Bos taurus	retro_btau_1194
Sus scrofa	retro_sscr_662
Canis familiaris	retro_cfam_1023
Equus caballus	retro_ecab_941

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Dipodomys ordii	ENSDORG00000006029	1 retrocopy	retro_dord_38,
Erinaceus europaeus	ENSEEUG00000015625	1 retrocopy	retro_eeur_248,
Latimeria chalumnae	ENSLACG00000007365	1 retrocopy	retro_lcha_17,
Macropus eugenii	ENSMEUG00000013934	1 retrocopy	retro_meug_203,
Myotis lucifugus	ENSMLUG00000004457	1 retrocopy	retro_mluc_396,
Oryctolagus cuniculus	ENSOCUG00000016554	1 retrocopy	retro_ocun_80,
Procavia capensis	ENSPCAG00000008973	1 retrocopy	retro_pcap_361,
Pan troglodytes	ENSPTRG00000024398	1 retrocopy	retro_ptro_534 ,