RetrogeneDB ID: retro_ptro_158

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 1:68669179..68669687(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SIRT5
• Ensembl ID: ENSPTRG00000017736
• Aliases: None
• Description: NAD-dependent protein deacylase sirtuin-5, mitochondrial [Source:UniProtKB/TrEMBL;Acc:H2QSB4]

Sequence

>retro_ptro_158
CAGAATATCCATGGGCGGCACCCAAGGCTGGCGCCAAGAACCTTCTTGAAATCCACCGTAGCTTACGTTAAACTCCATGT
ACCTCTTGTGGAGTCGTGTCTGAGAATTATGAGAGTCGGTCGGTCCACCTTTATCAGGAGAAGGTGCTCCAGGACCTGGA
ACTCAAGATGCCAGAATCCCAGTTGGGAAACTTGCCGGGTGTGAGAGGCAGAGAGCAGGGGCTTGCCGCAACCTCACGCC
CTGTGGTTTGGCAAAAACTTGGATCCTGCCTTTCTGGAGGAGGTTGACAGACAGCTCACCCTTGTGACTATGTCTAGTGG
CACATACTCCCCCTGTGGTGTACCCCGCAGCTGTGTTTGCCCACCAGATGTCTGCCAAGGGAGTGCCAGTGACCGAATTT
AACATGGAGACCACCTCAGCCATGAGAAGATTCAGGTTTCATTTCCAGGGACCCCGTGGTAGGATGCTTCCTGAACCCCT
TGCTGGTCATGAAAATGAAACTGTTTCT

Alignment

ORF - retro_ptro_158 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.48 %
• Parental protein coverage: 55.16 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  QNIDELHR-KAGTKNLLEIHGSLFKTRCTSCGVVAENYKS-PICPALSGKGAPEPGTQDASIPIEKLPRC
          QNI...H..KAG.KNLLEIH.SL..T.CTSCGVV.ENY.S....P.LSG.GAP.PGTQDA.IP..KL..C
Retrocopy QNIHGRHP<KAGAKNLLEIHRSLR*TPCTSCGVVSENYES<SVGPPLSGEGAPGPGTQDARIPVGKLAGC

Parental  EETGCG-GLLRPHVVWFGENLDPAILEEVDRELA-HCD-LCLVVGTSSVVYPAAMFAPQVAARGVPVAEF
          E....G.GL..PH..WFG.NLDPA.LEEVDR.L...CD.LCLV..T..VVYPAA.FA.Q..A.GVPV.EF
Retrocopy ERQRAG<GLPQPHALWFGKNLDPAFLEEVDRQLT<PCD<LCLVAHTPPVVYPAAVFAHQMSAKGVPVTEF

Parental  NTETTPATNRFRFHFQGPCGTTLPEALAHHENETVS
          N.ETT.A..RFRFHFQGP.G..LPE.LA.HENETVS
Retrocopy NMETTSAMRRFRFHFQGPRGRMLPEPLAGHENETVS

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	40.20 RPM
SRP007412_cerebellum	0.00 RPM	28.50 RPM
SRP007412_heart	0.00 RPM	49.81 RPM
SRP007412_kidney	0.16 RPM	40.25 RPM
SRP007412_liver	0.13 RPM	30.61 RPM
SRP007412_testis	0.00 RPM	24.03 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_158 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_158 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_158 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_167

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000019802	1 retrocopy	retro_cjac_2923,
Erinaceus europaeus	ENSEEUG00000005650	1 retrocopy	retro_eeur_209,
Homo sapiens	ENSG00000124523	1 retrocopy	retro_hsap_167,
Macropus eugenii	ENSMEUG00000008671	1 retrocopy	retro_meug_733,
Nomascus leucogenys	ENSNLEG00000000843	1 retrocopy	retro_nleu_977,
Pan troglodytes	ENSPTRG00000017736	1 retrocopy	retro_ptro_158 ,
Tursiops truncatus	ENSTTRG00000007786	1 retrocopy	retro_ttru_944,