RetrogeneDB ID: retro_ptro_3216

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: X:51913705..51914266(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CENPV
• Ensembl ID: ENSPTRG00000008810
• Aliases: CENPV, PRR6
• Description: None

Sequence

>retro_ptro_3216
CCGCTGCCCTCCGCGCCACTCCCGGACCCGCCGGCGCCCGCCGAGTCCCCTAAGGAGCTGGACCTGGGCGCACAGCGGGA
GCGCTGGGAGACGTTCAGGAAACTGTGGGGCCTCAGCTGCGAGGGCGCCGCCACTGTCCTGCTGGACACCTTCGAGTACC
CGGGCCTCGTGCATCACACCGGGGGCTGCCACTGCGGCGCGGTCCGCTTTGCGGTCTGGGCCCCTGCAGATCTGCGCGTC
GTGGATTGCAGCTGCAGGCTGTGCAGGAAGAAGCAGCACCGCCACTTCCTCGTCCCGGCCTCGCGCTTCACGCTGCTCCA
GGGCGCAGAAAGCATCGTCACCTATCGGTCCAACACGCACCCGGCGCTGCACAGCTTCTGCAGCAGGTGCGGGGTGCAGA
GTTTCCACGCAGCTGTCTCTGACCCCCGCGTGTACGGCGTCGCCCCGCACTGCCTGGACGAGGGCACCGTGCGCAGCGTG
GTCATCGAGGAGGTCGGCGGTGGCGACCCGGGGGAGGAGGCCGCCGAGGAGCACAAGGCCATCCACAAGACGTCCTCCCA
G

Alignment

ORF - retro_ptro_3216 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.1 %
• Parental protein coverage: 68.38 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  PPPPPPPPTPATPTSSASNLDLGEQRERWETFQKRQKLTSEGAAKLLLDTFEYQGLVKHTGGCHCGAVRF
          P.P..P.P.P..P..S...LDLG.QRERWETF.K...L..EGAA..LLDTFEY.GLV.HTGGCHCGAVRF
Retrocopy PLPSAPLPDPPAPAESPKELDLGAQRERWETFRKLWGLSCEGAATVLLDTFEYPGLVHHTGGCHCGAVRF

Parental  EVWASADLHIFDCNCSICKKKQNRHFIVPASRFKLLKGAEHITTYTFNTHKAQHTFCKRCGVQSFYTPRS
          .VWA.ADL...DC.C..C.KKQ.RHF.VPASRF.LL.GAE.I.TY..NTH.A.H.FC.RCGVQSF....S
Retrocopy AVWAPADLRVVDCSCRLCRKKQHRHFLVPASRFTLLQGAESIVTYRSNTHPALHSFCSRCGVQSFHAAVS

Parental  NPGGFGIAPHCLDEGTVRSMVTEEFNGSD-WEKAMKEHKTIKNMSKE
          .P...G.APHCLDEGTVRS.V.EE..G.D..E.A..EHK.I...S..
Retrocopy DPRVYGVAPHCLDEGTVRSVVIEEVGGGDPGEEAAEEHKAIHKTSSQ

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	0.50 RPM	21.15 RPM
SRP007412_cerebellum	0.07 RPM	16.38 RPM
SRP007412_heart	0.00 RPM	3.15 RPM
SRP007412_kidney	0.00 RPM	11.45 RPM
SRP007412_liver	0.00 RPM	14.14 RPM
SRP007412_testis	0.00 RPM	14.33 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_3216 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_3216 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_3216 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000004716	5 retrocopies	retro_amel_1859, retro_amel_1870, retro_amel_1909, retro_amel_1926, retro_amel_924,
Canis familiaris	ENSCAFG00000018019	2 retrocopies	retro_cfam_2153, retro_cfam_2155,
Homo sapiens	ENSG00000166582	3 retrocopies	retro_hsap_4683, retro_hsap_4833, retro_hsap_4834,
Macropus eugenii	ENSMEUG00000002027	1 retrocopy	retro_meug_519,
Microcebus murinus	ENSMICG00000007166	1 retrocopy	retro_mmur_1491,
Mustela putorius furo	ENSMPUG00000010146	2 retrocopies	retro_mputfur_1195, retro_mputfur_39,
Nomascus leucogenys	ENSNLEG00000014726	1 retrocopy	retro_nleu_2709,
Otolemur garnettii	ENSOGAG00000029365	1 retrocopy	retro_ogar_99,
Pan troglodytes	ENSPTRG00000008810	1 retrocopy	retro_ptro_3216 ,
Ictidomys tridecemlineatus	ENSSTOG00000012221	2 retrocopies	retro_itri_110, retro_itri_1540,