RetrogeneDB ID: retro_ptro_2194

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 5:140209817..140210282(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NTPCR
• Ensembl ID: ENSPTRG00000002116
• Aliases: None
• Description: nucleoside-triphosphatase, cancer-related [Source:HGNC Symbol;Acc:28204]

Sequence

>retro_ptro_2194
GGATTTTATAGAAAGGAAGTCAGACAGGGAGGGAGAATAGGATTTGATGTCATCATGTTGTCCGGCATCCAGGGGCCTTT
ATTTAGAGTTGGGTTAGAGCCTCCACCTGGAAAATGTGGATGCCAAGTTGGGCATTATGTGGTTAACCTGACTTATTTTG
AGCAGTTGGCGCTCCCTATCTTGAGGAATGCAGATTCCAGCAGTGGCCCAGGGCAGAGAGTGTGCGTCACTGATGAGAGT
GGGAAAATGAAACTCTTTAGTTAGCCTTTCATCCAAGCTGTTTGTCAGATGCTATCTACCCCAGGGACTATAATCGCTGG
CACAATCCCAGTCCCTAAAGGAAAGTCACTGGCCGTTGTAGAAGAAATCAGAAACAGAAATGACGTGAAAGTGTTTAATG
TCTCCAAGGAAGACAGAAACCACCTTCTGCCAGATATTGTGATGTGTGTGCAGAGCAGCAGGAAG

Alignment

ORF - retro_ptro_2194 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.77 %
• Parental protein coverage: 82.11 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GFYTEEVRQGGRRIGFDVVTLSGTRGPLSRVGLEPPPGKRECRVGQYVVDLTSFEQLALPVLRNADCSSG
          GFY..EVRQGGR.IGFDV..LSG..GPL.RVGLEPPPGK..C.VG.YVV.LT.FEQLALP.LRNAD.SSG
Retrocopy GFYRKEVRQGGR-IGFDVIMLSGIQGPLFRVGLEPPPGKCGCQVGHYVVNLTYFEQLALPILRNADSSSG

Parental  PGQRVCVIDEIGKMELFSQLFIQAVRQTLSTPGTIILGTIPVPKGKPLALVEEIRNRKDVKVFNVTKENR
          PGQRVCV.DE.GKM.LFS..FIQAV.Q.LSTPGTII.GTIPVPKGK.LA.VEEIRNR.DVKVFNV.KE.R
Retrocopy PGQRVCVTDESGKMKLFS*PFIQAVCQMLSTPGTIIAGTIPVPKGKSLAVVEEIRNRNDVKVFNVSKEDR

Parental  NHLLPDIVTCVQSSRK
          NHLLPDIV.CVQSSRK
Retrocopy NHLLPDIVMCVQSSRK

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	23.45 RPM
SRP007412_cerebellum	0.00 RPM	14.34 RPM
SRP007412_heart	0.00 RPM	21.77 RPM
SRP007412_kidney	0.00 RPM	28.92 RPM
SRP007412_liver	0.00 RPM	19.71 RPM
SRP007412_testis	0.00 RPM	27.29 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2194 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2194 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2194 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3246
Gorilla gorilla	retro_ggor_2209
Pongo abelii	retro_pabe_2691

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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	ENSCJAG00000018274	1 retrocopy	retro_cjac_1773,
Felis catus	ENSFCAG00000014211	1 retrocopy	retro_fcat_708,
Homo sapiens	ENSG00000135778	1 retrocopy	retro_hsap_3246,
Gorilla gorilla	ENSGGOG00000015198	1 retrocopy	retro_ggor_2209,
Macaca mulatta	ENSMMUG00000012614	1 retrocopy	retro_mmul_741,
Pongo abelii	ENSPPYG00000000108	1 retrocopy	retro_pabe_2691,
Pan troglodytes	ENSPTRG00000002116	1 retrocopy	retro_ptro_2194 ,