RetrogeneDB ID: retro_ptro_3015

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: GL391762.1:4725..5006(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NAA50
• Ensembl ID: ENSPTRG00000015233
• Aliases: None
• Description: N(Alpha)-acetyltransferase 50, NatE catalytic subunit [Source:UniProtKB/TrEMBL;Acc:K7DL89]

Sequence

>retro_ptro_3015
ATGGAGCTGGGAGATGGGACACCACACAATATTAAACAGTAGAAGAGAAGGAATCGGGTTATCTTTTCAGTCAGCTACAA
TGGTAAGTTCCACAAGGATGTGATGGAGGTGGTGAACGATCAAAACTTGCCTATTTCAGTGATGTTCCTGTAGGTGCATT
GTACTCTAGTGTGGCTCATTCACAGAATCAGAAAAGACTTTACATCATGACACTTGGATATCTGGCACCTTACCAAAGGC
TAGGAATAGGAACTACAATGTTAAATCATGTCTTAAACATG

Alignment

ORF - retro_ptro_3015 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.74 %
• Parental protein coverage: 56.97 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  IELGDVTPHNIKQLKRLNQVIFPVSYNDKFYKDVLEV-GELAKLAYFNDIAVGAVCCRVDHSQNQKRLYI
          .ELGD.TPHNIKQ.KR.N.VIF.VSYN.KF.KDV.EV.GE..KLAYF.D..VGA....V.HSQNQKRLYI
Retrocopy MELGDGTPHNIKQ*KRRNRVIFSVSYNGKFHKDVMEV<GERSKLAYFSDVPVGALYSSVAHSQNQKRLYI

Parental  MTLGCLAPYRRLGIGTKMLNHVLNI
          MTLG.LAPY.RLGIGT.MLNHVLN.
Retrocopy MTLGYLAPYQRLGIGTTMLNHVLNM

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	7.54 RPM
SRP007412_cerebellum	0.00 RPM	29.11 RPM
SRP007412_heart	0.00 RPM	26.09 RPM
SRP007412_kidney	0.00 RPM	20.76 RPM
SRP007412_liver	0.00 RPM	18.23 RPM
SRP007412_testis	0.00 RPM	44.16 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_3015 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_3015 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_3015 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Erinaceus europaeus	ENSEEUG00000014852	1 retrocopy	retro_eeur_547,
Procavia capensis	ENSPCAG00000009780	2 retrocopies	retro_pcap_205, retro_pcap_459,
Pan troglodytes	ENSPTRG00000015233	2 retrocopies	retro_ptro_3015 , retro_ptro_3031,
Ictidomys tridecemlineatus	ENSSTOG00000009438	1 retrocopy	retro_itri_1703,