RetrogeneDB ID: retro_ptro_806

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 13:22376735..22377143(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RFESD
• Ensembl ID: ENSPTRG00000017085
• Aliases: None
• Description: Rieske (Fe-S) domain containing [Source:UniProtKB/TrEMBL;Acc:K7D8E3]

Sequence

>retro_ptro_806
ATGAATCTTGATGGCTCTGCACAAGATACTGAAAAGAGGGAATATTCTTCTGTCTGGGTGGGCAGAGAAGATGACATTAA
AAAATCTGAAAGAATAACAGCTGTTGTCCATGCTAGAGAAGTGGTCATTTTCTATCACAAGGGAGAATATCATGCTATAG
ATATTCGCTGTTACCACTCAGGAGGACCTTTACATTTGGGAGATATAGAGGATTTTGATGGATGACCGTGTATAGTTTGC
CGCTGGCATAAGTACAAAATTACTTTGGCAACAGGAGAAGGTCTGTACCAGACTATAAACTCTAAAGATCCATCAGCAAA
ACCCAAGTAGTGCTCCAAAGGAATAAAGCAAAGGATTCACACAGTGACAGTGGACAATGGGAATATTTATGTGACTCTTT
CTAATGAA

Alignment

ORF - retro_ptro_806 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.65 %
• Parental protein coverage: 86.62 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MNLDGSAQDPEKREYSSVCVGREDDIKKSERMTAVVHDREVVIFYHKGEYHAMDIRCYHSGGPLHLGDIE
          MNLDGSAQD.EKREYSSV.VGREDDIKKSER.TAVVH.REVVIFYHKGEYHA.DIRCYHSGGPLHLGDIE
Retrocopy MNLDGSAQDTEKREYSSVWVGREDDIKKSERITAVVHAREVVIFYHKGEYHAIDIRCYHSGGPLHLGDIE

Parental  DFDGRPCIVCPWHKYKITLATGEGLYQSINPKDPSAKPKWCSKGIKQRIHTVTVDNGNIYVTLSNE
          DFDG.PCIVC.WHKYKITLATGEGLYQ.IN.KDPSAKPK.CSKGIKQRIHTVTVDNGNIYVTLSNE
Retrocopy DFDG*PCIVCRWHKYKITLATGEGLYQTINSKDPSAKPK*CSKGIKQRIHTVTVDNGNIYVTLSNE

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	0.54 RPM
SRP007412_cerebellum	0.00 RPM	0.97 RPM
SRP007412_heart	0.00 RPM	0.70 RPM
SRP007412_kidney	0.00 RPM	0.89 RPM
SRP007412_liver	0.00 RPM	0.26 RPM
SRP007412_testis	0.00 RPM	14.12 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_806 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_806 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_806 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1173

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000175449	1 retrocopy	retro_hsap_1173,
Gorilla gorilla	ENSGGOG00000027350	1 retrocopy	retro_ggor_913,
Pan troglodytes	ENSPTRG00000017085	1 retrocopy	retro_ptro_806 ,