RetrogeneDB ID: retro_pabe_1663

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 19:20794559..20794811(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: COX16
• Ensembl ID: ENSPPYG00000005951
• Aliases: None
• Description: COX16 cytochrome c oxidase assembly homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:20213]

Sequence

>retro_pabe_1663
ATGTTGTTGCTAATTGTTGGAGTTTCTTTTGGTCTTCATGAGTTTTTACAAATCTGACATGATACTGTGAAGATTAAAAT
TGATCCTGAGTTGGAAAAAAACTGAAAGCAAATAGTATCATTAGAGTCAGAATATGAGAAAATAAGAGACTCCACTTTTG
ATGACTGGAAGAATATCCAAGGACCCAAGCCTTGGAAAGATCCTGACCTCCTCCAAGAAAGAAATCCAGAAATCGTTAAG
ACTAAGACAACT

Alignment

ORF - retro_pabe_1663 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.94 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MLLLIIGGSFGLREFSQIRYDAVKTKMDPELEKKLKENKISLESEYEKIKDSKFDDWKNIRGPRPWEDPD
          MLLLI.G.SFGL.EF.QI..D.VK.K.DPELEK..K....SLESEYEKI.DS.FDDWKNI.GP.PW.DPD
Retrocopy MLLLIVGVSFGLHEFLQI*HDTVKIKIDPELEKN*KQI-VSLESEYEKIRDSTFDDWKNIQGPKPWKDPD

Parental  LLQGRNPESLKTKTT
          LLQ.RNPE..KTKTT
Retrocopy LLQERNPEIVKTKTT

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	0.22 RPM	4.92 RPM
SRP007412_cerebellum	0.00 RPM	6.57 RPM
SRP007412_heart	0.00 RPM	10.93 RPM
SRP007412_kidney	0.07 RPM	13.13 RPM
SRP007412_liver	0.00 RPM	10.28 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1663 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1663 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1663 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000133983	1 retrocopy	retro_hsap_2038,
Macaca mulatta	ENSMMUG00000011089	2 retrocopies	retro_mmul_1368, retro_mmul_1391,
Nomascus leucogenys	ENSNLEG00000001776	1 retrocopy	retro_nleu_2908,
Otolemur garnettii	ENSOGAG00000028663	1 retrocopy	retro_ogar_3045,
Pongo abelii	ENSPPYG00000005951	2 retrocopies	retro_pabe_1663 , retro_pabe_1664,
Pan troglodytes	ENSPTRG00000006494	1 retrocopy	retro_ptro_1355,
Rattus norvegicus	ENSRNOG00000047115	1 retrocopy	retro_rnor_1546,
Tarsius syrichta	ENSTSYG00000013313	1 retrocopy	retro_tsyr_1700,
Tursiops truncatus	ENSTTRG00000014791	1 retrocopy	retro_ttru_1513,