RetrogeneDB ID: retro_pabe_2697

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 5:147651975..147652353(+)
• Located in intron of: ENSPPYG00000015906

Retrocopy information

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

Parental gene information

• Parental gene symbol: APOOL
• Ensembl ID: ENSPPYG00000020516
• Aliases: None
• Description: apolipoprotein O-like [Source:HGNC Symbol;Acc:24009]

Sequence

>retro_pabe_2697
GGAAAACTGACAACCATTCCTGCAAGTCTGATACGTGCATCTGTAAGTGTACATGCAGCCAAAGAAGAGGAATCCAAAAA
GCAGCTAGTGAAACCAGAGCAGCTCCCCGTATATACTGCACCACCGCTCCAGTCTAAATATGTTGAAGAGCAGCCTGGTC
ATTTACAAACGGGCTTTGCTTCCATCTACACTGCAACTGGTCATTATACTGGCTGGTGCAAGGGTGTTTATGTCTTTGTG
AAAAATGTGATAATGGATACAGTACAATTTGGAAAAGATGCTTATGTCTATCTGAAGAATCCTCCTCGAGATTTTCTTCC
GAAAATGGGAGTTATTACGGTTTCAGGATTGGCAGGCTTGGTTTCAGCGAGAAAGGTT

Alignment

ORF - retro_pabe_2697 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.27 %
• Parental protein coverage: 53.16 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GKLTTMPAGLIYASVSVHAAKEEESKKQLVKPEQLPIYTVPPLQSKYVEEQPGHLQMGFASIRTATGCYI
          GKLTT.PA.LI.ASVSVHAAKEEESKKQLVKPEQLP.YT.PPLQSKYVEEQPGHLQ.GFASI.TATG.Y.
Retrocopy GKLTTIPASLIRASVSVHAAKEEESKKQLVKPEQLPVYTAPPLQSKYVEEQPGHLQTGFASIYTATGHYT

Parental  GWCKGVYVFVKNGIMDTVQFGKDAYVYMKNPPRDFLPKMGVITVSGLAGLVSARKV
          GWCKGVYVFVKN.IMDTVQFGKDAYVY.KNPPRDFLPKMGVITVSGLAGLVSARKV
Retrocopy GWCKGVYVFVKNVIMDTVQFGKDAYVYLKNPPRDFLPKMGVITVSGLAGLVSARKV

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	0.06 RPM	2.27 RPM
SRP007412_cerebellum	0.00 RPM	2.07 RPM
SRP007412_heart	0.00 RPM	2.20 RPM
SRP007412_kidney	0.07 RPM	1.99 RPM
SRP007412_liver	0.00 RPM	1.68 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2697 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2697 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2697 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3253
Pan troglodytes	retro_ptro_2200
Gorilla gorilla	retro_ggor_2213
Macaca mulatta	retro_mmul_2045

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Parental genes homology:

Parental genes homology involve 18 parental genes, and 27 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000000829	1 retrocopy	retro_amel_1035,
Canis familiaris	ENSCAFG00000017383	1 retrocopy	retro_cfam_1490,
Callithrix jacchus	ENSCJAG00000008249	2 retrocopies	retro_cjac_1783, retro_cjac_2464,
Dipodomys ordii	ENSDORG00000011045	1 retrocopy	retro_dord_373,
Equus caballus	ENSECAG00000009229	1 retrocopy	retro_ecab_577,
Homo sapiens	ENSG00000155008	1 retrocopy	retro_hsap_3253,
Gorilla gorilla	ENSGGOG00000016329	1 retrocopy	retro_ggor_2213,
Loxodonta africana	ENSLAFG00000008844	1 retrocopy	retro_lafr_1035,
Microcebus murinus	ENSMICG00000015844	1 retrocopy	retro_mmur_1511,
Myotis lucifugus	ENSMLUG00000011384	1 retrocopy	retro_mluc_1364,
Macaca mulatta	ENSMMUG00000004335	1 retrocopy	retro_mmul_2045,
Mustela putorius furo	ENSMPUG00000001899	3 retrocopies	retro_mputfur_606, retro_mputfur_734, retro_mputfur_874,
Nomascus leucogenys	ENSNLEG00000002634	1 retrocopy	retro_nleu_1702,
Pongo abelii	ENSPPYG00000020191	7 retrocopies	retro_pabe_1394, retro_pabe_1417, retro_pabe_2215, retro_pabe_2417, retro_pabe_2434, retro_pabe_2702, retro_pabe_856,
Pongo abelii	ENSPPYG00000020516	1 retrocopy	retro_pabe_2697 ,
Pan troglodytes	ENSPTRG00000022067	1 retrocopy	retro_ptro_2200,
Sus scrofa	ENSSSCG00000012459	1 retrocopy	retro_sscr_610,
Tursiops truncatus	ENSTTRG00000000429	1 retrocopy	retro_ttru_1337,