RetrogeneDB ID: retro_ptro_2200

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 5:146828325..146828896(+)
• Located in intron of: ENSPTRG00000017369

Retrocopy information

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

Parental gene information

• Parental gene symbol: APOOL
• Ensembl ID: ENSPTRG00000022067
• Aliases: None
• Description: apolipoprotein O-like [Source:HGNC Symbol;Acc:24009]

Sequence

>retro_ptro_2200
GGAAAACTGACAACCATGCCTGCAAGTCTGATACATGCATCTGTAAGTGTACATGCAACCAAAGAAGAGGAATCCAAAAA
GCAGCTAGTGAAACCAGAGCAGCTCCCCGTATATATTGCACCACCGCTCCAGTCTAAATATGTTGAAGAGCAGCCTGGTC
ATTTACAAACGGGCTTTGCTTCCATCTACACTGCAACTGGTCATTATACTGGCTGGTGCAAGGGTGTTTATGTCTTTGTG
AAAAATGGGATAATGGATACAGTACAATTTGGGAAAGATGCTTATGTCTATCTGAAGAATCCTCCTCGAGATTTTCTTTC
GAAAATGGGAGTTATTACGGTTTCAGGATTGGCGGGCTTGATTTCAGCGAGAAAAGGTTTTAAGTTTAAGAAAATTACTT
ATCCTCTGGGACTGGCCACGTTATGAGCAACTGTTTGCTACCCAGTTCAGTCAGTAATAATTGCTAAGGTAACAGGGAAA
AAGGTATATGCTACAAGCCAGCAAATTTTTGAAGCAGTTAAATCATTGTGGACAAAAAGCAGCAAAGAAAGAGTCACTCC
CTAAACCTAAA

Alignment

ORF - retro_ptro_2200 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.1 %
• Parental protein coverage: 70.9 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GKLTTMPAGLIYASVSVHAAKQEESKKQLVKPEQLPIYTAPPLQSKYVEEQPGHLQMGFASIRTATGCYI
          GKLTTMPA.LI.ASVSVHA.K.EESKKQLVKPEQLP.Y.APPLQSKYVEEQPGHLQ.GFASI.TATG.Y.
Retrocopy GKLTTMPASLIHASVSVHATKEEESKKQLVKPEQLPVYIAPPLQSKYVEEQPGHLQTGFASIYTATGHYT

Parental  GWCKGVYVFVKNGIMDTVQFGKDAYVYLKNPPRDFLAKMGVITVSGLAGLVSARKGSKFKKITYPLGLAT
          GWCKGVYVFVKNGIMDTVQFGKDAYVYLKNPPRDFL.KMGVITVSGLAGL.SARKG.KFKKITYPLGLAT
Retrocopy GWCKGVYVFVKNGIMDTVQFGKDAYVYLKNPPRDFLSKMGVITVSGLAGLISARKGFKFKKITYPLGLAT

Parental  LGATVCYPVQSVIIAKVTAKKVYATSQQIFGAVKSLWTKSSKE-ESLPKPK
          L.ATVCYPVQSVIIAKVT.KKVYATSQQIF.AVKSLWTKSSKE.ESLPKPK
Retrocopy L*ATVCYPVQSVIIAKVTGKKVYATSQQIFEAVKSLWTKSSKE>ESLPKPK

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	1.95 RPM
SRP007412_cerebellum	0.04 RPM	2.58 RPM
SRP007412_heart	0.09 RPM	8.54 RPM
SRP007412_kidney	0.05 RPM	7.17 RPM
SRP007412_liver	0.03 RPM	3.96 RPM
SRP007412_testis	0.32 RPM	0.95 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2200 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2200 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2200 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3253
Gorilla gorilla	retro_ggor_2213
Pongo abelii	retro_pabe_2697
Macaca mulatta	retro_mmul_2045

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Parental genes homology:

Parental genes homology involve 18 parental genes, and 25 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	ENSPPYG00000020516	1 retrocopy	retro_pabe_2697,
Pan troglodytes	ENSPTRG00000021742	5 retrocopies	retro_ptro_1147, retro_ptro_1799, retro_ptro_1992, retro_ptro_2205, retro_ptro_746,
Pan troglodytes	ENSPTRG00000022067	1 retrocopy	retro_ptro_2200 ,
Sus scrofa	ENSSSCG00000012459	1 retrocopy	retro_sscr_610,
Tursiops truncatus	ENSTTRG00000000429	1 retrocopy	retro_ttru_1337,