RetrogeneDB ID: retro_pabe_3257

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 8:52430950..52431393(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PDCD10
• Ensembl ID: ENSPPYG00000029750
• Aliases: None
• Description: programmed cell death 10 [Source:HGNC Symbol;Acc:8761]

Sequence

>retro_pabe_3257
GTAAATCTGTCTGCAGCTCAGATACTGAGAGTGGCTTTCATTAAGGCCAATAAGGAAACCCCGGTCTCACACAATACGTT
GTTTTGGCAACTTTAGAGAAAAAAAATAGAAACATTAAGATCACAGGATTTCTTCTTATGGCAGCTGTTAATGTATAATA
GTAGATAATTGAATGACTAGAGCCAGAATTCCAGGATGCAAATGAAAGGCACAAGTACTTATACAAATTCTCAGTAAGTT
TCCAGTGAGCTCAATGACAGCGTGAGAATTCTGCAGACAATTAAGGATATAAAGAGTGCAATAAAAGAGCTCGATATAGT
GAATAATGTCTTCAAGAAATATCAATACCAGAACCACGGGCACCTGAACACCAAAAGAAAGTATTTTTAAAGTATTCTAA
AAGTTTCAATGGTATTCTGAAAACTTATTTCAAAGATGACAAA

Alignment

ORF - retro_pabe_3257 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.45 %
• Parental protein coverage: 81.18 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  VNLSAAQTLRAAFIKAEKE-NPGLTQDIIMKILEKKSVEVNFTESLLRMAADDVEEYMIERPEPEFQDLN
          VNLSAAQ.LR.AFIKA.KE.NPGLTQ......LE........T..LL.MAA..V....IE..EPEFQD.N
Retrocopy VNLSAAQILRVAFIKANKE<NPGLTQYVVLATLEXXXRNIKITGFLL-MAAVNV***IIE*LEPEFQDAN

Parental  E-KARALKQILSKIP-DEINDRVRFLQTIKDIASAIKELLDTVNNVFKKYQYQNR-RALEHQKKEFVKYS
          E.KA..L.QILSK.P..E.ND.VR.LQTIKDI.SAIKEL.D.VNNVFKKYQYQN..RA.EHQKK.F.KYS
Retrocopy E<KAQVLIQILSKFP<SELNDSVRILQTIKDIKSAIKEL-DIVNNVFKKYQYQNH<RAPEHQKKVFLKYS

Parental  KSFSDTLKTYFKDGK
          KSF...LKTYFKD.K
Retrocopy KSFNGILKTYFKDDK

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	13.05 RPM
SRP007412_cerebellum	0.00 RPM	6.57 RPM
SRP007412_heart	0.00 RPM	4.85 RPM
SRP007412_kidney	0.00 RPM	10.01 RPM
SRP007412_liver	0.00 RPM	6.79 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3257 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3257 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3257 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3953
Pan troglodytes	retro_ptro_2683
Gorilla gorilla	retro_ggor_2656
Macaca mulatta	retro_mmul_2288

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Parental genes homology:

Parental genes homology involve 24 parental genes, and 38 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000002181	1 retrocopy	retro_amel_420,
Bos taurus	ENSBTAG00000031709	2 retrocopies	retro_btau_1623, retro_btau_713,
Canis familiaris	ENSCAFG00000014569	2 retrocopies	retro_cfam_1988, retro_cfam_687,
Callithrix jacchus	ENSCJAG00000002763	2 retrocopies	retro_cjac_1442, retro_cjac_4178,
Dasypus novemcinctus	ENSDNOG00000015854	1 retrocopy	retro_dnov_351,
Homo sapiens	ENSG00000114209	1 retrocopy	retro_hsap_3953,
Gorilla gorilla	ENSGGOG00000008621	1 retrocopy	retro_ggor_2656,
Loxodonta africana	ENSLAFG00000006823	1 retrocopy	retro_lafr_409,
Microcebus murinus	ENSMICG00000007004	1 retrocopy	retro_mmur_1008,
Myotis lucifugus	ENSMLUG00000016978	1 retrocopy	retro_mluc_1331,
Macaca mulatta	ENSMMUG00000005938	2 retrocopies	retro_mmul_1090, retro_mmul_2288,
Mustela putorius furo	ENSMPUG00000017075	1 retrocopy	retro_mputfur_298,
Mus musculus	ENSMUSG00000027835	1 retrocopy	retro_mmus_2113,
Nomascus leucogenys	ENSNLEG00000004874	1 retrocopy	retro_nleu_532,
Otolemur garnettii	ENSOGAG00000013887	1 retrocopy	retro_ogar_540,
Oreochromis niloticus	ENSONIG00000005553	1 retrocopy	retro_onil_40,
Procavia capensis	ENSPCAG00000010385	1 retrocopy	retro_pcap_283,
Pongo abelii	ENSPPYG00000029750	1 retrocopy	retro_pabe_3257 ,
Pan troglodytes	ENSPTRG00000015598	1 retrocopy	retro_ptro_2683,
Sarcophilus harrisii	ENSSHAG00000005443	1 retrocopy	retro_shar_414,
Ictidomys tridecemlineatus	ENSSTOG00000028442	3 retrocopies	retro_itri_1208, retro_itri_1377, retro_itri_322,
Tupaia belangeri	ENSTBEG00000000240	9 retrocopies	retro_tbel_1498, retro_tbel_1690, retro_tbel_2223, retro_tbel_2903, retro_tbel_3430, retro_tbel_3898, retro_tbel_3900, retro_tbel_4532, retro_tbel_95,
Tarsius syrichta	ENSTSYG00000000708	1 retrocopy	retro_tsyr_1786,
Tursiops truncatus	ENSTTRG00000016315	1 retrocopy	retro_ttru_635,