RetrogeneDB ID: retro_pabe_2215

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 3:54711667..54712204(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: APOO
• Ensembl ID: ENSPPYG00000020191
• Aliases: None
• Description: apolipoprotein O [Source:HGNC Symbol;Acc:28727]

Sequence

>retro_pabe_2215
TTCAAGGCAACTCAGAGGTGCATAGGGTAAGCTGGCATGAGTTTGCTCATCTTCAAACTCTGTGCAGCACCAAGAAAGGA
CTCACGTCCCAAATATCCCATGAAGCTTGATGAGCTTTCACTCTACTCAGTTCCTAAGGGTGAATTTGAATATATGGAGG
AGTGGAGGACCCAGTTTGAAGAAAGCATCTCTCAGCTCCAACATTACTGTAGGCCATGTACAAGTTGGTGTCAGGAAACA
TACTCCCAAACTAATTCCAAGATGCAAAGTTTGGGTCAATGAGGGTTAGACAGCTATGAATATCTCCAAATGCACCTCCA
GGATTTTTTCCAAGACTTGGTGTTATTGGTTTTGCTGGTCTTTTTGGACTCTTTTTGGCAAAAGGTTACAAAATTAAAGA
AGCTGGTATAGCCTTCTGGTTTCATGGGATTAGCTGCCTCTGCCTATTATCTACAACAATTCATTGCATTTGCCCAGGTC
AGTGGGGAGAGTTTACATGGTTGGGATTTATGAAGATACATAGTCCTATAAGATTTG

Alignment

ORF - retro_pabe_2215 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.17 %
• Parental protein coverage: 90.4 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  FKVIQRSVGPASLSLLTFKVYAAPKKDSPPKNSVKVDELSLYSVPEGQSKYVEEARSQLEESISQLRHYC
          FK..QR..G.A..SLL.FK..AAP.KDS.PK...K.DELSLYSVP.G...Y.EE.R.Q.EESISQL.HYC
Retrocopy FKATQRCIG*AGMSLLIFKLCAAPRKDSRPKYPMKLDELSLYSVPKGEFEYMEEWRTQFEESISQLQHYC

Parental  EPYTTWCQETYSQTKPKMQSLVQWGLDSYDYLQ-NAPPGFFPRLGVIGFAGLIGLLLARG-SKIKKLVYP
          .P.T.WCQETYSQT..KMQSL.Q.GLDSY.YLQ.NAPPGFFPRLGVIGFAGL.GL.LA.G..K.KKLV.P
Retrocopy RPCTSWCQETYSQTNSKMQSLGQ*GLDSYEYLQ<NAPPGFFPRLGVIGFAGLFGLFLAKG>TKLKKLV*P

Parental  PGFMGLAASLYYPQQAIVFAQVSGERLYDWGLRGYIVIEDL
          .GFMGLAAS.YY.QQ.I.FAQVSGE.L..W.L..YIV..DL
Retrocopy SGFMGLAASAYYLQQFIAFAQVSGESLHGWDL*RYIVL*DL

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	15.15 RPM
SRP007412_cerebellum	0.00 RPM	13.01 RPM
SRP007412_heart	0.00 RPM	15.44 RPM
SRP007412_kidney	0.00 RPM	13.89 RPM
SRP007412_liver	0.00 RPM	3.43 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2215 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2215 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2215 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 23 parental genes, and 61 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000012749	1 retrocopy	retro_amel_1282,
Choloepus hoffmanni	ENSCHOG00000000226	2 retrocopies	retro_chof_2372, retro_chof_839,
Callithrix jacchus	ENSCJAG00000004909	8 retrocopies	retro_cjac_1360, retro_cjac_1417, retro_cjac_1448, retro_cjac_1767, retro_cjac_1792, retro_cjac_1896, retro_cjac_2038, retro_cjac_2063,
Dasypus novemcinctus	ENSDNOG00000006710	1 retrocopy	retro_dnov_2450,
Equus caballus	ENSECAG00000013441	1 retrocopy	retro_ecab_145,
Echinops telfairi	ENSETEG00000014150	3 retrocopies	retro_etel_1052, retro_etel_516, retro_etel_711,
Felis catus	ENSFCAG00000000029	3 retrocopies	retro_fcat_1203, retro_fcat_1657, retro_fcat_1798,
Homo sapiens	ENSG00000184831	5 retrocopies	retro_hsap_1018, retro_hsap_1693, retro_hsap_2670, retro_hsap_3047, retro_hsap_3259,
Gorilla gorilla	ENSGGOG00000001200	4 retrocopies	retro_ggor_1269, retro_ggor_1863, retro_ggor_2098, retro_ggor_806,
Loxodonta africana	ENSLAFG00000029070	1 retrocopy	retro_lafr_1114,
Macropus eugenii	ENSMEUG00000014222	1 retrocopy	retro_meug_700,
Macaca mulatta	ENSMMUG00000016361	4 retrocopies	retro_mmul_1584, retro_mmul_1886, retro_mmul_2051, retro_mmul_814,
Monodelphis domestica	ENSMODG00000025554	1 retrocopy	retro_mdom_1510,
Mustela putorius furo	ENSMPUG00000000109	1 retrocopy	retro_mputfur_109,
Mus musculus	ENSMUSG00000079508	1 retrocopy	retro_mmus_282,
Nomascus leucogenys	ENSNLEG00000010026	5 retrocopies	retro_nleu_1167, retro_nleu_1338, retro_nleu_1944, retro_nleu_456, retro_nleu_898,
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	ENSPTRG00000021742	5 retrocopies	retro_ptro_1147, retro_ptro_1799, retro_ptro_1992, retro_ptro_2205, retro_ptro_746,
Pteropus vampyrus	ENSPVAG00000002530	2 retrocopies	retro_pvam_128, retro_pvam_594,
Sarcophilus harrisii	ENSSHAG00000008734	1 retrocopy	retro_shar_125,
Sus scrofa	ENSSSCG00000012174	1 retrocopy	retro_sscr_774,
Tarsius syrichta	ENSTSYG00000010239	2 retrocopies	retro_tsyr_1089, retro_tsyr_2155,