RetrogeneDB ID: retro_pabe_2242

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 3:109613116..109613654(+)
• Located in intron of: ENSPPYG00000014020

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSPPYG00000013315
• Aliases: None
• Description: None

Sequence

>retro_pabe_2242
ATGCTGACACCTGTAAGCAAACTGAAGTGCGATGACAGTCTTAAACGGTCTGGGACGTCAGCCATAGCATCCGGCCCAAC
TCAGAGGGTTCTGTGAGAGACAAGTTGATTGTTAAAGAGGTTGCAGAGCTTGAGCTTATTTACCTTGTACATGTCAAGTG
TATTTCCTGATCTAAAAAGCTTCATTGCTTTCTGCTGACTGTAACCCCAGACGAGGGTTACTACTAGGGTGGAAAATTTC
AGCTCGAAACTGGACTTCCTGATGCATACAACATGGTGCCTTCCAAAGTGAAATGCCTGACCAGGATCTGGTACCCTAAC
ATCACAGAAATGGGGGAAATATGTCTAAAGTTTACTGAGGACATTCAATTGACAGCACTGGCTGGGCTCCCACAAGAACA
TTAAAGGATGTTATTTGGAGATTAAATTATTTGTTTACTAATCTTCTGAATTTTGACGATCCACTGAATGTTGAAGCTGC
AGAACATCATTTGTGGGACAAGGAGGACTTCTTGAATAAAGTCGATGACTACATCAAG

Alignment

ORF - retro_pabe_2242 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.34 %
• Parental protein coverage: 97.84 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  MLTLASKLKRDDGLKGSRTAATASDSTRRV-SVRDKLLVKEVAELE-ANLPCTCKVHF-PD-PNKLHCFQ
          MLT..SKLK.DD.LK.S.T.A.AS..T.RV.SVRDKL.VKEVAELE.A.LPCTC.V.F.PD...KLHCF.
Retrocopy MLTPVSKLKCDDSLKRSGTSAIASGPTQRV<SVRDKLIVKEVAELE<AYLPCTCQVYF<PD<SKKLHCFL

Parental  LTVTPDEGYYQGGKFQFETEVPDAYNMVPPKVKCLTKIWHPNITETGEICLSLLRE-HSIDGTGWAPTRT
          LTVTPDEGYY.GGKFQ.ET..PDAYNMVP.KVKCLT.IW.PNITE.GEICL......HSID.TGWAPTRT
Retrocopy LTVTPDEGYY*GGKFQLETGLPDAYNMVPSKVKCLTRIWYPNITEMGEICLKFTED<HSIDSTGWAPTRT

Parental  LKDVVWGLNSLFTDLLNFDDPLNIEAAEHHLRDKEDFRNKVDDYIK
          LKDV.W.LN.LFT.LLNFDDPLN.EAAEHHL.DKEDF.NKVDDYIK
Retrocopy LKDVIWRLNYLFTNLLNFDDPLNVEAAEHHLWDKEDFLNKVDDYIK

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	9.23 RPM
SRP007412_cerebellum	0.36 RPM	6.69 RPM
SRP007412_heart	0.18 RPM	6.41 RPM
SRP007412_kidney	0.17 RPM	6.36 RPM
SRP007412_liver	0.15 RPM	12.00 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2242 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2242 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2242 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 24 parental genes, and 59 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000008551	1 retrocopy	retro_amel_572,
Bos taurus	ENSBTAG00000026114	2 retrocopies	retro_btau_1698, retro_btau_948,
Canis familiaris	ENSCAFG00000012363	1 retrocopy	retro_cfam_1275,
Callithrix jacchus	ENSCJAG00000000476	3 retrocopies	retro_cjac_2378, retro_cjac_2980, retro_cjac_3219,
Cavia porcellus	ENSCPOG00000006368	1 retrocopy	retro_cpor_1122,
Dasypus novemcinctus	ENSDNOG00000000506	2 retrocopies	retro_dnov_1301, retro_dnov_132,
Equus caballus	ENSECAG00000011687	1 retrocopy	retro_ecab_158,
Echinops telfairi	ENSETEG00000009230	1 retrocopy	retro_etel_1534,
Homo sapiens	ENSG00000184182	2 retrocopies	retro_hsap_2439, retro_hsap_2773,
Gorilla gorilla	ENSGGOG00000010709	3 retrocopies	retro_ggor_1518, retro_ggor_1519, retro_ggor_1930,
Microcebus murinus	ENSMICG00000012075	5 retrocopies	retro_mmur_1014, retro_mmur_114, retro_mmur_1365, retro_mmur_584, retro_mmur_815,
Myotis lucifugus	ENSMLUG00000001286	5 retrocopies	retro_mluc_1237, retro_mluc_1674, retro_mluc_1747, retro_mluc_1789, retro_mluc_2627,
Macaca mulatta	ENSMMUG00000018482	4 retrocopies	retro_mmul_1450, retro_mmul_1585, retro_mmul_254, retro_mmul_628,
Mustela putorius furo	ENSMPUG00000000101	1 retrocopy	retro_mputfur_782,
Mus musculus	ENSMUSG00000034343	3 retrocopies	retro_mmus_2161, retro_mmus_255, retro_mmus_845,
Nomascus leucogenys	ENSNLEG00000011152	2 retrocopies	retro_nleu_1340, retro_nleu_677,
Otolemur garnettii	ENSOGAG00000005308	7 retrocopies	retro_ogar_1109, retro_ogar_1995, retro_ogar_2491, retro_ogar_2551, retro_ogar_2715, retro_ogar_639, retro_ogar_761,
Pongo abelii	ENSPPYG00000013315	3 retrocopies	retro_pabe_1395, retro_pabe_1785, retro_pabe_2242 ,
Pan troglodytes	ENSPTRG00000013081	2 retrocopies	retro_ptro_1410, retro_ptro_1876,
Rattus norvegicus	ENSRNOG00000019953	1 retrocopy	retro_rnor_2696,
Sus scrofa	ENSSSCG00000027723	3 retrocopies	retro_sscr_291, retro_sscr_423, retro_sscr_542,
Tarsius syrichta	ENSTSYG00000011510	3 retrocopies	retro_tsyr_1718, retro_tsyr_1944, retro_tsyr_2133,
Tursiops truncatus	ENSTTRG00000011528	2 retrocopies	retro_ttru_1297, retro_ttru_1455,
Vicugna pacos	ENSVPAG00000010485	1 retrocopy	retro_vpac_361,