RetrogeneDB ID: retro_pabe_3339

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 8:66768793..66769033(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NDUFA4
• Ensembl ID: ENSPPYG00000017780
• Aliases: None
• Description: NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 4, 9kDa [Source:HGNC Symbol;Acc:7687]

Sequence

>retro_pabe_3339
ATGCTCCGCTAGATTCTCAGTCAGGCCAAGAAGCATCCGAGCTTGATCCCCCTCTTTACATTTATTGGAGCTGGAGGTAC
TGGAGCAGCACAATTTGTCTTGCATCTGGCATCGTTCAATACAGATGTTAGCTGGGACAGAAAGAACCCAGAGCCCTGGA
ACAAATGGGGTCCCAATGATCAATACAAGTTTTACTCAATGAATGTAGATTACAGCAAACTGAAGAAAGAAGGTCCAGAT

Alignment

ORF - retro_pabe_3339 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.75 %
• Parental protein coverage: 98.77 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MLRQILSQAKKHPSLIPLFVFIGTGASGATLYLLRLALFNPDVCWDRNNPEPWNKLGPNDQYKFYSVNVD
          MLR.ILSQAKKHPSLIPLF.FIG.G..GA....L.LA.FN.DV.WDR.NPEPWNK.GPNDQYKFYS.NVD
Retrocopy MLR*ILSQAKKHPSLIPLFTFIGAGGTGAAQFVLHLASFNTDVSWDRKNPEPWNKWGPNDQYKFYSMNVD

Parental  YSKLKKERPD
          YSKLKKE.PD
Retrocopy YSKLKKEGPD

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	157.08 RPM
SRP007412_cerebellum	0.00 RPM	123.06 RPM
SRP007412_heart	0.00 RPM	305.28 RPM
SRP007412_kidney	0.00 RPM	125.86 RPM
SRP007412_liver	0.00 RPM	57.07 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3339 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3339 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3339 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4067
Pan troglodytes	retro_ptro_2756

---

Parental genes homology:

Parental genes homology involve 28 parental genes, and 193 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000002493	10 retrocopies	retro_amel_1356, retro_amel_1633, retro_amel_18, retro_amel_1800, retro_amel_1866, retro_amel_533, retro_amel_608, retro_amel_638, retro_amel_845, retro_amel_955,
Bos taurus	ENSBTAG00000011145	7 retrocopies	retro_btau_1075, retro_btau_1155, retro_btau_1375, retro_btau_1454, retro_btau_1710, retro_btau_645, retro_btau_800,
Choloepus hoffmanni	ENSCHOG00000012330	1 retrocopy	retro_chof_2667,
Callithrix jacchus	ENSCJAG00000000748	3 retrocopies	retro_cjac_3291, retro_cjac_36, retro_cjac_90,
Dasypus novemcinctus	ENSDNOG00000011217	12 retrocopies	retro_dnov_1874, retro_dnov_1921, retro_dnov_2015, retro_dnov_2258, retro_dnov_2566, retro_dnov_2567, retro_dnov_2641, retro_dnov_349, retro_dnov_506, retro_dnov_725, retro_dnov_744, retro_dnov_764,
Equus caballus	ENSECAG00000026987	1 retrocopy	retro_ecab_370,
Felis catus	ENSFCAG00000024790	4 retrocopies	retro_fcat_261, retro_fcat_449, retro_fcat_459, retro_fcat_905,
Homo sapiens	ENSG00000189043	18 retrocopies	retro_hsap_1459, retro_hsap_200, retro_hsap_2374, retro_hsap_2386, retro_hsap_259, retro_hsap_2685, retro_hsap_2726, retro_hsap_285, retro_hsap_3241, retro_hsap_4067, retro_hsap_4188, retro_hsap_4292, retro_hsap_4699, retro_hsap_4700, retro_hsap_4750, retro_hsap_4856, retro_hsap_650, retro_hsap_877,
Gorilla gorilla	ENSGGOG00000001437	3 retrocopies	retro_ggor_249, retro_ggor_30, retro_ggor_567,
Microcebus murinus	ENSMICG00000013999	5 retrocopies	retro_mmur_1225, retro_mmur_1314, retro_mmur_133, retro_mmur_341, retro_mmur_696,
Myotis lucifugus	ENSMLUG00000006470	6 retrocopies	retro_mluc_1778, retro_mluc_1821, retro_mluc_329, retro_mluc_450, retro_mluc_517, retro_mluc_849,
Macaca mulatta	ENSMMUG00000020894	2 retrocopies	retro_mmul_272, retro_mmul_274,
Monodelphis domestica	ENSMODG00000014107	2 retrocopies	retro_mdom_1095, retro_mdom_1593,
Mustela putorius furo	ENSMPUG00000014152	8 retrocopies	retro_mputfur_1127, retro_mputfur_1600, retro_mputfur_416, retro_mputfur_696, retro_mputfur_711, retro_mputfur_790, retro_mputfur_827, retro_mputfur_880,
Mus musculus	ENSMUSG00000029632	4 retrocopies	retro_mmus_2172, retro_mmus_3219, retro_mmus_3412, retro_mmus_3620,
Oryctolagus cuniculus	ENSOCUG00000029372	1 retrocopy	retro_ocun_41,
Otolemur garnettii	ENSOGAG00000000358	17 retrocopies	retro_ogar_1023, retro_ogar_1026, retro_ogar_1319, retro_ogar_1403, retro_ogar_1566, retro_ogar_1960, retro_ogar_1976, retro_ogar_2050, retro_ogar_2350, retro_ogar_2528, retro_ogar_3023, retro_ogar_3413, retro_ogar_3434, retro_ogar_3457, retro_ogar_694, retro_ogar_731, retro_ogar_997,
Ochotona princeps	ENSOPRG00000014186	3 retrocopies	retro_opri_1138, retro_opri_275, retro_opri_633,
Pongo abelii	ENSPPYG00000017780	5 retrocopies	retro_pabe_2296, retro_pabe_24, retro_pabe_301, retro_pabe_3339 , retro_pabe_678,
Pan troglodytes	ENSPTRG00000018934	19 retrocopies	retro_ptro_1134, retro_ptro_1736, retro_ptro_1745, retro_ptro_1811, retro_ptro_182, retro_ptro_1842, retro_ptro_219, retro_ptro_2191, retro_ptro_235, retro_ptro_2756, retro_ptro_2844, retro_ptro_2908, retro_ptro_3034, retro_ptro_3123, retro_ptro_3165, retro_ptro_3233, retro_ptro_473, retro_ptro_766, retro_ptro_993,
Pteropus vampyrus	ENSPVAG00000006660	5 retrocopies	retro_pvam_1092, retro_pvam_1436, retro_pvam_1441, retro_pvam_545, retro_pvam_798,
Rattus norvegicus	ENSRNOG00000005512	3 retrocopies	retro_rnor_1880, retro_rnor_2327, retro_rnor_2985,
Sorex araneus	ENSSARG00000011125	8 retrocopies	retro_sara_160, retro_sara_203, retro_sara_316, retro_sara_339, retro_sara_49, retro_sara_536, retro_sara_659, retro_sara_747,
Sus scrofa	ENSSSCG00000024313	6 retrocopies	retro_sscr_1155, retro_sscr_367, retro_sscr_552, retro_sscr_642, retro_sscr_682, retro_sscr_733,
Tupaia belangeri	ENSTBEG00000016629	16 retrocopies	retro_tbel_1049, retro_tbel_1848, retro_tbel_2008, retro_tbel_2058, retro_tbel_2194, retro_tbel_2274, retro_tbel_2423, retro_tbel_2761, retro_tbel_3262, retro_tbel_4255, retro_tbel_4309, retro_tbel_436, retro_tbel_4380, retro_tbel_4426, retro_tbel_4719, retro_tbel_815,
Tarsius syrichta	ENSTSYG00000000041	15 retrocopies	retro_tsyr_1427, retro_tsyr_1650, retro_tsyr_1766, retro_tsyr_1948, retro_tsyr_1973, retro_tsyr_1974, retro_tsyr_198, retro_tsyr_270, retro_tsyr_425, retro_tsyr_473, retro_tsyr_492, retro_tsyr_659, retro_tsyr_685, retro_tsyr_821, retro_tsyr_937,
Tursiops truncatus	ENSTTRG00000013045	8 retrocopies	retro_ttru_1057, retro_ttru_132, retro_ttru_1709, retro_ttru_1745, retro_ttru_1841, retro_ttru_218, retro_ttru_257, retro_ttru_308,
Vicugna pacos	ENSVPAG00000010003	1 retrocopy	retro_vpac_262,