RetrogeneDB ID: retro_pabe_3366

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 8:117861385..117861755(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NDUFB9
• Ensembl ID: ENSPPYG00000018869
• Aliases: None
• Description: NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 9, 22kDa [Source:HGNC Symbol;Acc:7704]

Sequence

>retro_pabe_3366
CAGAATGAAAAGGATATAATCAGGACCACCCAGCTGCTGAGGGGGACAGACGAAGAATTCTGGCACTGTCAGCCTCCACA
GCCATGTATCTTCCATGCTGTCTGGAGAGTACCTCCAATGAGAGATATAAGTGCTACAAGGTTCCAGAGTGGTTCTTAGA
TGATTGGCTTCCTTCTGAGAAAGCAATGCATCCTGACTACTGTGCCAAGAGACAGCAGTGGAAATAACTGTGGAGAGAAA
GCTGGGAGTGAGAAGTTAAGCAGCTGCAAGAGGAAATCCCACCTGGTGGTCCTAAGATTAAGCTCTCCTCCCTTCAGGAA
AGGAAAGCAATTTTCTCCCACTGCAGTTGTGTATTGTGACCAGACTCCGG

Alignment

ORF - retro_pabe_3366 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.11 %
• Parental protein coverage: 68. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  KNEKDMARA-QLLKEAEEEFWYRQHPQPYIF-PDSPGGTSYERYDC-KVPEWCLDDWHPSEK-MYPDYFA
          .NEKD..R..QLL....EEFW..Q.PQP.IF.P.....TS.ERY.C.KVPEW.LDDW.PSEK.M.PDY.A
Retrocopy QNEKDIIRTTQLLRGTDEEFWHCQPPQPCIF<PCCLESTSNERYKCYKVPEWFLDDWLPSEKAMHPDYCA

Parental  KREQWK-KQRESWR-EVKQLQEETPPGGPLTE-ALPPARKEGDLPPLWWYIVTRPR
          KR.QWK...RESW..EVKQLQEE.PPGGP....AL.P..KE....PL...IVTR.R
Retrocopy KRQQWK*LWRESWE*EVKQLQEEIPPGGPKIK<ALLPSGKESNFLPLQLCIVTRLR

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	6.03 RPM
SRP007412_cerebellum	0.00 RPM	3.65 RPM
SRP007412_heart	0.00 RPM	10.51 RPM
SRP007412_kidney	0.00 RPM	14.92 RPM
SRP007412_liver	0.00 RPM	8.60 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3366 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3366 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3366 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4112
Pan troglodytes	retro_ptro_2791
Gorilla gorilla	retro_ggor_2759

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Parental genes homology:

Parental genes homology involve 18 parental genes, and 30 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000010022	1 retrocopy	retro_acar_132,
Ailuropoda melanoleuca	ENSAMEG00000015852	2 retrocopies	retro_amel_1680, retro_amel_553,
Callithrix jacchus	ENSCJAG00000012818	1 retrocopy	retro_cjac_2125,
Equus caballus	ENSECAG00000018238	1 retrocopy	retro_ecab_541,
Felis catus	ENSFCAG00000004678	1 retrocopy	retro_fcat_689,
Homo sapiens	ENSG00000147684	2 retrocopies	retro_hsap_3905, retro_hsap_4112,
Gorilla gorilla	ENSGGOG00000015883	2 retrocopies	retro_ggor_2632, retro_ggor_2759,
Microcebus murinus	ENSMICG00000017481	1 retrocopy	retro_mmur_1494,
Myotis lucifugus	ENSMLUG00000003765	1 retrocopy	retro_mluc_1339,
Macaca mulatta	ENSMMUG00000015493	1 retrocopy	retro_mmul_1736,
Monodelphis domestica	ENSMODG00000001831	3 retrocopies	retro_mdom_1176, retro_mdom_1193, retro_mdom_1582,
Nomascus leucogenys	ENSNLEG00000005484	2 retrocopies	retro_nleu_1141, retro_nleu_578,
Otolemur garnettii	ENSOGAG00000030772	2 retrocopies	retro_ogar_1654, retro_ogar_925,
Pongo abelii	ENSPPYG00000018869	3 retrocopies	retro_pabe_2643, retro_pabe_3182, retro_pabe_3366 ,
Pan troglodytes	ENSPTRG00000020569	2 retrocopies	retro_ptro_2656, retro_ptro_2791,
Pteropus vampyrus	ENSPVAG00000009153	1 retrocopy	retro_pvam_243,
Ictidomys tridecemlineatus	ENSSTOG00000021955	1 retrocopy	retro_itri_611,
Tupaia belangeri	ENSTBEG00000006895	3 retrocopies	retro_tbel_1901, retro_tbel_2663, retro_tbel_610,