RetrogeneDB ID: retro_pabe_2879

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 6:71189852..71190312(+)
• Located in intron of: ENSPPYG00000016763

Retrocopy information

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

Parental gene information

• Parental gene symbol: NDUFAB1
• Ensembl ID: ENSPPYG00000007192
• Aliases: None
• Description: NADH dehydrogenase (ubiquinone) 1, alpha/beta subcomplex, 1, 8kDa [Source:HGNC Symbol;Acc:7694]

Sequence

>retro_pabe_2879
ATGGCAGCTTGTGTCTGCCACCTGCCCTTGGCCATCACACTGATGCCCCGGGTCCCATGCTGGCCACAGCCTGCTGCTCA
GCATCACTTGTGCTCTGTGGGGACTCTGATGAGGCTGGGGCTTTGCAGCTGGCTCCACAGCGGGCTTTGGTGCTTGTGCA
CGTGCTGGGTAGAAGTTACACAGTTGTGCTGTCAGTATAGTGACATGCCCCCTTTGACGTTAGAGGGAATCAAAGACTGT
CTTCTTTATATCTTGAAACCCTGTGACAAGATTGACCCAGAGAAGCTCTCAGTGAATTCTTACTTTATGAAAGACCTGTG
CTTTGACAGTTTGGACCAAGTAGAGAGTACGCATGGTCATGGAAGATAAATTTGGGTTTGAAATTCCTGATATAGATGTG
GAAAAGTTAATATGTCCACAAGAAATTGTAGATTATATTGCAGATAAGAGAGATGTATAT

Alignment

ORF - retro_pabe_2879 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.97 %
• Parental protein coverage: 96.15 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  LSAYVRRLPAAFAPLPRVR-MLAVARPLSTALCSAGTQTRLGPL----QPASVLAQVPGR-VTQLCRQYS
          ..A.V..LP.A....PRV..MLA.A...S..L...G.....G.L....Q.A.VL..V.GR.VTQLC.QYS
Retrocopy MAACVCHLPLAITLMPRVP<MLATAC-CSASLVLCGDSDEAGALQLAPQRALVLVHVLGR>VTQLCCQYS

Parental  DMPPLTLEGIQDRVLYVLKLYDKIDPEKLSVNSHFMKDLGLDSLDQVE-IIMAMEDEFGFEIPDIDAEKL
          DMPPLTLEGI.D..LY.LK..DKIDPEKLSVNS.FMKDL..DSLDQVE...M.MED.FGFEIPDID.EKL
Retrocopy DMPPLTLEGIKDCLLYILKPCDKIDPEKLSVNSYFMKDLCFDSLDQVE>VRMVMEDKFGFEIPDIDVEKL

Parental  MCPQEIVDYIADKKDVY
          .CPQEIVDYIADK.DVY
Retrocopy ICPQEIVDYIADKRDVY

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	23.94 RPM
SRP007412_cerebellum	0.00 RPM	26.02 RPM
SRP007412_heart	0.00 RPM	44.88 RPM
SRP007412_kidney	0.07 RPM	28.61 RPM
SRP007412_liver	0.00 RPM	20.75 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2879 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2879 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2879 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3484
Pan troglodytes	retro_ptro_2358
Gorilla gorilla	retro_ggor_2349

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Parental genes homology:

Parental genes homology involve 17 parental genes, and 34 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000014304	1 retrocopy	retro_amel_1692,
Canis familiaris	ENSCAFG00000017667	3 retrocopies	retro_cfam_1738, retro_cfam_1821, retro_cfam_450,
Callithrix jacchus	ENSCJAG00000020616	2 retrocopies	retro_cjac_2635, retro_cjac_3099,
Cavia porcellus	ENSCPOG00000012038	2 retrocopies	retro_cpor_728, retro_cpor_767,
Felis catus	ENSFCAG00000013241	3 retrocopies	retro_fcat_1104, retro_fcat_1181, retro_fcat_2012,
Homo sapiens	ENSG00000004779	1 retrocopy	retro_hsap_3484,
Gorilla gorilla	ENSGGOG00000006320	1 retrocopy	retro_ggor_2349,
Macropus eugenii	ENSMEUG00000012681	3 retrocopies	retro_meug_1780, retro_meug_303, retro_meug_830,
Microcebus murinus	ENSMICG00000007778	2 retrocopies	retro_mmur_1193, retro_mmur_120,
Macaca mulatta	ENSMMUG00000020522	1 retrocopy	retro_mmul_101,
Monodelphis domestica	ENSMODG00000016352	1 retrocopy	retro_mdom_389,
Mus musculus	ENSMUSG00000030869	6 retrocopies	retro_mmus_1724, retro_mmus_2073, retro_mmus_2188, retro_mmus_2947, retro_mmus_3094, retro_mmus_3332,
Otolemur garnettii	ENSOGAG00000005562	2 retrocopies	retro_ogar_2916, retro_ogar_325,
Pongo abelii	ENSPPYG00000007192	1 retrocopy	retro_pabe_2879 ,
Pan troglodytes	ENSPTRG00000007889	1 retrocopy	retro_ptro_2358,
Rattus norvegicus	ENSRNOG00000018129	2 retrocopies	retro_rnor_1353, retro_rnor_2058,
Ictidomys tridecemlineatus	ENSSTOG00000024657	2 retrocopies	retro_itri_281, retro_itri_916,