RetrogeneDB ID: retro_pabe_2519

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 4:62910948..62911485(-)
• Located in intron of: ENSPPYG00000014742

Retrocopy information

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

Parental gene information

• Parental gene symbol: UBE2C
• Ensembl ID: ENSPPYG00000011071
• Aliases: None
• Description: ubiquitin-conjugating enzyme E2C [Source:HGNC Symbol;Acc:15937]

Sequence

>retro_pabe_2519
ATAGCCTCTCAAAACCTTGACCCAGCTGCCACCAGCATTGCTGCTGCCTATAAAGGTACCACCCCCAGCAGGGGTGCTGC
CCGGGACCCTGTGGGCAAAAGGCTACAGCAGGAGTTGGTGACCTTCACAATGCCTGGTGACGCAGGGATTTCTGCCTTCC
CTGAATCAGGCAACCTTTTCAAATGGGTGGGGATCATCCATTGAGCAGCTGGCACAGCATATGAAGACCTGAGGTTTAAG
CTTTCCCTAGAGTTCCCCAGGGGCTACTCTTACAATGTACCCATGGTGAAGTTCCTCAGGCCCTGCTACCACCCCAACAT
GGACACCCAGGGTAACATCTGCCTGGACATCCTGAAGGACAAGTGGTCTGCCCTGTATGATGTCAGGACCATCCTGCTCT
CCATCCACAGCCTTCGAGGAGAACCCAACATTGATAGCCCTTTGAACAGGCATGCTGCCAAGCTCTGGAAAACCCCCACA
GCTTTTAAGAAGCACCTGTAAGAAACCTACTTAAAGCAGGTCACCAGCCAGGAGCCC

Alignment

ORF - retro_pabe_2519 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.56 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MASQNRDPAATSVAAARKGAEPSGGAARGPVGKRLQQELMTLMMSGDKGISAFPESDNLFKWVGTIHGAA
          .ASQN.DPAATS.AAA.KG..PS.GAAR.PVGKRLQQEL.T..M.GD.GISAFPES.NLFKWVG.IH.AA
Retrocopy IASQNLDPAATSIAAAYKGTTPSRGAARDPVGKRLQQELVTFTMPGDAGISAFPESGNLFKWVGIIH*AA

Parental  GTVYEDLRYKLSLEFPSGYPYNAPTVKFLTPCYHPNVDTQGNICLDILKEKWSALYDVRTILLSIQSLLG
          GT.YEDLR.KLSLEFP.GY.YN.P.VKFL.PCYHPN.DTQGNICLDILK.KWSALYDVRTILLSI.SL.G
Retrocopy GTAYEDLRFKLSLEFPRGYSYNVPMVKFLRPCYHPNMDTQGNICLDILKDKWSALYDVRTILLSIHSLRG

Parental  EPNIDSPLNTHAAELWKNPTAFKKYLQETYSKQVTSQEP
          EPNIDSPLN.HAA.LWK.PTAFKK.L.ETY.KQVTSQEP
Retrocopy EPNIDSPLNRHAAKLWKTPTAFKKHL*ETYLKQVTSQEP

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	0.39 RPM
SRP007412_cerebellum	0.00 RPM	0.00 RPM
SRP007412_heart	0.09 RPM	0.66 RPM
SRP007412_kidney	0.43 RPM	0.27 RPM
SRP007412_liver	0.03 RPM	1.01 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2519 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2519 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2519 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2935
Gorilla gorilla	retro_ggor_2035
Macaca mulatta	retro_mmul_1951

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 64 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000014102	2 retrocopies	retro_cpor_1007, retro_cpor_211,
Dipodomys ordii	ENSDORG00000011774	4 retrocopies	retro_dord_157, retro_dord_386, retro_dord_421, retro_dord_84,
Homo sapiens	ENSG00000175063	3 retrocopies	retro_hsap_1474, retro_hsap_1922, retro_hsap_2935,
Gorilla gorilla	ENSGGOG00000026061	3 retrocopies	retro_ggor_1130, retro_ggor_1402, retro_ggor_2035,
Macropus eugenii	ENSMEUG00000007177	14 retrocopies	retro_meug_1021, retro_meug_1128, retro_meug_1203, retro_meug_1398, retro_meug_1435, retro_meug_145, retro_meug_1476, retro_meug_1504, retro_meug_1575, retro_meug_1773, retro_meug_1808, retro_meug_2034, retro_meug_334, retro_meug_645,
Myotis lucifugus	ENSMLUG00000006715	4 retrocopies	retro_mluc_2164, retro_mluc_2220, retro_mluc_600, retro_mluc_636,
Macaca mulatta	ENSMMUG00000021023	4 retrocopies	retro_mmul_1345, retro_mmul_170, retro_mmul_1951, retro_mmul_777,
Monodelphis domestica	ENSMODG00000013661	6 retrocopies	retro_mdom_1549, retro_mdom_1552, retro_mdom_1732, retro_mdom_1970, retro_mdom_2020, retro_mdom_415,
Mus musculus	ENSMUSG00000001403	5 retrocopies	retro_mmus_1344, retro_mmus_1593, retro_mmus_1770, retro_mmus_2881, retro_mmus_3512,
Otolemur garnettii	ENSOGAG00000004989	3 retrocopies	retro_ogar_2347, retro_ogar_249, retro_ogar_3067,
Ochotona princeps	ENSOPRG00000014284	4 retrocopies	retro_opri_1009, retro_opri_1055, retro_opri_222, retro_opri_50,
Pongo abelii	ENSPPYG00000011071	4 retrocopies	retro_pabe_1155, retro_pabe_1221, retro_pabe_1589, retro_pabe_2519 ,
Pan troglodytes	ENSPTRG00000013564	1 retrocopy	retro_ptro_38,
Pteropus vampyrus	ENSPVAG00000000369	1 retrocopy	retro_pvam_423,
Rattus norvegicus	ENSRNOG00000015131	5 retrocopies	retro_rnor_1390, retro_rnor_2131, retro_rnor_2470, retro_rnor_719, retro_rnor_864,
Tursiops truncatus	ENSTTRG00000015987	1 retrocopy	retro_ttru_1752,