RetrogeneDB ID: retro_pabe_179

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 17_random:11296883..11297189(-)
• Located in intron of: ENSPPYG00000008874

Retrocopy information

• Ensembl ID: ENSPPYG00000008875
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSPPYG00000025876
• Aliases: None
• Description: None

Sequence

>retro_pabe_179
ATGGCAGGACAAGCGTTTAGAAAGTTTCTTCCACTCTTTGACCGAGTATTGGTTGAAAGGAGTGCTGCTGAAACTGTAAC
CAAAGGAGGCATTATGCTTCCAGAAAAATCTCAAGGAAAAGTATTGCAAGCAACAGTAGTCGCTGTTGGATCGGGTTCCA
AAGGAAAGGGTGGAGAGATCCAACCAGTTAGCGTGAAAGTTGGAGATAAAGTTCTTCTCCCAGAATATGGAGGCACCAAA
GTAGTTCTAGATGACAAGGATTATTTCCTATTTAGAGATGGTGACATTCTTGGAAAGTACGTAGAC

Alignment

ORF - retro_pabe_179 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 100. %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAGQAFRKFLPLFDRVLVERSAAETVTKGGIMLPEKSQGKVLQATVVAVGSGSKGKGGEIQPVSVKVGDK
          MAGQAFRKFLPLFDRVLVERSAAETVTKGGIMLPEKSQGKVLQATVVAVGSGSKGKGGEIQPVSVKVGDK
Retrocopy MAGQAFRKFLPLFDRVLVERSAAETVTKGGIMLPEKSQGKVLQATVVAVGSGSKGKGGEIQPVSVKVGDK

Parental  VLLPEYGGTKVVLDDKDYFLFRDGDILGKYVD
          VLLPEYGGTKVVLDDKDYFLFRDGDILGKYVD
Retrocopy VLLPEYGGTKVVLDDKDYFLFRDGDILGKYVD

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	9.73 RPM
SRP007412_cerebellum	0.12 RPM	8.39 RPM
SRP007412_heart	0.00 RPM	12.64 RPM
SRP007412_kidney	0.00 RPM	29.50 RPM
SRP007412_liver	0.03 RPM	31.15 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_179 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_179 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_179 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 87 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000007417	17 retrocopies	retro_chof_1048, retro_chof_1160, retro_chof_143, retro_chof_1476, retro_chof_1561, retro_chof_1755, retro_chof_1880, retro_chof_2052, retro_chof_2053, retro_chof_226, retro_chof_303, retro_chof_414, retro_chof_420, retro_chof_86, retro_chof_907, retro_chof_91, retro_chof_940,
Dasypus novemcinctus	ENSDNOG00000013246	27 retrocopies	retro_dnov_1088, retro_dnov_1117, retro_dnov_1214, retro_dnov_1375, retro_dnov_1391, retro_dnov_1405, retro_dnov_1412, retro_dnov_1428, retro_dnov_1445, retro_dnov_1546, retro_dnov_1647, retro_dnov_1652, retro_dnov_1686, retro_dnov_1821, retro_dnov_2176, retro_dnov_2291, retro_dnov_2413, retro_dnov_2569, retro_dnov_2625, retro_dnov_2652, retro_dnov_418, retro_dnov_481, retro_dnov_483, retro_dnov_490, retro_dnov_524, retro_dnov_554, retro_dnov_966,
Erinaceus europaeus	ENSEEUG00000005040	6 retrocopies	retro_eeur_132, retro_eeur_278, retro_eeur_474, retro_eeur_611, retro_eeur_657, retro_eeur_698,
Macaca mulatta	ENSMMUG00000010491	1 retrocopy	retro_mmul_344,
Mus musculus	ENSMUSG00000073676	11 retrocopies	retro_mmus_1005, retro_mmus_1719, retro_mmus_1750, retro_mmus_1934, retro_mmus_2483, retro_mmus_2485, retro_mmus_301, retro_mmus_3077, retro_mmus_386, retro_mmus_872, retro_mmus_877,
Pongo abelii	ENSPPYG00000025876	1 retrocopy	retro_pabe_179 ,
Pan troglodytes	ENSPTRG00000012774	17 retrocopies	retro_ptro_1033, retro_ptro_1117, retro_ptro_1152, retro_ptro_1591, retro_ptro_1752, retro_ptro_1907, retro_ptro_1908, retro_ptro_2343, retro_ptro_2406, retro_ptro_2485, retro_ptro_2847, retro_ptro_287, retro_ptro_374, retro_ptro_667, retro_ptro_726, retro_ptro_786, retro_ptro_926,
Sus scrofa	ENSSSCG00000016078	7 retrocopies	retro_sscr_103, retro_sscr_1059, retro_sscr_106, retro_sscr_1088, retro_sscr_294, retro_sscr_298, retro_sscr_401,