RetrogeneDB ID: retro_pabe_1795

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 20:61207825..61208068(+)
• Located in intron of: ENSPPYG00000011219

Retrocopy information

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

Parental gene information

• Parental gene symbol: DPH3
• Ensembl ID: ENSPPYG00000014083
• Aliases: None
• Description: DPH3 homolog [Source:UniProtKB/Swiss-Prot;Acc:Q5R7N8]

Sequence

>retro_pabe_1795
ATGGCAGTATTTCACGGGGTGGAAATTGAGGACTTCCAATATGACGAGGACTCGGAGACGTATTTCTGTCCCTGCCCAAG
TGGAGATAACTTCTCCATCACCAAGGAGGAGTTGGAGAATGGGGAAGGCGTGGCAATGTGTCCAGGCTGCTCTCTCATTA
TAAAAGTGATTTATGACAAAGATCAGTTTGCGTGTGGAGAAACAGTCCCAGTGCCTTCAGCCAACAAAGAATGAGTTAAA
TGC

Alignment

ORF - retro_pabe_1795 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.59 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAVFHDEVEIEDFQYDEDSETYFYPCPCGDNFSITKEDLENGEDVATCPSCSLIIKVIYDKDQFVCGETV
          MAVFH..VEIEDFQYDEDSETYF.PCP.GDNFSITKE.LENGE.VA.CP.CSLIIKVIYDKDQF.CGETV
Retrocopy MAVFHG-VEIEDFQYDEDSETYFCPCPSGDNFSITKEELENGEGVAMCPGCSLIIKVIYDKDQFACGETV

Parental  PAPSANKELVKC
          P.PSANKE.VKC
Retrocopy PVPSANKE*VKC

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	0.17 RPM	13.49 RPM
SRP007412_cerebellum	0.24 RPM	19.33 RPM
SRP007412_heart	0.24 RPM	14.06 RPM
SRP007412_kidney	0.00 RPM	11.77 RPM
SRP007412_liver	0.12 RPM	16.65 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1795 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1795 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1795 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2438
Pan troglodytes	retro_ptro_1409
Gorilla gorilla	retro_ggor_174

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 23 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000012030	1 retrocopy	retro_dnov_39,
Dipodomys ordii	ENSDORG00000011642	1 retrocopy	retro_dord_167,
Erinaceus europaeus	ENSEEUG00000009790	1 retrocopy	retro_eeur_502,
Echinops telfairi	ENSETEG00000016272	1 retrocopy	retro_etel_1879,
Homo sapiens	ENSG00000154813	1 retrocopy	retro_hsap_2438,
Gorilla gorilla	ENSGGOG00000022108	1 retrocopy	retro_ggor_174,
Loxodonta africana	ENSLAFG00000025650	3 retrocopies	retro_lafr_31, retro_lafr_545, retro_lafr_87,
Macaca mulatta	ENSMMUG00000022692	2 retrocopies	retro_mmul_2085, retro_mmul_497,
Monodelphis domestica	ENSMODG00000025472	3 retrocopies	retro_mdom_131, retro_mdom_1434, retro_mdom_609,
Mus musculus	ENSMUSG00000021905	1 retrocopy	retro_mmus_196,
Nomascus leucogenys	ENSNLEG00000001096	2 retrocopies	retro_nleu_2876, retro_nleu_2913,
Pongo abelii	ENSPPYG00000014083	1 retrocopy	retro_pabe_1795 ,
Pan troglodytes	ENSPTRG00000014671	1 retrocopy	retro_ptro_1409,
Tupaia belangeri	ENSTBEG00000011675	1 retrocopy	retro_tbel_58,
Tursiops truncatus	ENSTTRG00000007739	3 retrocopies	retro_ttru_1474, retro_ttru_31, retro_ttru_907,