RetrogeneDB ID: retro_pabe_1376

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 16:23764760..23764952(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ACBD7
• Ensembl ID: ENSPPYG00000002111
• Aliases: None
• Description: acyl-CoA binding domain containing 7 [Source:HGNC Symbol;Acc:17715]

Sequence

>retro_pabe_1376
GATAATAAAGAACTGAAAAAACTCGATGGATTTTACAAACAAGCTATAATTGGAGACATTACTATTGAGTATCCGAGAAT
GCTGGATTTAAAGGGCAAGGCCAAATGGGCAGCATGGACTCTCCAAAAAAGGTTGTCAAAGGAAGATACAATGAGTGTCT
CTATTTCTAAGGCAAAAGAGCCGATAGAAAAA

Alignment

ORF - retro_pabe_1376 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.75 %
• Parental protein coverage: 72.73 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  DDGELKELYGLYKQVIVGDINIACPGMLDLKGKAKWEAWNLKKGLSTEDAMSAYISKAKELIEK
          D..ELK.L.G.YKQ.I.GDI.I..P.MLDLKGKAKW.AW.L.K.LS.ED.MS..ISKAKE.IEK
Retrocopy DNKELKKLDGFYKQAIIGDITIEYPRMLDLKGKAKWAAWTLQKRLSKEDTMSVSISKAKEPIEK

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	6.30 RPM
SRP007412_cerebellum	0.00 RPM	0.97 RPM
SRP007412_heart	0.00 RPM	0.03 RPM
SRP007412_kidney	0.00 RPM	0.10 RPM
SRP007412_liver	0.06 RPM	0.06 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1376 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1376 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1376 has 5 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1669
Pan troglodytes	retro_ptro_1132
Gorilla gorilla	retro_ggor_1257
Macaca mulatta	retro_mmul_1577
Callithrix jacchus	retro_cjac_1017

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000009249	1 retrocopy	retro_cjac_1017,
Felis catus	ENSFCAG00000027337	1 retrocopy	retro_fcat_683,
Homo sapiens	ENSG00000176244	2 retrocopies	retro_hsap_1501, retro_hsap_1669,
Gorilla gorilla	ENSGGOG00000015777	3 retrocopies	retro_ggor_1152, retro_ggor_1257, retro_ggor_625,
Macaca mulatta	ENSMMUG00000010587	2 retrocopies	retro_mmul_1577, retro_mmul_2141,
Nomascus leucogenys	ENSNLEG00000012353	2 retrocopies	retro_nleu_1147, retro_nleu_1720,
Pongo abelii	ENSPPYG00000002111	2 retrocopies	retro_pabe_1252, retro_pabe_1376 ,
Pongo abelii	ENSPPYG00000012788	2 retrocopies	retro_pabe_2755, retro_pabe_2968,
Pan troglodytes	ENSPTRG00000041316	3 retrocopies	retro_ptro_1018, retro_ptro_1132, retro_ptro_530,
Pteropus vampyrus	ENSPVAG00000007153	1 retrocopy	retro_pvam_649,