RetrogeneDB ID: retro_ptro_530

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 11:3868818..3869040(+)
• Located in intron of: ENSPTRG00000003204

Retrocopy information

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

Parental gene information

• Parental gene symbol: ACBD7
• Ensembl ID: ENSPTRG00000041316
• Aliases: None
• Description: acyl-CoA binding domain containing 7 [Source:HGNC Symbol;Acc:17715]

Sequence

>retro_ptro_530
CTGCAGGCTGATTTTGACAGTGTTGCAGAAGATGTGAGGAAGCTGAAAACAAGACCAGATGAGGAAGGACTGAAACAACT
CTATGGGCTTTAGAAACAAGCTATAACTGGGGACATTAATATTGAGTGTTCAGGAATGCTAGATTTAAAAGGCAAGGCCA
AATGAGAAGCATTGAATTTCCAAAATGGGATATCAAAGGACAATGTGATGAGTATATATATA

Alignment

ORF - retro_ptro_530 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.27 %
• Parental protein coverage: 84.09 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LQADFDRAAEDVRKLKARPDAGELKELYGLYKQAIVGDINIACPGMLDLKGKAKWEAWNLKKGLSTEDAM
          LQADFD..AEDVRKLK.RPD...LK.LYGL.KQAI.GDINI.C.GMLDLKGKAK.EA.N...G.S....M
Retrocopy LQADFDSVAEDVRKLKTRPDEEGLKQLYGL*KQAITGDINIECSGMLDLKGKAK*EALNFQNGISKDNVM

Parental  SAYI
          S.YI
Retrocopy SIYI

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	3.63 RPM
SRP007412_cerebellum	0.00 RPM	3.80 RPM
SRP007412_heart	0.00 RPM	0.03 RPM
SRP007412_kidney	0.00 RPM	0.16 RPM
SRP007412_liver	0.00 RPM	0.07 RPM
SRP007412_testis	0.00 RPM	1.26 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_530 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_530 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_530 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Gorilla gorilla	retro_ggor_625

---

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,
Pan troglodytes	ENSPTRG00000012401	2 retrocopies	retro_ptro_2140, retro_ptro_2446,
Pan troglodytes	ENSPTRG00000041316	3 retrocopies	retro_ptro_1018, retro_ptro_1132, retro_ptro_530 ,
Pteropus vampyrus	ENSPVAG00000007153	1 retrocopy	retro_pvam_649,