RetrogeneDB ID: retro_pabe_3412

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 9:56963197..56963559(+)
• Located in intron of: ENSPPYG00000019234

Retrocopy information

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

Parental gene information

• Parental gene symbol: AK4
• Ensembl ID: ENSPPYG00000001269
• Aliases: AK3, AK 4, AK3L1, AK4
• Description: Adenylate kinase isoenzyme 4, mitochondrial [Source:UniProtKB/Swiss-Prot;Acc:Q5R421]

Sequence

>retro_pabe_3412
GACAAAATGTATGAAGTGGATTTAGTGATCTGTTTGAAGATTCCATTCGAAACACTTAAAGATTGTCTCAGCCGACGTTG
GATTCACCCTCCCTGCAGCAGGGTGTATAACCTGGGCTTCAATCCACCTGGTGTACATGGGATTGATGACATCTCTGGGG
AACCATTAATCCAGCAGGAAGATGATAGACTCGAAGCGGTTGCTGCCAGGATAAGACAGTACAAGGTTGTGGCAAAGCCA
GTCATTTAATTATGGAAGAGCCCAGGCGTGCTCCACCATTTTTCTGGGATGGAGACTGATAAAATCTGGCCCTAAGTCTA
CATATTTTTCTTAACAAGATCACACCTATTCAGTCCAAAGAA

Alignment

ORF - retro_pabe_3412 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.87 %
• Parental protein coverage: 54.26 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  DKICEVDLVISLNIPFETLKDRLSRRWIHPPSGRVYNLDFNPPHVHGIDDVTGEPLVQQEDDKPEAVAAR
          DK..EVDLVI.L.IPFETLKD.LSRRWIHPP..RVYNL.FNPP.VHGIDD..GEPL.QQEDD..EAVAAR
Retrocopy DKMYEVDLVICLKIPFETLKDCLSRRWIHPPCSRVYNLGFNPPGVHGIDDISGEPLIQQEDDRLEAVAAR

Parental  LRQYKDVAKPVIELYKSRGVLHQFSGTETNKIWPYVYT-LFSNKITPIQSKE
          .RQYK.VAKPVI.L.KS.GVLH.FSG.ET.KIWP.VY...F.NKITPIQSKE
Retrocopy IRQYKVVAKPVI*LWKSPGVLHHFSGMETDKIWP*VYI<IFLNKITPIQSKE

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	0.06 RPM	25.99 RPM
SRP007412_cerebellum	0.00 RPM	32.95 RPM
SRP007412_heart	0.00 RPM	21.76 RPM
SRP007412_kidney	0.13 RPM	108.46 RPM
SRP007412_liver	0.09 RPM	16.46 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3412 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3412 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3412 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4225
Pan troglodytes	retro_ptro_2870
Gorilla gorilla	retro_ggor_2829

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 50 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000016835	1 retrocopy	retro_cjac_1856,
Homo sapiens	ENSG00000162433	6 retrocopies	retro_hsap_1101, retro_hsap_1744, retro_hsap_2993, retro_hsap_3320, retro_hsap_3619, retro_hsap_4225,
Gorilla gorilla	ENSGGOG00000026644	4 retrocopies	retro_ggor_1301, retro_ggor_2073, retro_ggor_2444, retro_ggor_2829,
Myotis lucifugus	ENSMLUG00000009622	1 retrocopy	retro_mluc_1708,
Macaca mulatta	ENSMMUG00000001079	3 retrocopies	retro_mmul_104, retro_mmul_1680, retro_mmul_2080,
Mus musculus	ENSMUSG00000028527	1 retrocopy	retro_mmus_1933,
Nomascus leucogenys	ENSNLEG00000015163	3 retrocopies	retro_nleu_1666, retro_nleu_2481, retro_nleu_743,
Otolemur garnettii	ENSOGAG00000016024	1 retrocopy	retro_ogar_3375,
Ochotona princeps	ENSOPRG00000010345	17 retrocopies	retro_opri_1094, retro_opri_153, retro_opri_291, retro_opri_328, retro_opri_357, retro_opri_417, retro_opri_438, retro_opri_442, retro_opri_666, retro_opri_724, retro_opri_73, retro_opri_743, retro_opri_752, retro_opri_765, retro_opri_889, retro_opri_892, retro_opri_947,
Pongo abelii	ENSPPYG00000001269	6 retrocopies	retro_pabe_1021, retro_pabe_2479, retro_pabe_2735, retro_pabe_2970, retro_pabe_3412 , retro_pabe_3483,
Pongo abelii	ENSPPYG00000019245	3 retrocopies	retro_pabe_2676, retro_pabe_3588, retro_pabe_967,
Pan troglodytes	ENSPTRG00000000827	4 retrocopies	retro_ptro_2024, retro_ptro_2154, retro_ptro_2449, retro_ptro_2870,