RetrogeneDB ID: retro_pabe_840

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 12:49280727..49281269(+)
• Located in intron of: ENSPPYG00000004491

Retrocopy information

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

Parental gene information

• Parental gene symbol: PARK7
• Ensembl ID: ENSPPYG00000001925
• Aliases: None
• Description: parkinson protein 7 [Source:HGNC Symbol;Acc:16369]

Sequence

>retro_pabe_840
TTGGCTAAAGGAGCAGAGGAAATGGAGACGGTCATCCTGTAGATGTCATGAGGCGAGCTGGGATTAAGGTCACCATTGCA
GGTCTGGCTGGAAAAGACCCAGTACAGTGTAGCCATGATGTTTTCATTTGTCCTGATGCCAGTCTTGAAGATGCAAAAAA
AGAGGGACCATATGACATAGCAAGTTCTACCAGGAGGTAATCTGGGTGCACAGAATTTACCTGAGTCTGCTTCTGTGAAG
GAGATACTAAAGGAGCAGGAGAACCAGAAGGGCCTTATAGCCACCATCTGTGTAGGTCCTACTGCTCTGATGGCTCATGA
AATCAGTTTTGGAAGTAAAGTTACAACACTCCCGCTTGCTAAGGACAAAATAATGAATGGAAGTCATTACACCTACTCTG
AGAATCGTGTGGAAAAGGACGGCCTGAAATTCTTACAAGCCCAGGGCCTAAGACCAGCTTTGAGTTTGTGCTTACAATTG
TTGAAGCCCTGAGCAGCAAGGAGATGGCAGCTCAAGTGAAGCCTCCACTTGTTCTTAAAGAC

Alignment

ORF - retro_pabe_840 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.78 %
• Parental protein coverage: 95.24 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  LAKGAEEMETVI-PVDVMRRAGIKVTIAGLAGKDPVQCSRDVVICPDASLEDAKKEGPYDVV-VLPGGNL
          LAKGAEEMETVI.PVDVMRRAGIKVTIAGLAGKDPVQCS.DV.ICPDASLEDAKKEGPYD...VLPGGNL
Retrocopy LAKGAEEMETVI<PVDVMRRAGIKVTIAGLAGKDPVQCSHDVFICPDASLEDAKKEGPYDIA>VLPGGNL

Parental  GAQNLSESAAVKEILKEQENQKGLIAAICAGPTALLAHEIGFGSKVTTHPLAKDKMMNGGHYTYSENRVE
          GAQNL.ESA.VKEILKEQENQKGLIA.IC.GPTAL.AHEI.FGSKVTT.PLAKDK.MNG.HYTYSENRVE
Retrocopy GAQNLPESASVKEILKEQENQKGLIATICVGPTALMAHEISFGSKVTTLPLAKDKIMNGSHYTYSENRVE

Parental  KDGL-ILTSRG-PGTSFEFALAIVEALNGKEVAAQVKAPLVLKD
          KDGL..L...G.P.TSFEF.L.IVEAL..KE.AAQVK.PLVLKD
Retrocopy KDGLKFLQAQG<PKTSFEFVLTIVEALSSKEMAAQVKPPLVLKD

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	0.22 RPM	72.21 RPM
SRP007412_cerebellum	0.49 RPM	72.72 RPM
SRP007412_heart	0.27 RPM	82.97 RPM
SRP007412_kidney	0.36 RPM	97.72 RPM
SRP007412_liver	0.18 RPM	90.89 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_840 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_840 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_840 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_995
Gorilla gorilla	retro_ggor_795

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Parental genes homology:

Parental genes homology involve 18 parental genes, and 49 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000003703	1 retrocopy	retro_amel_854,
Canis familiaris	ENSCAFG00000019674	1 retrocopy	retro_cfam_1150,
Choloepus hoffmanni	ENSCHOG00000004364	7 retrocopies	retro_chof_1725, retro_chof_1877, retro_chof_2047, retro_chof_2123, retro_chof_2220, retro_chof_279, retro_chof_63,
Callithrix jacchus	ENSCJAG00000000319	4 retrocopies	retro_cjac_1348, retro_cjac_2729, retro_cjac_3210, retro_cjac_4225,
Erinaceus europaeus	ENSEEUG00000013141	1 retrocopy	retro_eeur_233,
Echinops telfairi	ENSETEG00000010915	1 retrocopy	retro_etel_215,
Homo sapiens	ENSG00000116288	2 retrocopies	retro_hsap_4195, retro_hsap_995,
Gorilla gorilla	ENSGGOG00000012105	2 retrocopies	retro_ggor_2812, retro_ggor_795,
Microcebus murinus	ENSMICG00000008470	2 retrocopies	retro_mmur_1294, retro_mmur_690,
Nomascus leucogenys	ENSNLEG00000008790	3 retrocopies	retro_nleu_1025, retro_nleu_2320, retro_nleu_233,
Oryctolagus cuniculus	ENSOCUG00000016511	1 retrocopy	retro_ocun_1405,
Ochotona princeps	ENSOPRG00000002151	2 retrocopies	retro_opri_104, retro_opri_1173,
Pongo abelii	ENSPPYG00000001925	2 retrocopies	retro_pabe_3433, retro_pabe_840 ,
Pan troglodytes	ENSPTRG00000000102	3 retrocopies	retro_ptro_2848, retro_ptro_3270, retro_ptro_755,
Rattus norvegicus	ENSRNOG00000018289	2 retrocopies	retro_rnor_1229, retro_rnor_2463,
Tupaia belangeri	ENSTBEG00000009474	13 retrocopies	retro_tbel_1182, retro_tbel_1306, retro_tbel_1405, retro_tbel_1790, retro_tbel_2059, retro_tbel_220, retro_tbel_2247, retro_tbel_2551, retro_tbel_3013, retro_tbel_4047, retro_tbel_4486, retro_tbel_4538, retro_tbel_561,
Tarsius syrichta	ENSTSYG00000001455	1 retrocopy	retro_tsyr_1883,
Vicugna pacos	ENSVPAG00000011076	1 retrocopy	retro_vpac_364,