RetrogeneDB ID: retro_pabe_229

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 1:26978154..26978600(+)
• Located in intron of: ENSPPYG00000000197

Retrocopy information

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

Parental gene information

• Parental gene symbol: PFDN5
• Ensembl ID: ENSPPYG00000004575
• Aliases: None
• Description: prefoldin subunit 5 [Source:RefSeq peptide;Acc:NP_001125627]

Sequence

>retro_pabe_229
TCCAAGACTATCACGGAGATGAATCTGCCACAGCTAGAAATGCTCAAGAACCAGCTGGACCAGGAAATGGAGTTCTTGTC
CACCTCCACTGCCCAGCTCAAAGTGGTACAGACCAAGTATGTAGAAGCCAAGGACTGTCTGAACATGCTGAGTAAGAGCA
ATGAGGGAAGAGAATTACTCCTCCCACTGACGAGTTTGATGTATGTCCATGAGAAGCTGCATGATGTGGAACATGTGCTC
ACTGATGTAGGAACTGGGTACTATGTAGATAAGATAGCTGAGGATGCCAAGGACTTCTTCAAGAGGAAGACAGACTTCCT
AACCAAGCAGATAGAGAAAATCCACCAGCTCTCCAGGAGCACGCCATGGAACCGGCTGTCATGGAAATGATGAGCCAGAC
GATTCAGCAGCCCAGAGCCCTAGGGGCAGCTCAGGCTACTGCTAAG

Alignment

ORF - retro_pabe_229 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.44 %
• Parental protein coverage: 97.4 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SINITELNLPQLEMLKNQLDQEVEFLSTSIAQLKVVQTKYVEAKDCLNVLNKSNEGKELLVPLTSSMYVP
          S..ITE.NLPQLEMLKNQLDQE.EFLSTS.AQLKVVQTKYVEAKDCLN.L.KSNEG.ELL.PLTS.MYV.
Retrocopy SKTITEMNLPQLEMLKNQLDQEMEFLSTSTAQLKVVQTKYVEAKDCLNMLSKSNEGRELLLPLTSLMYVH

Parental  GKLHDVEHVLIDVGTGYYVEKTAEDAKDFFKRKIDFLTKQMEKIQ-PALQEKHAMKQAVMEMMSQKIQQL
          .KLHDVEHVL.DVGTGYYV.K.AEDAKDFFKRK.DFLTKQ.EKI..PALQE.HAM..AVMEMMSQ.IQQ.
Retrocopy EKLHDVEHVLTDVGTGYYVDKIAEDAKDFFKRKTDFLTKQIEKIH<PALQE-HAMEPAVMEMMSQTIQQP

Parental  TALGAAQATAK
          .ALGAAQATAK
Retrocopy RALGAAQATAK

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	55.18 RPM
SRP007412_cerebellum	0.24 RPM	75.88 RPM
SRP007412_heart	0.06 RPM	52.29 RPM
SRP007412_kidney	0.36 RPM	100.14 RPM
SRP007412_liver	0.55 RPM	57.81 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_229 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_229 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_229 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_515
Gorilla gorilla	retro_ggor_475
Macaca mulatta	retro_mmul_428

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Parental genes homology:

Parental genes homology involve 20 parental genes, and 42 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000012402	2 retrocopies	retro_amel_322, retro_amel_99,
Canis familiaris	ENSCAFG00000007016	4 retrocopies	retro_cfam_1382, retro_cfam_1421, retro_cfam_1639, retro_cfam_919,
Callithrix jacchus	ENSCJAG00000018477	6 retrocopies	retro_cjac_1590, retro_cjac_1614, retro_cjac_1707, retro_cjac_2274, retro_cjac_42, retro_cjac_993,
Dasypus novemcinctus	ENSDNOG00000013002	1 retrocopy	retro_dnov_1994,
Echinops telfairi	ENSETEG00000002111	3 retrocopies	retro_etel_1815, retro_etel_372, retro_etel_950,
Felis catus	ENSFCAG00000005871	4 retrocopies	retro_fcat_1215, retro_fcat_1468, retro_fcat_1566, retro_fcat_828,
Homo sapiens	ENSG00000123349	1 retrocopy	retro_hsap_515,
Gorilla gorilla	ENSGGOG00000026308	1 retrocopy	retro_ggor_475,
Macropus eugenii	ENSMEUG00000012110	1 retrocopy	retro_meug_1682,
Macaca mulatta	ENSMMUG00000022030	2 retrocopies	retro_mmul_1677, retro_mmul_428,
Mustela putorius furo	ENSMPUG00000006059	1 retrocopy	retro_mputfur_18,
Mus musculus	ENSMUSG00000001289	1 retrocopy	retro_mmus_3707,
Nomascus leucogenys	ENSNLEG00000017706	3 retrocopies	retro_nleu_1369, retro_nleu_1370, retro_nleu_1549,
Otolemur garnettii	ENSOGAG00000009463	2 retrocopies	retro_ogar_1820, retro_ogar_292,
Ochotona princeps	ENSOPRG00000015638	1 retrocopy	retro_opri_394,
Procavia capensis	ENSPCAG00000012413	2 retrocopies	retro_pcap_132, retro_pcap_167,
Pongo abelii	ENSPPYG00000004575	1 retrocopy	retro_pabe_229 ,
Pan troglodytes	ENSPTRG00000005010	1 retrocopy	retro_ptro_384,
Sorex araneus	ENSSARG00000006221	1 retrocopy	retro_sara_439,
Tupaia belangeri	ENSTBEG00000016436	4 retrocopies	retro_tbel_1068, retro_tbel_2415, retro_tbel_3132, retro_tbel_768,