RetrogeneDB ID: retro_ptro_384

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 1:201908190..201908618(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PFDN5
• Ensembl ID: ENSPTRG00000005010
• Aliases: None
• Description: None

Sequence

>retro_ptro_384
ATGAATCTGCCGCAGCTAGAAATGCTCAAGAACCAGCTGGACCAGGAAATGGAGTTCTTGTCCACCTCCATTGCCCAGCT
CAAAGTGGTACAGACCAAGTATGTAGAAGCCAAGGACTGTCTGAACATGCTGAGTAAGAACAATGAGGGAAGAGAATTAC
TCCTCCCACTGACGAGTTTAATATATGTCCCTGAGAAGCTGCATGATGTGGAACATGTGCTCATTGATGTAGGAACTGGG
TACTATGTAGATAAGATAGCTGAGGATGCCAAGGACTTCTTGAAGAGGAAGACAGACTTCCTAACCAAGCAGATAGAGAA
AATCCACCAGCTCTCCAGGAGCACACCATGACACCGGCTGTCATGGAAATGATGAGCCAGACGATTCAGCAGCCCAGAGC
CCTGGGGGCAGCTCAGGCTGCTGCTAAG

Alignment

ORF - retro_ptro_384 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.76 %
• Parental protein coverage: 93.51 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LNLPQLEMLKNQLDQEVEFLSTSIAQLKVVQTKYVEAKDCLNVLNKSNEGKELLVPLTSSMYVPGKLHDV
          .NLPQLEMLKNQLDQE.EFLSTSIAQLKVVQTKYVEAKDCLN.L.K.NEG.ELL.PLTS..YVP.KLHDV
Retrocopy MNLPQLEMLKNQLDQEMEFLSTSIAQLKVVQTKYVEAKDCLNMLSKNNEGRELLLPLTSLIYVPEKLHDV

Parental  EHVLIDVGTGYYVEKTAEDAKDFFKRKIDFLTKQMEKIQ-PALQEKHAMKQAVMEMMSQKIQQLTALGAA
          EHVLIDVGTGYYV.K.AEDAKDF.KRK.DFLTKQ.EKI..PALQE.H.M..AVMEMMSQ.IQQ..ALGAA
Retrocopy EHVLIDVGTGYYVDKIAEDAKDFLKRKTDFLTKQIEKIH<PALQE-HTMTPAVMEMMSQTIQQPRALGAA

Parental  QATAK
          QA.AK
Retrocopy QAAAK

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	0.04 RPM	96.70 RPM
SRP007412_cerebellum	0.00 RPM	65.78 RPM
SRP007412_heart	0.09 RPM	57.71 RPM
SRP007412_kidney	0.03 RPM	143.81 RPM
SRP007412_liver	0.13 RPM	56.53 RPM
SRP007412_testis	0.00 RPM	107.49 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_384 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_384 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_384 has 0 orthologous retrocopies within eutheria group .

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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,