RetrogeneDB ID: retro_ggor_475

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 1:203083886..203084305(-)
• Located in intron of: ENSGGOG00000015271

Retrocopy information

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

Parental gene information

• Parental gene symbol: PFDN5
• Ensembl ID: ENSGGOG00000026308
• Aliases: None
• Description: None

Sequence

>retro_ggor_475
CCGCAGCTAGAAATGCTCAAGAACCAGCTGGACCAGGAAATGGAGTTCTTGTCCACCTCCATTGCCCAGCTCAAAGTGGT
ACAGACCAAGTATGTAGAAGCCAAGGACTGTCTGAACATGCTGAGTAAGAACAATGAGGGAAGAGAATTACTCCTCCCAC
TGACAAGTTTAATGTGTGTCCCTGAGAAGCTGCATGATGTGGAACATGTGCTCATTGATGTAGGAACTGGGTACTATGTA
GATAAGATAGCTGAGGATGCCAAGGACTTCTTCAAGAGGAAGACAGACTTCCTAACCAAGCAGATAGAGAAAATCCACCA
GCTCTCCAGGAGCACACCATGAAACCGGCTGTCATGGAAATGACGAGCCAGACGATTCAGCAGCCCAGAGCCCTGGGGGC
AGCTCAGGCTACTGCTAAG

Alignment

ORF - retro_ggor_475 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.51 %
• Parental protein coverage: 88.68 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  PQLEMLKNQLDQEVEFLSTSIAQLKVVQTKYVEAKDCLNVLNKSNEGKELLVPLTSSMYVPGKLHDVEHV
          PQLEMLKNQLDQE.EFLSTSIAQLKVVQTKYVEAKDCLN.L.K.NEG.ELL.PLTS.M.VP.KLHDVEHV
Retrocopy PQLEMLKNQLDQEMEFLSTSIAQLKVVQTKYVEAKDCLNMLSKNNEGRELLLPLTSLMCVPEKLHDVEHV

Parental  LIDVGTGYYVEKTAEDAKDFFKRKIDFLTKQMEKIQ-PALQEKHAMKQAVMEMMSQKIQQLTALGAAQAT
          LIDVGTGYYV.K.AEDAKDFFKRK.DFLTKQ.EKI..PALQE.H.MK.AVMEM.SQ.IQQ..ALGAAQAT
Retrocopy LIDVGTGYYVDKIAEDAKDFFKRKTDFLTKQIEKIH<PALQE-HTMKPAVMEMTSQTIQQPRALGAAQAT

Parental  AK
          AK
Retrocopy AK

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	0.05 RPM	74.23 RPM
SRP007412_cerebellum	0.16 RPM	68.51 RPM
SRP007412_heart	0.00 RPM	34.52 RPM
SRP007412_kidney	0.04 RPM	188.50 RPM
SRP007412_liver	0.11 RPM	94.22 RPM
SRP007412_testis	0.00 RPM	109.30 RPM

ChIP-Seq

Gorilla gorilla was not studied using ChIP-Seq data.

EST

Gorilla gorilla was not studied using EST data.

TSS

Gorilla gorilla was not studied using FANTOM5 data.

Lab

retro_ggor_475 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_475 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_515
Pongo abelii	retro_pabe_229
Macaca mulatta	retro_mmul_428

---

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,