RetrogeneDB ID: retro_ptro_1958

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 3:186965173..186965519(-)
• Located in intron of: ENSPTRG00000015661

Retrocopy information

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

Parental gene information

• Parental gene symbol: C9orf85
• Ensembl ID: ENSPTRG00000021018
• Aliases: None
• Description: chromosome 9 open reading frame 85 [Source:HGNC Symbol;Acc:28784]

Sequence

>retro_ptro_1958
GATGGAGTATGTCAGCACTGTAAAGAAGTTCTTGAGTGGCGTGTAAAATATAGCAAATACAAACCATTATCCAACCTAAA
AAATGTGTTAAATGTTTACAATAGACAGTGGAGGATTCTTATCTCATAACGTGTAGACCATGTGCCTATGAACTTGAAGT
TTGCACAAAATGTGGAAAGAAGAAGACATTGCTATTCTGTTCAATAAAGAACCAGGAAAAACAGAGAATATTGAAAATAA
TCTAAGTTCCAACCATAGAAGAAGCTGCAGAAGAAGTGAAGAAAGTGATGATGATTTGGATTTTGATATTGGTTTAGAAA
ACACAGGAGGAGACCCTCAAGTGAAT

Alignment

ORF - retro_ptro_1958 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.51 %
• Parental protein coverage: 73.89 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  DGVCQRCKEVLEWRVKYSKYKPLS-KPKKCVKCLQKTVKDSYHIMCRPCACELEVCAKCGKK-EDIVIPL
          DGVCQ.CKEVLEWRVKYSKYKPLS..PKKCVKCLQ.TV.DSY.I.CRPCA.ELEVC.KCGKK.EDI.I..
Retrocopy DGVCQHCKEVLEWRVKYSKYKPLS<QPKKCVKCLQ*TVEDSYLITCRPCAYELEVCTKCGKK<EDIAILF

Parental  NKETEKIEHTENNLSSNHRRSCRRNEESDDDLDFDIDLEDTGGDHQMN
          NKE..K.E..ENNLSSNHRRSCRR.EESDDDLDFDI.LE.TGGD.Q.N
Retrocopy NKEPGKTENIENNLSSNHRRSCRRSEESDDDLDFDIGLENTGGDPQVN

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	0.13 RPM	1.18 RPM
SRP007412_cerebellum	0.14 RPM	1.72 RPM
SRP007412_heart	0.03 RPM	1.89 RPM
SRP007412_kidney	0.00 RPM	2.54 RPM
SRP007412_liver	0.03 RPM	2.62 RPM
SRP007412_testis	0.00 RPM	5.80 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1958 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1958 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1958 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2895

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Parental genes homology:

Parental genes homology involve 19 parental genes, and 41 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000007254	1 retrocopy	retro_amel_730,
Bos taurus	ENSBTAG00000006831	1 retrocopy	retro_btau_39,
Canis familiaris	ENSCAFG00000001820	1 retrocopy	retro_cfam_2126,
Callithrix jacchus	ENSCJAG00000001441	2 retrocopies	retro_cjac_1283, retro_cjac_1374,
Cavia porcellus	ENSCPOG00000025848	2 retrocopies	retro_cpor_1538, retro_cpor_316,
Felis catus	ENSFCAG00000031942	1 retrocopy	retro_fcat_1955,
Homo sapiens	ENSG00000155621	2 retrocopies	retro_hsap_2104, retro_hsap_2895,
Myotis lucifugus	ENSMLUG00000024309	2 retrocopies	retro_mluc_2449, retro_mluc_2526,
Macaca mulatta	ENSMMUG00000018881	2 retrocopies	retro_mmul_670, retro_mmul_988,
Mustela putorius furo	ENSMPUG00000008971	1 retrocopy	retro_mputfur_1413,
Mus musculus	ENSMUSG00000035171	6 retrocopies	retro_mmus_1049, retro_mmus_2254, retro_mmus_2286, retro_mmus_2781, retro_mmus_2941, retro_mmus_3698,
Nomascus leucogenys	ENSNLEG00000001023	1 retrocopy	retro_nleu_1272,
Oryctolagus cuniculus	ENSOCUG00000024578	2 retrocopies	retro_ocun_703, retro_ocun_766,
Otolemur garnettii	ENSOGAG00000011302	1 retrocopy	retro_ogar_979,
Pongo abelii	ENSPPYG00000029745	2 retrocopies	retro_pabe_1996, retro_pabe_2397,
Pan troglodytes	ENSPTRG00000021018	2 retrocopies	retro_ptro_1543, retro_ptro_1958 ,
Rattus norvegicus	ENSRNOG00000027161	5 retrocopies	retro_rnor_1898, retro_rnor_2010, retro_rnor_2242, retro_rnor_2859, retro_rnor_2960,
Sorex araneus	ENSSARG00000004523	1 retrocopy	retro_sara_260,
Tupaia belangeri	ENSTBEG00000015556	6 retrocopies	retro_tbel_1998, retro_tbel_200, retro_tbel_2406, retro_tbel_2410, retro_tbel_3539, retro_tbel_940,