RetrogeneDB ID: retro_ptro_1543

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 2A:55348251..55348700(+)
• Located in intron of: ENSPTRG00000011924

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_1543
AGCTCCCAGAAAGGCACAATGTGGCTCGTTCCAGGCCTCAAGCACCAGAATACGTTTAGCTTCAAAAATGACAAGTTTGA
TAAGAGTGTTCAGACCAAGAAAATTAATGCAAAACTTCCTGATATAGTATGTCAGCGCTATAAAGAAGTTCTTGAGTGTC
ATGTAAAATACAAAAAATACAAACCATTATCAAACCTAAAAAATGTGTTAAATGTTTATGAAAGACAGTGAAGGATTCTT
ATCACACAATGTGTAGACCATGCGCTTATGAACTTGAAGTTTGCACAAAATGTGGAAAGAAAGAAGACATTGTTATTCCG
TTCAGTAAGGAACCAGAAAAAATAAAATATTGAAACAATCTAAGTTCTAACCATAGAAGAAGCTGCAGAAGAAATGAAGA
AAGGGATGATAATTTAGATTTTGATGTTGATTTAGAAGACACAGGAGGA

Alignment

ORF - retro_ptro_1543 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.92 %
• Parental protein coverage: 96.18 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SSQKGNVARSRPQKHQNTFSFKNDKFDKSVQTKKINAKLHDGVCQRCKEVLEWRVKYSKYKPLS-KPKKC
          SSQKG........KHQNTFSFKNDKFDKSVQTKKINAKL.D.VCQR.KEVLE..VKY.KYKPLS.KPKKC
Retrocopy SSQKGTMWLVPGLKHQNTFSFKNDKFDKSVQTKKINAKLPDIVCQRYKEVLECHVKYKKYKPLS<KPKKC

Parental  VKCLQKTVKDSYHIMCRPCACELEVCAKCGKKEDIVIPLNKETEKIEHTENNLSSNHRRSCRRNEESDDD
          VKCL.KTVKDSYH.MCRPCA.ELEVC.KCGKKEDIVIP..KE.EKI....NNLSSNHRRSCRRNEE.DD.
Retrocopy VKCL*KTVKDSYHTMCRPCAYELEVCTKCGKKEDIVIPFSKEPEKIKY-*NNLSSNHRRSCRRNEERDDN

Parental  LDFDIDLEDTGG
          LDFD.DLEDTGG
Retrocopy LDFDVDLEDTGG

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	0.07 RPM	1.18 RPM
SRP007412_cerebellum	0.00 RPM	1.72 RPM
SRP007412_heart	0.17 RPM	1.89 RPM
SRP007412_kidney	0.00 RPM	2.54 RPM
SRP007412_liver	0.00 RPM	2.62 RPM
SRP007412_testis	0.11 RPM	5.80 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1543 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1543 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1543 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2104
Pongo abelii	retro_pabe_1996
Macaca mulatta	retro_mmul_988
Callithrix jacchus	retro_cjac_1283

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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,