RetrogeneDB ID: retro_ptro_1493

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 22:40867315..40867633(+)
• Located in intron of: ENSPTRG00000042031

Retrocopy information

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

Parental gene information

• Parental gene symbol: C6ORF108
• Ensembl ID: ENSPTRG00000029662
• Aliases: None
• Description: Chromosome 6 open reading frame 108 [Source:UniProtKB/TrEMBL;Acc:K7CVK4]

Sequence

>retro_ptro_1493
GATAAGTCCGCTGGGGGTGACAGGCTCATCCATGAGTGGTACTTGATGTGGCTGCAGAAGGCGGATGTGGTGGTGGCAGA
AGTGACACAACTGTCCCTGGGTATAGGCTATGATCTGGGCCAAGCCACAGCCCTCAATAAGTGAATCCTGTGTCTGCTCC
AGCCGCAGTCTGGTGGAGTGCTGTCGGCCATGATCTGGGAAGAGGCAGATGGCTCTGGGTTCCAGGTGTGGGACTACGGA
GAGGGAAAGGTGGAGGCCCTGCTGCATGGATAGGTTGAGGCTGATCCTCTCGAGCAGGTTGCCTCCCCTAACCCAACC

Alignment

ORF - retro_ptro_1493 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.03 %
• Parental protein coverage: 99.07 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EEAAGGDRLIHEQDLEWLQQADVVVAEVTQPSLGVGYELGRAVAFNKRILCLFRPQSGRVLSAMIRGAAD
          ...AGGDRLIHE..L.WLQ.ADVVVAEVTQ.SLG.GY.LG.A.A.NK.ILCL..PQSG.VLSAMI...AD
Retrocopy DKSAGGDRLIHEWYLMWLQKADVVVAEVTQLSLGIGYDLGQATALNK*ILCLLQPQSGGVLSAMIWEEAD

Parental  GSRFQVWDYEEGEVEALLDRYFEADPPGQVAASPDPT
          GS.FQVWDY.EG.VEALL....EADP..QV.ASP.PT
Retrocopy GSGFQVWDYGEGKVEALLHG*VEADPLEQV-ASPNPT

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	0.98 RPM	22.72 RPM
SRP007412_cerebellum	1.61 RPM	9.11 RPM
SRP007412_heart	0.17 RPM	8.69 RPM
SRP007412_kidney	1.12 RPM	95.66 RPM
SRP007412_liver	2.55 RPM	56.27 RPM
SRP007412_testis	1.69 RPM	2.11 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1493 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1493 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1493 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2562

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000012390	1 retrocopy	retro_amel_1012,
Bos taurus	ENSBTAG00000019913	1 retrocopy	retro_btau_518,
Canis familiaris	ENSCAFG00000001837	1 retrocopy	retro_cfam_1148,
Callithrix jacchus	ENSCJAG00000005337	1 retrocopy	retro_cjac_3948,
Equus caballus	ENSECAG00000006660	1 retrocopy	retro_ecab_595,
Felis catus	ENSFCAG00000009722	1 retrocopy	retro_fcat_365,
Homo sapiens	ENSG00000112667	1 retrocopy	retro_hsap_2562,
Nomascus leucogenys	ENSNLEG00000000516	1 retrocopy	retro_nleu_1515,
Pongo abelii	ENSPPYG00000016635	1 retrocopy	retro_pabe_1888,
Pan troglodytes	ENSPTRG00000029662	1 retrocopy	retro_ptro_1493 ,
Pteropus vampyrus	ENSPVAG00000008743	1 retrocopy	retro_pvam_1400,
Rattus norvegicus	ENSRNOG00000018397	1 retrocopy	retro_rnor_580,
Tursiops truncatus	ENSTTRG00000007022	1 retrocopy	retro_ttru_1520,