RetrogeneDB ID: retro_ptro_267

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 1:219985786..219986143(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FDX1L
• Ensembl ID: ENSPTRG00000010465
• Aliases: None
• Description: ferredoxin 1-like [Source:HGNC Symbol;Acc:30546]

Sequence

>retro_ptro_267
CCCAGGGATGTGGTGAACGTGGTGTTTGTAGACCTGTCAGGCTGGCGGATCCAGTGAGCTGCAGAGTCGGAGGACAATAT
TCTCCACCTGACCCAATGCCATGGGGTGAACCTGGAAGGTGCCTGTGAAGCCTTCCTGGCATGCTCCACCTGCCATGTGC
ATGTGAGCAAAGACCTGGACCTTCTGCCTCCTCCCGAAGAGAGGGAAGACAGCATGCTAGACATGGCCTCCCTCCTCCGG
GAGAACTCCCTGCTGGGCTGGCAGATCGTGCTGATGCTGGAGCTGGAAGGGGCAGAATTCAGTCTGCCCTAGAACGCCAG
GAACTTCTACGTGGACTGCCACATCCCCAGGCCCCAC

Alignment

ORF - retro_ptro_267 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.05 %
• Parental protein coverage: 65.57 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  PGDVVNVVFVDRSGQRI-PVSGRVG-DNVLHLAQRHGVDLEGACEASLACSTCHVYVSEDHLDLLPPPEE
          P.DVVNVVFVD.SG.RI.PVS.RVG.DN.LHL.Q.HGV.LEGACEA.LACSTCHV.VS.D.LDLLPPPEE
Retrocopy PRDVVNVVFVDLSGWRI<PVSCRVG>DNILHLTQCHGVNLEGACEAFLACSTCHVHVSKD-LDLLPPPEE

Parental  REDDMLDMAPLLQENSRLGCQIVLTPELEGAEFTLPKITRNFYVDGHVPKPH
          RED.MLDMA.LL.ENS.LG.QIVL..ELEGAEF.LP...RNFYVD.H.P.PH
Retrocopy REDSMLDMASLLRENSLLGWQIVLMLELEGAEFSLP*NARNFYVDCHIPRPH

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	0.00 RPM	23.67 RPM
SRP007412_cerebellum	0.00 RPM	9.50 RPM
SRP007412_heart	0.00 RPM	2.45 RPM
SRP007412_kidney	0.00 RPM	8.53 RPM
SRP007412_liver	0.03 RPM	6.42 RPM
SRP007412_testis	0.00 RPM	1.69 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_267 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_267 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_267 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_331
Gorilla gorilla	retro_ggor_355
Macaca mulatta	retro_mmul_584
Callithrix jacchus	retro_cjac_1753

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000267673	1 retrocopy	retro_hsap_331,
Gorilla gorilla	ENSGGOG00000006009	1 retrocopy	retro_ggor_355,
Macaca mulatta	ENSMMUG00000022896	1 retrocopy	retro_mmul_584,
Mus musculus	ENSMUSG00000079677	1 retrocopy	retro_mmus_2676,
Nomascus leucogenys	ENSNLEG00000012175	1 retrocopy	retro_nleu_1773,
Pan troglodytes	ENSPTRG00000004260	2 retrocopies	retro_ptro_1428, retro_ptro_1452,
Pan troglodytes	ENSPTRG00000010465	1 retrocopy	retro_ptro_267 ,