RetrogeneDB ID: retro_ptro_1453

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 21:17558020..17558604(+)
• Located in intron of: ENSPTRG00000013846

Retrocopy information

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

Parental gene information

• Parental gene symbol: C6orf203
• Ensembl ID: ENSPTRG00000018464
• Aliases: None
• Description: chromosome 6 open reading frame 203 [Source:HGNC Symbol;Acc:17971]

Sequence

>retro_ptro_1453
GTTATAAGCGCCATGGCTATGACTAGTGTCAAATTGCTTGCCGTTGTTTTAAGAAAACCAGATACCTGGATTGGACTCTG
GGGTGTTCTCCGAGGGACACCTCCGTCACACAAACTCTGTACTTCCTGGAATCGATATAGCACTAAGTTACGTGCACCAA
ATTATAAAAGACTTATCCATAATATTTTCTCACTGAAATTCTCAGGGCTTTTAATATCTCCAGAATATATTTTTCCATTT
TCCATAAGACTCAAAAGTAATAAAAGCTCTAATAAATCTACTACAAAGTCACCGCAAAAAGTAGAAGATGAAGAGGACTC
TGATGAAGACAGCGATCATGATGAGATGAGTGAGCAGGAAGAGGAGCTTGAGGATGACCCTACGATAGTCAAAGACTATC
AAGACCTGGAAAAAGAGTGCAGTCTTTTTGGTATGACGATGTCCTGAAGACAGGCCTAGATATTGGGAGAAACAAAGTGG
AAGATGCGTTCTACAAAGGTGAACTCAGGCTGAATGGGGAAAAGTTGTGGAAGAAAAACAGAACGGTCAAAGTGGGAGAT
ACACTGGATCTTCTCATTGGAGAT

Alignment

ORF - retro_ptro_1453 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82. %
• Parental protein coverage: 80.82 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  IISAMAMASVKLLAGVLRKPDAWIGLWGVLRGTPSSYKLCTSWNRYLYFSSTKLRAPNYKTLFYNIFSLR
          .ISAMAM.SVKLLA.VLRKPD.WIGLWGVLRGTP.S.KLCTSWNRY....STKLRAPNYK.L..NIFSL.
Retrocopy VISAMAMTSVKLLAVVLRKPDTWIGLWGVLRGTPPSHKLCTSWNRY----STKLRAPNYKRLIHNIFSLK

Parental  LPGLLLSPECIFPFSVRLKSNIRSTKSTKKSLQKV-DEEDSDEESDHDEMSEQEEELEDDPTVVKNYKDL
          ..GLL.SPE.IFPFS.RLKSN..S.KST.KS.QKV.DEEDSDE.SDHDEMSEQEEELEDDPT.VK.Y.DL
Retrocopy FSGLLISPEYIFPFSIRLKSNKSSNKSTTKSPQKVEDEEDSDEDSDHDEMSEQEEELEDDPTIVKDYQDL

Parental  EKA-VQSFRYDVVLKTGLDIGRNKVEDAFYKGELRLNEEKLWKKSRTVKVGDTLDLLIGE
          EK..VQSF.YD.VLKTGLDIGRNKVEDAFYKGELRLN.EKLWKK.RTVKVGDTLDLLIG.
Retrocopy EKE<VQSFWYDDVLKTGLDIGRNKVEDAFYKGELRLNGEKLWKKNRTVKVGDTLDLLIGD

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	6.43 RPM
SRP007412_cerebellum	0.11 RPM	6.52 RPM
SRP007412_heart	0.00 RPM	10.26 RPM
SRP007412_kidney	0.00 RPM	10.85 RPM
SRP007412_liver	0.00 RPM	6.45 RPM
SRP007412_testis	0.21 RPM	7.06 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1453 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1453 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1453 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2502

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000003732	1 retrocopy	retro_cfam_1818,
Homo sapiens	ENSG00000130349	1 retrocopy	retro_hsap_3538,
Gorilla gorilla	ENSGGOG00000006113	1 retrocopy	retro_ggor_2389,
Macropus eugenii	ENSMEUG00000013534	1 retrocopy	retro_meug_2181,
Microcebus murinus	ENSMICG00000004137	1 retrocopy	retro_mmur_1269,
Macaca mulatta	ENSMMUG00000007391	1 retrocopy	retro_mmul_115,
Nomascus leucogenys	ENSNLEG00000013450	2 retrocopies	retro_nleu_1433, retro_nleu_499,
Otolemur garnettii	ENSOGAG00000008839	2 retrocopies	retro_ogar_1396, retro_ogar_390,
Pongo abelii	ENSPPYG00000016885	1 retrocopy	retro_pabe_2922,
Pan troglodytes	ENSPTRG00000018464	2 retrocopies	retro_ptro_1453 , retro_ptro_2405,
Tursiops truncatus	ENSTTRG00000008837	2 retrocopies	retro_ttru_324, retro_ttru_432,