RetrogeneDB ID: retro_ptro_2357

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 6:70991546..70992298(+)
• Located in intron of: ENSPTRG00000018333

Retrocopy information

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

Parental gene information

• Parental gene symbol: TMEM192
• Ensembl ID: ENSPTRG00000016571
• Aliases: None
• Description: None

Sequence

>retro_ptro_2357
GGTTTCTTGGGTATCACTCAAAGTATTGAAGATGACCCATCTTGGGATACCCAGCTTCTCTTAACATTACTCACTAGAAG
CTCATTTTAGACCCTGATTCTATCTTTTTCCTACAGTCATCATAACAAATCTTTTGTTTATTCATGTTGTGTTATTTTTA
GCATTTTTAACAGATGTGGTTTGTTCTTACCCTAATCTAAATGAAGACAGGTGCCCAGGAAACTATACCAACCCTCTTGA
AGTTCAAATGGTTGTAATCCTTTGGAAAGTTACTTTGTGGTGGATTTTCTGTTTACATCTTGAATGCTACATCCAGTATC
ACCACAGCAAAGTCAGAAATCGAGGCTATAACTTGATCTACTGACGGATAAGGCATCTCAAGAGATTTGCGTTAATGATA
CACTCCACTGGCAACACAATAATTCTCTTCATACTGTGTTGCAGCATTCCTTCCTGGAAACCCGCAGATCAGATTATATC
TTGATCTCCTTCTGGCCATCCTGGCCCTGGTGCTGATCTGTTTTCTGATGTGTCTGCTCATATACACAGTGAAAATCTGG
AAATTTAATAAAGCTAAGCCATATCCTGATGTACTTGAAGAAGGAAAAATCTGTACTTAACCCAGCAGTATTACCTCAGA
GACTGGATTCAGGACTATTTGAAACCTAGAAGAAGTTGTTGAAAAGCAAGGAGACATAATAGTATATATGAAGTGACACA
ATGAAGTGTTGAGTGACTGTTGGCTCTCACTT

Alignment

ORF - retro_ptro_2357 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.5 %
• Parental protein coverage: 92.25 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  GSLDITQSIEDDPLLDAQLLP-HHSLQAHFRPRFHPLPTVIIMNLLWFIHLVFVVLAFLTGVLCSYPNPN
          G.L.ITQSIEDDP..D.QLL..H.SL.AHFRP.F...PTVII.NLL.FIH.V...LAFLT.V.CSYPN.N
Retrocopy GFLGITQSIEDDPSWDTQLLL>HYSLEAHFRP*FYLFPTVIITNLL-FIHVV-LFLAFLTDVVCSYPNLN

Parental  EDKCPGNYTNPLKVQTVIILGKVILW-ILHLLLECYIQYHHSKIRNRGYNLIYRSTRHLKRLALMIQSSG
          ED.CPGNYTNPL.VQ.V.IL.KV.LW.I..L.LECYIQYHHSK.RNRGYNLIY...RHLKR.ALMI.S.G
Retrocopy EDRCPGNYTNPLEVQMVVILWKVTLWWIFCLHLECYIQYHHSKVRNRGYNLIY*RIRHLKRFALMIHSTG

Parental  NTV-LLLILCMQHSFPEPG-RLYLDLILAILALELICSLICLLIYTVKIRRFNKAKPEPDILEEEKIYAY
          NT..L....C...S......RLYLDL.LAILAL.LIC.L.CLLIYTVKI..FNKAKP.PD.LEE.KI...
Retrocopy NTIILFILCCSIPSWKPAD>RLYLDLLLAILALVLICFLMCLLIYTVKIWKFNKAKPYPDVLEEGKICT*

Parental  PSNITSETGFRTISSLEEIVEKQGDTIEYLKRHNALLSKRLLAL
          PS.ITSETGFRTI..LEE.VEKQGD.I.Y.K.HN..LS...L.L
Retrocopy PSSITSETGFRTI*NLEEVVEKQGDIIVYMK*HNEVLSDCWLSL

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	16.68 RPM
SRP007412_cerebellum	0.00 RPM	32.48 RPM
SRP007412_heart	0.00 RPM	19.06 RPM
SRP007412_kidney	0.00 RPM	69.17 RPM
SRP007412_liver	0.00 RPM	37.58 RPM
SRP007412_testis	0.11 RPM	12.75 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2357 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2357 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2357 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3483
Pongo abelii	retro_pabe_2878
Macaca mulatta	retro_mmul_1769

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000009198	1 retrocopy	retro_cjac_2346,
Homo sapiens	ENSG00000170088	1 retrocopy	retro_hsap_3483,
Macaca mulatta	ENSMMUG00000021912	1 retrocopy	retro_mmul_1769,
Nomascus leucogenys	ENSNLEG00000006475	1 retrocopy	retro_nleu_2203,
Pongo abelii	ENSPPYG00000015175	1 retrocopy	retro_pabe_2878,
Pan troglodytes	ENSPTRG00000016571	1 retrocopy	retro_ptro_2357 ,
Ictidomys tridecemlineatus	ENSSTOG00000000402	1 retrocopy	retro_itri_1414,