RetrogeneDB ID: retro_ptro_2369

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 6:89930589..89931401(+)
• Located in intron of: ENSPTRG00000018418

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSPTRG00000008496
• Aliases: None
• Description: None

Sequence

>retro_ptro_2369
ATGAGGGAGATCGTGCACATTCAGGCCGGCCAGTGCGGCAACTAGATCGGGGCCAAGTTCTGGGAAGTCATCAGTGATGA
GCATGGCATAGACCCCAGCGGCAACTACGTGGGGAACTCGGACTTGGAGCCGGAGCAGATCAGCATCTACTACAACGAGG
CCTCTTCTCACAAGTATGTGCCTCGGGCCATGCGTCGACCTGGAGCCCGGGACCATGGACAGTGTCCGCTCGGGGCCTTT
TGGACATTTTTTCAGGCCTGACAATTTAATCTTTGGTCAGAGTGGGGCCGTTAATAACTGGGCCAGGGGTCACTACACGG
AGTGTGCGGAGCTGGTGGATTCCGTCCTGGATGTGCGGAAGAAGTGTGAGAACTGCGACGGTCTGTAGGGTTTCCAGCTG
ACCCTCTCGCTGGGCAGGGGCACAAGCTCGGGTATGGGCACGCTGCTCATCAGCAAGATGCATGAGGAGTATCCCAACTG
CATTATGAACACCTTCAGCATAGTGCCCTCGCCCAAGGTGTCAGACACTGTGGTGGAGCCCTACAACCCCACGCTGTCCA
TCCACCAGCTGGTGGAGAATACAGATGAGACCTACTGCATCAACAAGGAGGCGCTCTAGGACATCTGCGTCAGCACCCTC
AGGCTGGCCACGCCCACCTACGGGGACCTCAGCCACCTGATGTTGGCCACCATGAGCAGGATCACTACCTCCTTGTGCTT
CCTGGGCCAGCTCAATGCGCACCTGCACAAGCTGGTGGTGAACATGGGTGCCCTTCCCCCGCCTGCACTTCTTCATGCCA
GGCATGTAGCCC

Alignment

ORF - retro_ptro_2369 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.99 %
• Parental protein coverage: 60.44 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MREIVHIQAGQCGNQIGAKFWEVISDEHGIDPSGNYVGDSDLQLERISVYYNEASSHKYVPRAILVDLEP
          MREIVHIQAGQCGN.IGAKFWEVISDEHGIDPSGNYVG.SDL..E.IS.YYNEASSHKYVPRA......P
Retrocopy MREIVHIQAGQCGN*IGAKFWEVISDEHGIDPSGNYVGNSDLEPEQISIYYNEASSHKYVPRAM---RRP

Parental  GTMDSVRS--GAF-GHLFRPDNFIFGQSGAGNNWAKGHYTEGAELVDSVLDVVRKECENCDCLQGFQLTH
          G..D......GAF.GH.FRPDN.IFGQSGA.NNWA.GHYTE.AELVDSVLD.VRK.CENCD.L.GFQLT.
Retrocopy GARDHGQCPLGAF>GHFFRPDNLIFGQSGAVNNWARGHYTECAELVDSVLD-VRKKCENCDGL*GFQLTL

Parental  SLGGGTGSGMGTLLISKVREEYPDRIMNTFSVVPSPKVSDTVVEPYNATLSIHQLVENTDETYCIDNEAL
          SLG.GT.SGMGTLLISK..EEYP..IMNTFS.VPSPKVSDTVVEPYN.TLSIHQLVENTDETYCI..EAL
Retrocopy SLGRGTSSGMGTLLISKMHEEYPNCIMNTFSIVPSPKVSDTVVEPYNPTLSIHQLVENTDETYCINKEAL

Parental  YDICFRTLKLATPTYGDLNHLVSATMSGVTTSLRFPGQLNADLRKLAVNM-VPFPRLHFFMPGFAP
          .DIC..TL.LATPTYGDL.HL..ATMS..TTSL.F.GQLNA.L.KL.VNM.VPFPRLHFFMPG..P
Retrocopy *DICVSTLRLATPTYGDLSHLMLATMSRITTSLCFLGQLNAHLHKLVVNM>VPFPRLHFFMPGM*P

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	261.66 RPM
SRP007412_cerebellum	0.04 RPM	115.83 RPM
SRP007412_heart	0.00 RPM	0.03 RPM
SRP007412_kidney	0.00 RPM	0.31 RPM
SRP007412_liver	0.00 RPM	0.07 RPM
SRP007412_testis	0.00 RPM	19.60 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2369 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2369 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2369 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Gorilla gorilla	retro_ggor_2364
Macaca mulatta	retro_mmul_1777

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Pan troglodytes	ENSPTRG00000008496	1 retrocopy	retro_ptro_2369 ,
Pan troglodytes	ENSPTRG00000017939	3 retrocopies	retro_ptro_151, retro_ptro_2527, retro_ptro_2677,
Pan troglodytes	ENSPTRG00000023373	2 retrocopies	retro_ptro_2403, retro_ptro_3166,