RetrogeneDB ID: retro_ptro_1056

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 15:52748209..52748932(-)
• Located in intron of: ENSPTRG00000007098

Retrocopy information

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

Parental gene information

• Parental gene symbol: THEM4
• Ensembl ID: ENSPTRG00000001301
• Aliases: None
• Description: None

Sequence

>retro_ptro_1056
ATGCTGAGGAGCTGCGCCAGGCGCCTCCGCACGCTGGGGGCCCTTTGCCAGCCGCCACCGGTAGGCAGGCGCCTGCTGGG
TAGTGAGCCGCGACCTGCGCTGAGGTCATTTTCTTCTGAGGAAGTCATTCTTAAGGACTATTCTGTCCCCAACCCCAGCT
GGAACAAGGACCTAAAACTGCTCTTTGACCAGTTTATGAAGAAATGTGAAGACGGCTCCTGGAAACGTTTGCCTTCATAT
AAACCTACACCTACTGAAAGGATTCAAGACTTTAAAACCCATTTTCTTGACCCAAAGCTTATGAAAGAAGAACAAGTGTC
ACAGGCCCAGCTCTTCACCAGAAGCTTTGATGATGGCCTGGGCTTTGAATACGTGATGTTCTACAATGACGTTGAGAAAA
GGATGGTTTGCTTATTTCAAGGAGTCCCTTACCTAGAAGGACCACCTGGATTGATTCATGGAGGTGCCATTGCAACCATG
ATTGATGCTACTGTTGGTATGTGTGCAATGATGGCTGGGGGAATCGTCATGACTGCCAATCTCAACATCAGTTGTAAAAG
ACCTATCCCTCTTTGTTCTGTTGTTACGATAAATAGCCAACTTGATAAAGTTGAAGGAAAGAAATTTTTTGTTTCCAGTA
ATGTTCAGAGTGTTGATGAGAAGACCCTATATTCAGAGGCGACAAGCTTACTTATAAAGCTGAATCCTGCTAAAAGTCTG
ACA

Alignment

ORF - retro_ptro_1056 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.46 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MLRSCAARLRTLWALCRPP-VGRRLPGSVPRPELRSFSSEEVILKDCSVPNPSWNKDLRLLFDQFMKKCE
          MLRSCA.RLRTL.ALC.PP.VGRRL.GS.PRP.LRSFSSEEVILKD.SVPNPSWNKDL.LLFDQFMKKCE
Retrocopy MLRSCARRLRTLGALCQPPPVGRRLLGSEPRPALRSFSSEEVILKDYSVPNPSWNKDLKLLFDQFMKKCE

Parental  DGSWKRLPSYKRTPTERIQDFKTRFLDPKLMKEEQMSQAQLFTRSFDDGLGFEYVMFYNDIEKRMVCLFQ
          DGSWKRLPSYK.TPTERIQDFKT.FLDPKLMKEEQ.SQAQLFTRSFDDGLGFEYVMFYND.EKRMVCLFQ
Retrocopy DGSWKRLPSYKPTPTERIQDFKTHFLDPKLMKEEQVSQAQLFTRSFDDGLGFEYVMFYNDVEKRMVCLFQ

Parental  GGPYLEGPPGFIHGGAIATMIDSTVGMCAMMAGGIVMTANLNINYKRPIPLCSVVMINSQLDEVEGRKFF
          G.PYLEGPPG.IHGGAIATMID.TVGMCAMMAGGIVMTANLNI..KRPIPLCSVV.INSQLD.VEG.KFF
Retrocopy GVPYLEGPPGLIHGGAIATMIDATVGMCAMMAGGIVMTANLNISCKRPIPLCSVVTINSQLDKVEGKKFF

Parental  VSCNVQSVDEKTLYSEATSLFIKLNPAKSLT
          VS.NVQSVDEKTLYSEATSL.IKLNPAKSLT
Retrocopy VSSNVQSVDEKTLYSEATSLLIKLNPAKSLT

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	21.18 RPM
SRP007412_cerebellum	0.00 RPM	17.46 RPM
SRP007412_heart	0.00 RPM	40.98 RPM
SRP007412_kidney	0.08 RPM	58.74 RPM
SRP007412_liver	0.00 RPM	9.62 RPM
SRP007412_testis	0.00 RPM	30.25 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1056 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1056 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1056 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1569
Gorilla gorilla	retro_ggor_1195
Pongo abelii	retro_pabe_1295

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000000355	1 retrocopy	retro_amel_1301,
Choloepus hoffmanni	ENSCHOG00000000818	1 retrocopy	retro_chof_841,
Dasypus novemcinctus	ENSDNOG00000005970	1 retrocopy	retro_dnov_710,
Felis catus	ENSFCAG00000003443	1 retrocopy	retro_fcat_387,
Homo sapiens	ENSG00000159445	2 retrocopies	retro_hsap_1569, retro_hsap_978,
Gorilla gorilla	ENSGGOG00000008114	2 retrocopies	retro_ggor_1195, retro_ggor_782,
Microcebus murinus	ENSMICG00000010696	4 retrocopies	retro_mmur_1241, retro_mmur_1436, retro_mmur_1505, retro_mmur_1574,
Nomascus leucogenys	ENSNLEG00000010322	1 retrocopy	retro_nleu_1737,
Oryctolagus cuniculus	ENSOCUG00000005194	1 retrocopy	retro_ocun_1341,
Pongo abelii	ENSPPYG00000000851	1 retrocopy	retro_pabe_1295,
Pan troglodytes	ENSPTRG00000001301	2 retrocopies	retro_ptro_1056 , retro_ptro_768,
Tupaia belangeri	ENSTBEG00000003352	2 retrocopies	retro_tbel_2412, retro_tbel_3266,
Tarsius syrichta	ENSTSYG00000005739	1 retrocopy	retro_tsyr_579,