RetrogeneDB ID: retro_ptro_2500

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 6:160673135..160673692(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: YKT6
• Ensembl ID: ENSPTRG00000019141
• Aliases: None
• Description: None

Sequence

>retro_ptro_2500
GTGAAGCTGTACAGCCTCAGTGTCCTCTACAAAGGCGAGGCCAATGTAGTGCTGCTCAAAGCCAGGTACGACGATGTCGC
TTCCTTCAGCTTTTTCCAGAGATCCAGCGTTCAGGAATTCATGACCTTCATGAATCAACTGATCGTGGAGCACTCATCCA
AAGGCACTAGAGCTTCTGTCGAAGAACAAGACTATATGTGGCACGTCTATGTCCGGAATGACAGTCTTGCAGGTGACAAT
GAATGCCCATCCCGGATGGCCTTTACCTTGCTGGAGAAAGTACTAGATGAATTCTCCAAGCAAGTCAACAGGATAGACTG
GCCAGTAGGATCCCCTGCTACAATCCATTCTGCAGCCCTGGATGGTCACCTCAGTAGACACCAGAACCCACGAGACGCTG
ACCCTGTGACTAACATGCAGGCCGAACCAGACAAGACCCAAATCGTTGTGCACAACACCATGGAGTATTTGTTAGAGCGA
GGTGAGAAGCGAGGTGGCTTGGTGTCCAAATCCGAGGGCTGGGAACACAGTCTAAAGCCTTCTATAAAACCGCCCGG

Alignment

ORF - retro_ptro_2500 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.15 %
• Parental protein coverage: 95.45 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MKLYSLSVLYKGEAKVVLLKAAYD-VSSFSFFQRSSVQEFMTFTSQLIVERSSKGTRASVKEQDYLCHVY
          .KLYSLSVLYKGEA.VVLLKA.YD.V.SFSFFQRSSVQEFMTF..QLIVE.SSKGTRASV.EQDY..HVY
Retrocopy VKLYSLSVLYKGEANVVLLKARYDDVASFSFFQRSSVQEFMTFMNQLIVEHSSKGTRASVEEQDYMWHVY

Parental  VRNDSLAGVVIADNEYPSRVAFTLLEKVLDEFSKQVDRIDWPVGSPATIHYPALDGHLSRYQNPREADPM
          VRNDSLAG....DNE.PSR.AFTLLEKVLDEFSKQV.RIDWPVGSPATIH..ALDGHLSR.QNPR.ADP.
Retrocopy VRNDSLAG----DNECPSRMAFTLLEKVLDEFSKQVNRIDWPVGSPATIHSAALDGHLSRHQNPRDADPV

Parental  TKVQAELDETKIILHNTMESLLERGEKLDDLVSKSE-VLGTQSKAFYKTAR
          T..QAE.D.T.I..HNTME.LLERGEK...LVSKSE..LGTQSKAFYKTAR
Retrocopy TNMQAEPDKTQIVVHNTMEYLLERGEKRGGLVSKSE<GLGTQSKAFYKTAR

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	0.13 RPM	64.44 RPM
SRP007412_cerebellum	0.04 RPM	68.22 RPM
SRP007412_heart	0.03 RPM	48.70 RPM
SRP007412_kidney	0.05 RPM	112.24 RPM
SRP007412_liver	0.03 RPM	86.25 RPM
SRP007412_testis	0.00 RPM	68.18 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2500 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2500 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2500 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3687
Gorilla gorilla	retro_ggor_2493
Pongo abelii	retro_pabe_3022

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Parental genes homology:

Parental genes homology involve 19 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000017618	1 retrocopy	retro_amel_967,
Bos taurus	ENSBTAG00000000274	1 retrocopy	retro_btau_601,
Canis familiaris	ENSCAFG00000002903	1 retrocopy	retro_cfam_740,
Choloepus hoffmanni	ENSCHOG00000011207	1 retrocopy	retro_chof_657,
Callithrix jacchus	ENSCJAG00000008053	2 retrocopies	retro_cjac_2394, retro_cjac_2492,
Dasypus novemcinctus	ENSDNOG00000015173	1 retrocopy	retro_dnov_1364,
Dipodomys ordii	ENSDORG00000016393	1 retrocopy	retro_dord_621,
Erinaceus europaeus	ENSEEUG00000001247	1 retrocopy	retro_eeur_267,
Felis catus	ENSFCAG00000014362	1 retrocopy	retro_fcat_1327,
Gorilla gorilla	ENSGGOG00000027036	1 retrocopy	retro_ggor_2493,
Macropus eugenii	ENSMEUG00000014769	1 retrocopy	retro_meug_2068,
Mustela putorius furo	ENSMPUG00000018200	2 retrocopies	retro_mputfur_141, retro_mputfur_165,
Mus musculus	ENSMUSG00000002741	1 retrocopy	retro_mmus_825,
Nomascus leucogenys	ENSNLEG00000003689	1 retrocopy	retro_nleu_2275,
Oryctolagus cuniculus	ENSOCUG00000002981	1 retrocopy	retro_ocun_15,
Pongo abelii	ENSPPYG00000017595	1 retrocopy	retro_pabe_3022,
Pan troglodytes	ENSPTRG00000019141	1 retrocopy	retro_ptro_2500 ,
Sus scrofa	ENSSSCG00000016750	1 retrocopy	retro_sscr_1063,
Tursiops truncatus	ENSTTRG00000006052	2 retrocopies	retro_ttru_1320, retro_ttru_417,