RetrogeneDB ID: retro_ptro_2106

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 4:156353958..156354498(-)
• Located in intron of: ENSPTRG00000016522

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSPTRG00000007132
• Aliases: None
• Description: None

Sequence

>retro_ptro_2106
GTCTACAAGGAAATGTACAAGACTGATCTGGAGAAGGACATTATTTCGGACACATCTGGTGACTTCTGCAAGCTGATGGT
TGCCCTGGCAAAGGGTAGAAGAGCAGAGGATGGCTCTGTCATTGATTATGAACTGATTGACCAAGATGCCCGGGATCTCT
ATGACGCTGGGGTGAAGAGGAAAGGAACTGAAGTTCCCAAGTGGATCAGCCTCATGACCGAGCGGAGCATGTCCCACTTC
CAGAAAGTATTTGATAGGTACAAGAGCTACAGTCCTTATGACATGTTGGAGAGCATCAAGAAAGAGGTTAAAGGAGACCT
GGAAAATGCTTTCCTGAACCTGGTCCAGTGTATTCAGAACAAGCCCCTGTATTTTGCTGACCGGCTGTACGACTCCATAA
CGGGCAAGGGGACTCAAGATAAGGTCCTGATCAGAATCATGGTCTCCCACAATGAAGTGGACATGTTGAAAATTAGGTCT
GAATTCAAGAGAAAGTATAGCAAGTCCCTGTACTATTACATCCAGCAAGACACTAAGGGT

Alignment

ORF - retro_ptro_2106 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.78 %
• Parental protein coverage: 52.02 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VYKEMYKTDLEKDIISDTSGDFRKLMVALAKGRRAEDGSVIDYELIDQDARDLYDAGVKRKGTDVPKWIS
          VYKEMYKTDLEKDIISDTSGDF.KLMVALAKGRRAEDGSVIDYELIDQDARDLYDAGVKRKGT.VPKWIS
Retrocopy VYKEMYKTDLEKDIISDTSGDFCKLMVALAKGRRAEDGSVIDYELIDQDARDLYDAGVKRKGTEVPKWIS

Parental  IMTERSVPHLQKVFDRYKSYSPYDMLESIRKEVKGDLENAFLNLVQCIQNKPLYFADRLYDSMKGKGTRD
          .MTERS..H.QKVFDRYKSYSPYDMLESI.KEVKGDLENAFLNLVQCIQNKPLYFADRLYDS..GKGT.D
Retrocopy LMTERSMSHFQKVFDRYKSYSPYDMLESIKKEVKGDLENAFLNLVQCIQNKPLYFADRLYDSITGKGTQD

Parental  KVLIRIMVSRSEVDMLKIRSEFKRKYGKSLYYYIQQDTKG
          KVLIRIMVS..EVDMLKIRSEFKRKY.KSLYYYIQQDTKG
Retrocopy KVLIRIMVSHNEVDMLKIRSEFKRKYSKSLYYYIQQDTKG

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	0.09 RPM	18.88 RPM
SRP007412_cerebellum	0.14 RPM	21.76 RPM
SRP007412_heart	0.41 RPM	127.84 RPM
SRP007412_kidney	0.73 RPM	208.35 RPM
SRP007412_liver	0.49 RPM	276.41 RPM
SRP007412_testis	0.00 RPM	64.49 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2106 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2106 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2106 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3114
Gorilla gorilla	retro_ggor_2137
Pongo abelii	retro_pabe_2572

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Parental genes homology:

Parental genes homology involve 20 parental genes, and 39 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000008055	2 retrocopies	retro_amel_1531, retro_amel_1836,
Bos taurus	ENSBTAG00000009615	2 retrocopies	retro_btau_634, retro_btau_985,
Canis familiaris	ENSCAFG00000016686	3 retrocopies	retro_cfam_1631, retro_cfam_367, retro_cfam_707,
Choloepus hoffmanni	ENSCHOG00000012143	3 retrocopies	retro_chof_1028, retro_chof_1965, retro_chof_815,
Equus caballus	ENSECAG00000012670	1 retrocopy	retro_ecab_759,
Homo sapiens	ENSG00000182718	3 retrocopies	retro_hsap_3114, retro_hsap_4150, retro_hsap_580,
Gorilla gorilla	ENSGGOG00000009738	3 retrocopies	retro_ggor_2137, retro_ggor_2788, retro_ggor_515,
Macropus eugenii	ENSMEUG00000008980	3 retrocopies	retro_meug_1000, retro_meug_312, retro_meug_389,
Myotis lucifugus	ENSMLUG00000002464	3 retrocopies	retro_mluc_1569, retro_mluc_2223, retro_mluc_2431,
Monodelphis domestica	ENSMODG00000011604	1 retrocopy	retro_mdom_1471,
Mustela putorius furo	ENSMPUG00000000762	2 retrocopies	retro_mputfur_73, retro_mputfur_79,
Nomascus leucogenys	ENSNLEG00000011678	2 retrocopies	retro_nleu_769, retro_nleu_802,
Otolemur garnettii	ENSOGAG00000009952	1 retrocopy	retro_ogar_3510,
Pongo abelii	ENSPPYG00000006526	2 retrocopies	retro_pabe_2572, retro_pabe_607,
Pan troglodytes	ENSPTRG00000007132	2 retrocopies	retro_ptro_2106 , retro_ptro_81,
Pteropus vampyrus	ENSPVAG00000011401	1 retrocopy	retro_pvam_389,
Tupaia belangeri	ENSTBEG00000001276	1 retrocopy	retro_tbel_3335,
Tarsius syrichta	ENSTSYG00000003719	1 retrocopy	retro_tsyr_2086,
Tursiops truncatus	ENSTTRG00000007705	1 retrocopy	retro_ttru_1725,
Vicugna pacos	ENSVPAG00000007888	2 retrocopies	retro_vpac_241, retro_vpac_27,