RetrogeneDB ID: retro_ptro_1204

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 17:4877102..4877507(-)
• Located in intron of: ENSPTRG00000008611

Retrocopy information

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

Parental gene information

• Parental gene symbol: ATP6V0C
• Ensembl ID: ENSPTRG00000007653
• Aliases: None
• Description: None

Sequence

>retro_ptro_1204
TCCAACAACAGCCCCGAGTATGCTTTGGTTTTCACCATCTCGGGTGCTATGGCCACCATGGTCTCCAGTGGCCTGGGTGC
TGCCTGTGGCATGGCCAAGAATGGCACCGGCATCGTGGCCATGTCTGTCATGTGGCCAGAGCTGATCCACATGAAGTCCA
TCATCCCAGTGGTCATGGCTGGTATCATCACCATCTATGGCCTAGTGGCGGCTGTCCCCCCTGCCAACTCCCTGAATGAT
GACAACAGTCTCTATAGCAGTTTCCTCCAGCTGGGCGCTGGCCTGAGTGGCCTGGCAGCCGGCTTCGCCATCGTCATCGT
GGGGGACACTGGCAAGTGTGGCACTGCCCAGCAGCCCTGACTATTTGTAGGCATGATACTGATCCTCATCTTTGCCAAGG
TGCTT

Alignment

ORF - retro_ptro_1204 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.54 %
• Parental protein coverage: 89.03 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SKSGPEYASFFAVMGASAAMVFSALGAAYGTAKSGTGIAAMSVMRPELI-MKSIIPVVMAGIIAIYGLVV
          S...PEYA..F...GA.A.MV.S.LGAA.G.AK.GTGI.AMSVM.PELI.MKSIIPVVMAGII.IYGLV.
Retrocopy SNNSPEYALVFTISGAMATMVSSGLGAACGMAKNGTGIVAMSVMWPELIHMKSIIPVVMAGIITIYGLVA

Parental  AVLIANSLNDDISLYKSFLQLGAGLSVGLSGLAAGFAIGIVGDAGVRGTAQQPRLFVGMILILIFAEVL
          AV..ANSLNDD.SLY.SFLQLGAGLS....GLAAGFAI.IVGD.G..GTAQQP.LFVGMILILIFA.VL
Retrocopy AVPPANSLNDDNSLYSSFLQLGAGLS----GLAAGFAIVIVGDTGKCGTAQQP*LFVGMILILIFAKVL

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	0.27 RPM	326.23 RPM
SRP007412_cerebellum	0.07 RPM	229.43 RPM
SRP007412_heart	0.09 RPM	41.88 RPM
SRP007412_kidney	0.05 RPM	231.78 RPM
SRP007412_liver	0.16 RPM	107.89 RPM
SRP007412_testis	0.00 RPM	34.04 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1204 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1204 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1204 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 31 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000026428	1 retrocopy	retro_btau_1638,
Homo sapiens	ENSG00000185883	2 retrocopies	retro_hsap_1798, retro_hsap_3462,
Gorilla gorilla	ENSGGOG00000028600	2 retrocopies	retro_ggor_1323, retro_ggor_2335,
Macropus eugenii	ENSMEUG00000004597	2 retrocopies	retro_meug_1428, retro_meug_1837,
Myotis lucifugus	ENSMLUG00000026715	2 retrocopies	retro_mluc_2507, retro_mluc_294,
Monodelphis domestica	ENSMODG00000015439	5 retrocopies	retro_mdom_1669, retro_mdom_1739, retro_mdom_507, retro_mdom_84, retro_mdom_982,
Mus musculus	ENSMUSG00000024121	2 retrocopies	retro_mmus_2726, retro_mmus_2888,
Nomascus leucogenys	ENSNLEG00000009416	2 retrocopies	retro_nleu_1692, retro_nleu_2770,
Procavia capensis	ENSPCAG00000015060	1 retrocopy	retro_pcap_148,
Pan troglodytes	ENSPTRG00000007653	2 retrocopies	retro_ptro_1204 , retro_ptro_2346,
Rattus norvegicus	ENSRNOG00000006542	1 retrocopy	retro_rnor_118,
Sarcophilus harrisii	ENSSHAG00000014251	1 retrocopy	retro_shar_194,
Ictidomys tridecemlineatus	ENSSTOG00000013420	3 retrocopies	retro_itri_119, retro_itri_387, retro_itri_691,
Drosophila melanogaster	FBgn0262736	3 retrocopies	retro_dmel_3, retro_dmel_38, retro_dmel_65,
Caenorhabditis elegans	R10E11.2	2 retrocopies	retro_cele_1, retro_cele_5,