RetrogeneDB ID: retro_ptro_60

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 15:87704293..87704647(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPTRG00000040709
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: GABARAP
• Ensembl ID: ENSPTRG00000034115
• Aliases: None
• Description: None

Sequence

>retro_ptro_60
ATGAAGTTCCAGTACAAGGAGGTCCATCCCTTTGAGTATCGGAAAAAGGAAGGAGAAAAGATCCGGAAGAAATATCCGGA
CAGGGTCCCCTTGATTGTAGAGAAGGCTCCAAAAGCAAGGGTGCCTGATCTGGACAAGAGGAAGTACCTAGTGCCCTCCG
ACCTTACCGATGGCCAGTTCTACTTTTTAATCCGGAAGAGAATCCACCTGAGACCTGAGGACGCCTTATTCTTCTTTGTC
AACAACACTATCCCTCCCACTAGTGCTACCATGGGCCAACTATATGAGGACAGTCATGAGGAAGATGATTTTCTGTATGT
GGCCTACAGTAATGAGAGTGTCTATGGGAAATGA

Alignment

ORF - retro_ptro_60 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.48 %
• Parental protein coverage: 99.15 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MKFVYKEEHPFEKRRSEGEKIRKKYPDRVPVIVEKAPKARIGDLDKKKYLVPSDLTVGQFYFLIRKRIHL
          MKF.YKE.HPFE.R..EGEKIRKKYPDRVP.IVEKAPKAR..DLDK.KYLVPSDLT.GQFYFLIRKRIHL
Retrocopy MKFQYKEVHPFEYRKKEGEKIRKKYPDRVPLIVEKAPKARVPDLDKRKYLVPSDLTDGQFYFLIRKRIHL

Parental  RAEDALFFFVNNVIPPTSATMGQLYQEHHEEDFFLYIAYSDESVYG
          R.EDALFFFVNN.IPPTSATMGQLY...HEED.FLY.AYS.ESVYG
Retrocopy RPEDALFFFVNNTIPPTSATMGQLYEDSHEEDDFLYVAYSNESVYG

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	0.36 RPM	148.88 RPM
SRP007412_cerebellum	1.61 RPM	107.55 RPM
SRP007412_heart	1.19 RPM	72.02 RPM
SRP007412_kidney	0.73 RPM	182.49 RPM
SRP007412_liver	0.59 RPM	107.30 RPM
SRP007412_testis	0.53 RPM	245.75 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_60 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_60 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_60 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_60

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Ciona intestinalis	ENSCING00000012473	1 retrocopy	retro_cint_25,
Callithrix jacchus	ENSCJAG00000016655	2 retrocopies	retro_cjac_2851, retro_cjac_3820,
Gorilla gorilla	ENSGGOG00000013770	1 retrocopy	retro_ggor_821,
Loxodonta africana	ENSLAFG00000000744	1 retrocopy	retro_lafr_61,
Macaca mulatta	ENSMMUG00000010545	1 retrocopy	retro_mmul_155,
Mus musculus	ENSMUSG00000018567	1 retrocopy	retro_mmus_3107,
Nomascus leucogenys	ENSNLEG00000008049	2 retrocopies	retro_nleu_1670, retro_nleu_4,
Oryctolagus cuniculus	ENSOCUG00000006997	1 retrocopy	retro_ocun_311,
Pongo abelii	ENSPPYG00000007901	1 retrocopy	retro_pabe_122,
Pan troglodytes	ENSPTRG00000008362	2 retrocopies	retro_ptro_250, retro_ptro_2794,
Pan troglodytes	ENSPTRG00000008445	3 retrocopies	retro_ptro_2505, retro_ptro_367, retro_ptro_63,
Pan troglodytes	ENSPTRG00000034115	1 retrocopy	retro_ptro_60 ,
Rattus norvegicus	ENSRNOG00000017417	2 retrocopies	retro_rnor_1818, retro_rnor_2093,
Sus scrofa	ENSSSCG00000017936	1 retrocopy	retro_sscr_163,
Drosophila melanogaster	FBgn0052672	1 retrocopy	retro_dmel_23,