RetrogeneDB ID: retro_ptro_250

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 1:199414268..199414516(+)
• Located in intron of: ENSPTRG00000001999

Retrocopy information

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

Parental gene information

• Parental gene symbol: GABARAPL2
• Ensembl ID: ENSPTRG00000008362
• Aliases: None
• Description: None

Sequence

>retro_ptro_250
GTGAAGTGGGTGTTCAGAGAGTCTCGCTCCTGGAACACAGGTGAGTGGAGTCCCCGAAGATCCACACAAAATAGCCCGGC
CAGTTCCAGCAATTATGAAAAAGTCCAGGCTCTCAGACCGCTGACACTGATAGGTAGAAGTCCTTGGTGCCACCTGGTAT
TCCAGTGGCTCAGTCCATGTGCATCATCACGAGTAGGATCCAGCTTGCTGCTGAAAAGGCCTCTGTCCCGTTTGTGGATA
AGACAGTG

Alignment

ORF - retro_ptro_250 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.95 %
• Parental protein coverage: 71.79 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MKWMFKEDHS-LEHRCVESAKIRAKYPDR-VPVIV-EKVS-GSQIVDIDKRKYLVPSDITVAQFMWIIRK
          .KW.F.E..S.LEHR.VES.KI..K.P...VP.I..EKV..GSQ..D.D..K.LVP..I.VAQ.M.II..
Retrocopy VKWVFRESRS<LEHR*VESPKIHTK*PGQ<VPAIM<EKVQ<GSQTADTDR*KSLVPPGIPVAQSMCIITS

Parental  RIQLPSEKAIFLFVDKTV
          RIQL..EKA...FVDKTV
Retrocopy RIQLAAEKASVPFVDKTV

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	101.90 RPM
SRP007412_cerebellum	0.04 RPM	92.31 RPM
SRP007412_heart	0.00 RPM	56.57 RPM
SRP007412_kidney	0.03 RPM	60.78 RPM
SRP007412_liver	0.00 RPM	19.15 RPM
SRP007412_testis	0.00 RPM	40.89 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_250 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_250 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_250 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000005453	2 retrocopies	retro_amel_1054, retro_amel_1238,
Callithrix jacchus	ENSCJAG00000014253	1 retrocopy	retro_cjac_146,
Dasypus novemcinctus	ENSDNOG00000002240	2 retrocopies	retro_dnov_1755, retro_dnov_2332,
Homo sapiens	ENSG00000034713	1 retrocopy	retro_hsap_4115,
Gorilla gorilla	ENSGGOG00000012299	2 retrocopies	retro_ggor_2761, retro_ggor_342,
Loxodonta africana	ENSLAFG00000017065	2 retrocopies	retro_lafr_234, retro_lafr_543,
Myotis lucifugus	ENSMLUG00000015112	1 retrocopy	retro_mluc_1207,
Macaca mulatta	ENSMMUG00000005759	2 retrocopies	retro_mmul_2369, retro_mmul_540,
Nomascus leucogenys	ENSNLEG00000013048	2 retrocopies	retro_nleu_1560, retro_nleu_580,
Pongo abelii	ENSPPYG00000007565	2 retrocopies	retro_pabe_3368, retro_pabe_372,
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	ENSRNOG00000019425	1 retrocopy	retro_rnor_57,