RetrogeneDB ID: retro_pabe_372

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 1:29499752..29500000(-)
• Located in intron of: ENSPPYG00000000207

Retrocopy information

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

Parental gene information

• Parental gene symbol: GABARAPL2
• Ensembl ID: ENSPPYG00000007565
• Aliases: None
• Description: GABA(A) receptor-associated protein-like 2 [Source:HGNC Symbol;Acc:13291]

Sequence

>retro_pabe_372
GTGAAGTGGGTGTTCAGAGAGGTTCGCTCCTGGAACACAGGTGAGTGGAGTCCCCAAAGATCCGCGCAAAATAGCCCAGC
CGGTTCCAGCAATTATGAAAAAGTCCAGGCTCTCAGACTGCTGACCCTGATAAGTAGAAGTCCTTGGTGCCACCTGGTAT
TCCAGTGGCTCAGTCCATGTGCGTCATCACGAGTAGGATCCAGCTTGCTGCTGAAAAGCCCTCTGTCCCGTTTGTGGATA
ACACAGTG

Alignment

ORF - retro_pabe_372 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 55.68 %
• Parental protein coverage: 71.79 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MKWMFKEDHS-LEHRCVESAKIRAKYPDR-VPVIV-EKVSGSQIV-DIDKRKYLVPSDITVAQFMWIIRK
          .KW.F.E..S.LEHR.VES.KIRAK.P.R.VP.I..EKV.......D.DK.K.LVP..I.VAQ.M..I..
Retrocopy VKWVFREVRS<LEHR*VESPKIRAK*PSR<VPAIM<EKVQALRLL<DPDK*KSLVPPGIPVAQSMCVITS

Parental  RIQLPSEKAIFLFVDKTV
          RIQL..EK....FVD.TV
Retrocopy RIQLAAEKPSVPFVDNTV

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	72.54 RPM
SRP007412_cerebellum	0.00 RPM	90.96 RPM
SRP007412_heart	0.03 RPM	44.28 RPM
SRP007412_kidney	0.00 RPM	39.48 RPM
SRP007412_liver	0.00 RPM	22.46 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_372 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_372 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_372 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Gorilla gorilla	retro_ggor_342
Macaca mulatta	retro_mmul_540

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 28 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 ,
Pongo abelii	ENSPPYG00000007628	7 retrocopies	retro_pabe_1280, retro_pabe_1566, retro_pabe_245, retro_pabe_3157, retro_pabe_3158, retro_pabe_940, retro_pabe_978,
Pongo abelii	ENSPPYG00000007901	1 retrocopy	retro_pabe_122,
Pan troglodytes	ENSPTRG00000008362	2 retrocopies	retro_ptro_250, retro_ptro_2794,
Rattus norvegicus	ENSRNOG00000019425	1 retrocopy	retro_rnor_57,