RetrogeneDB ID: retro_pabe_3177

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 7:120056052..120056589(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: LYPLA1
• Ensembl ID: ENSPPYG00000018590
• Aliases: None
• Description: acyl-protein thioesterase 1 [Source:RefSeq peptide;Acc:NP_001125450]

Sequence

>retro_pabe_3177
CCACATGTGCCAATTATGCCCATGACATTAATATGAACATGGCTATACCTTCTTGGTTTGATGTTTTTGGGCTTTCACCA
GATTCCCAGGAGGAGGAACCTGGAATTAAACAGGCAGCAGAAAATGTAAAACCTTTGGTAGATCAAGAGGTGTAGAATGG
CATTCTTTCCGACAGAATTATTTTGGGAGGATTTTCTCAGGGAGGAGCTTTTATTTTTATGTACTACTCTTACCACACAG
CAGAAACTGGCAGGTGTCATTGCATGCGACTGCTGGTTTCACTTTGGCCTTCCTTTCCAAAGGGTCCTATTAGTGGTACT
AATAGAGATATTTCTATTCTCCAGTGCCGTGGAGATTGTGACCCATTATTATCCCAATGTTTGGTTTCCTTATTTTTTTC
TTATTGTTTTATATTGGTAAATCCAGCCAATGTAAACTTTAAAACCTGTGAAAGCATAATGCACATTTCATGTCAACAGA
AAATGATTGGATGTCAAGCAATTTGCTGATAAAATTCTACAATTTTATCCAATTGAT

Alignment

ORF - retro_pabe_3177 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.76 %
• Parental protein coverage: 76.62 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  PCRPVRPVTL-NMNMAMPSWFDIIGLSPDSQEDESGIKQAAENIKALIDQEVKNGIPSNRIILGGFSQGG
          P..P..P.TL.NMNMA.PSWFD..GLSPDSQE.E.GIKQAAEN.K.L.DQEV.NGI.S.RIILGGFSQGG
Retrocopy PHVPIMPMTL<NMNMAIPSWFDVFGLSPDSQEEEPGIKQAAENVKPLVDQEV*NGILSDRIILGGFSQGG

Parental  A-LSLYTALTTQQKLAGVTALSCW-LPLRASFPQGPIGGANRDISILQCHGDCDPLVPLMFGSLTVEKLK
          A.L.L.T.LTTQQKLAGV.A..CW...L..SFP.GPI.G.NRDISILQC.GDCDPL......SL......
Retrocopy A>LFLCTTLTTQQKLAGVIACDCW<VSLWPSFPKGPISGTNRDISILQCRGDCDPLLSQCLVSLFFSYCF

Parental  TLVNPANVTFKTYEGMMHSSCQQEM-MDVKQFIDKLLP--PID
          .LVNPANV.FKT.E..MH.SCQQ.M..DVKQF.DK.L...PID
Retrocopy ILVNPANVNFKTCESIMHISCQQKM>LDVKQFADKILQFYPID

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	3.10 RPM
SRP007412_cerebellum	0.00 RPM	10.70 RPM
SRP007412_heart	0.00 RPM	11.47 RPM
SRP007412_kidney	0.00 RPM	14.09 RPM
SRP007412_liver	0.00 RPM	12.42 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3177 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3177 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3177 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3897
Gorilla gorilla	retro_ggor_2626
Macaca mulatta	retro_mmul_1734
Callithrix jacchus	retro_cjac_3100

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 39 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000006978	1 retrocopy	retro_cfam_523,
Callithrix jacchus	ENSCJAG00000011562	2 retrocopies	retro_cjac_1260, retro_cjac_3100,
Cavia porcellus	ENSCPOG00000022715	3 retrocopies	retro_cpor_142, retro_cpor_549, retro_cpor_782,
Dipodomys ordii	ENSDORG00000001479	1 retrocopy	retro_dord_88,
Equus caballus	ENSECAG00000016530	1 retrocopy	retro_ecab_238,
Echinops telfairi	ENSETEG00000001727	2 retrocopies	retro_etel_612, retro_etel_791,
Myotis lucifugus	ENSMLUG00000008208	1 retrocopy	retro_mluc_1683,
Macaca mulatta	ENSMMUG00000013157	3 retrocopies	retro_mmul_1734, retro_mmul_2459, retro_mmul_2474,
Nomascus leucogenys	ENSNLEG00000001027	4 retrocopies	retro_nleu_1137, retro_nleu_2015, retro_nleu_2817, retro_nleu_2869,
Oryctolagus cuniculus	ENSOCUG00000006751	3 retrocopies	retro_ocun_1510, retro_ocun_1623, retro_ocun_1679,
Pongo abelii	ENSPPYG00000001733	1 retrocopy	retro_pabe_142,
Pongo abelii	ENSPPYG00000018590	3 retrocopies	retro_pabe_2550, retro_pabe_3177 , retro_pabe_3565,
Pteropus vampyrus	ENSPVAG00000005246	2 retrocopies	retro_pvam_224, retro_pvam_838,
Rattus norvegicus	ENSRNOG00000008320	3 retrocopies	retro_rnor_1747, retro_rnor_2612, retro_rnor_406,
Tarsius syrichta	ENSTSYG00000012350	6 retrocopies	retro_tsyr_1287, retro_tsyr_1303, retro_tsyr_1465, retro_tsyr_1901, retro_tsyr_1996, retro_tsyr_2158,
Tursiops truncatus	ENSTTRG00000011836	3 retrocopies	retro_ttru_1643, retro_ttru_169, retro_ttru_291,