RetrogeneDB ID: retro_pabe_2550

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 4:115650538..115651227(-)
• 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_2550
ATGTGCAGCAATAACATGTCAGCCCCGCTGTCAGCCATCGTGCCCGCCTCCTGGAAGGCCGCCGCCGCGGTGATTTTCGT
TCATGGATTGGGAGATACTGGGCACAGATGGATAGAAGCCTTTGCAGGTATCAGAAGTTCACATATCAAATATGTCTGTC
CGCATGTGCCTGTTATGCCTTTACATTAAATATGAACATGGCTGTGCCTTCATAGTTTGATATTATTGGGCTTTCACCAG
ATTCACAGGAGGATGAACCTGGGATTAAACAGGCAGCAGAAAATATAAAAGCTTTGATTGATCAAGAAGTGAGGAACGGC
ATTCCTTCTAACCGAATTATTTTAGGAGGATTTTCTCAGGGAGGAGTTTTATCTTTATATACTGCCCTTACCACGTAGCA
GAAACTGGCGGGTGTCACTGCGCTCAGTTGCCGGCTTCCACTTCGGGCTTCATTTCCACAGGGTCCTATCAGTGGCGCTA
ATAGAGATATTCCTATTCTCCAGTGCCACGGAGATTGTGACCCGTTAGTTCCCCTGATGTTTGGTTCTCTTATGATTGAA
AAACTAAAAACACTGGTGAATCCAGCCGATGTGACCTTTAAAATCTATGAAGGTATGATGCATAGTTCATGTCAACAGGA
AATTATGGATGTCAAGCAATTCATTGATAAACTCCTACCTCCAATTGAT

Alignment

ORF - retro_pabe_2550 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.03 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MCGNNMSTPLPAIVPAARKATAAVIFLHGLGDTGGHGKQSFFMLCYSDFVVFSFPCRPVRPV-TLNMNMA
          MC.NNMS.PL.AIVPA..KA.AAVIF.HGLGDTG......F.....S.......P..PV.P..TLNMNMA
Retrocopy MCSNNMSAPLSAIVPASWKAAAAVIFVHGLGDTGHRWIEAFAGI-RSSHIKYVCPHVPVMPL<TLNMNMA

Parental  MPSWFDIIGLSPDSQEDESGIKQAAENIKALIDQEVKNGIPSNRIILGGFSQGGALSLYTALTTQQKLAG
          .PS.FDIIGLSPDSQEDE.GIKQAAENIKALIDQEV.NGIPSNRIILGGFSQGG.LSLYTALTT.QKLAG
Retrocopy VPS*FDIIGLSPDSQEDEPGIKQAAENIKALIDQEVRNGIPSNRIILGGFSQGGVLSLYTALTT*QKLAG

Parental  VTALSCWLPLRASFPQGPIGGANRDISILQCHGDCDPLVPLMFGSLTVEKLKTLVNPANVTFKTYEGMMH
          VTALSC.LPLRASFPQGPI.GANRDI.ILQCHGDCDPLVPLMFGSL..EKLKTLVNPA.VTFK.YEGMMH
Retrocopy VTALSCRLPLRASFPQGPISGANRDIPILQCHGDCDPLVPLMFGSLMIEKLKTLVNPADVTFKIYEGMMH

Parental  SSCQQEMMDVKQFIDKLLPPID
          SSCQQE.MDVKQFIDKLLPPID
Retrocopy SSCQQEIMDVKQFIDKLLPPID

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_2550 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2550 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2550 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3078
Gorilla gorilla	retro_ggor_2114

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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,