RetrogeneDB ID: retro_pabe_2080

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 2b:104399947..104400739(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PCED1A
• Ensembl ID: ENSPPYG00000010833
• Aliases: None
• Description: PC-esterase domain containing 1A [Source:HGNC Symbol;Acc:16212]

Sequence

>retro_pabe_2080
CGCCCTGCCTCCGCCGCCATGGCCCAGCTGCGAGCCTGCGAAGTCCGGCAGCTGCTGCACAACAAGTTCGTGGTGGTCAT
GGGGGACTCGGTCCAGCTGGCCGTGTACAAGGACCTGGTGCTCCTGCTTCAGAAGGACTGCCTGCTGTCCTCCAGTCAGC
TGAAGGCCAAGGGCGAGCTGAGCTTCGAGCGCGACATGCTGCTGGTGGGCTGCAGCAGCGGCCGCATGCACTACGACAGC
CACTACCGCGAGGTGCGCCAGTTCCGCTCGGGCCACCACCTGGTGCGCTTCTACTTCCTCACGCGCGTGTACTCGCACTA
CGCGGAGCGCGTCGTGGAGGAGCTGCGTAGGGCCGAGCCCGCCCCGGACGTGGTGATCATGAACTCCTGCCTCTGGGACC
TCGCCAGGGATGGCCGGGGCTTCCCCAGGAGCTACCGGCGTGACGTGGAGAGCCTGTTCGTGCGGCTGGACTGGGCGCTG
CCCACGTCCTGCCTCCTGATGTGGAACACCGCCATGCCCGTGGCCGAAACCATCTCGGGAAGCTGCCTCCCATGCGCGCG
CCAGCTCCGCCGCGCCCGCCTGCGCGAAGAGGTGATGGAGGCCAACTTCTACAGCTCCGCCGAGGCGGCGAGGCGCGGCT
TCGACGTGCTGGACCTGCATTTCCACTTCCGCCACGCCACGCGGCACCGGCTCGCCGACGGTGTGCACTGGGACGAGCGC
GCGCACCGCCACCTTTCCCAGCTGCTACTGGCCCACCTGGCAGACGCCTGGGGCGTGGACCTGCCCCGCCGC

Alignment

ORF - retro_pabe_2080 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.16 %
• Parental protein coverage: 58.37 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RPLRSDMVHFQASEVQQLLHNKFVVILGDSIQRAVYKDLVLLLQKDSLLTAAQLKAKGELSFEQDQLVAG
          RP....M....A.EV.QLLHNKFVV..GDS.Q.AVYKDLVLLLQKD.LL...QLKAKGELSFE.D.L..G
Retrocopy RPASAAMAQLRACEVRQLLHNKFVVVMGDSVQLAVYKDLVLLLQKDCLLSSSQLKAKGELSFERDMLLVG

Parental  GQLGELHNGTQYREVRQFCSGSGHHLVRFYFLTRVYSEYLEDVLEELTYG-PAPDLVIINSCLWDLSRYG
          ...G..H....YREVRQF...SGHHLVRFYFLTRVYS.Y.E.V.EEL....PAPD.VI.NSCLWDL.R.G
Retrocopy CSSGRMHYDSHYREVRQF--RSGHHLVRFYFLTRVYSHYAERVVEELRRAEPAPDVVIMNSCLWDLARDG

Parental  RCSMESYRENLERVFVRMDQVLPDSCLLVWNMAMPLGERITGGFLLPELQPLAGSLRRDVVEGNFYSATL
          R....SYR...E..FVR.D..LP.SCLL.WN.AMP..E.I.G..L....Q.....LR..V.E.NFYS...
Retrocopy RGFPRSYRRDVESLFVRLDWALPTSCLLMWNTAMPVAETISGSCLPCARQLRRARLREEVMEANFYSSAE

Parental  AGDHCFDVLDLHFHFRHAVQHRHRDGVHWDQHAHRHLSHLLLSHVADAWGVELPKR
          A....FDVLDLHFHFRHA..HR..DGVHWD..AHRHLS.LLL.H.ADAWGV.LP.R
Retrocopy AARRGFDVLDLHFHFRHATRHRLADGVHWDERAHRHLSQLLLAHLADAWGVDLPRR

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	34.61 RPM
SRP007412_cerebellum	0.00 RPM	33.32 RPM
SRP007412_heart	0.00 RPM	5.90 RPM
SRP007412_kidney	0.00 RPM	50.38 RPM
SRP007412_liver	0.00 RPM	18.36 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2080 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2080 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2080 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2207
Macaca mulatta	retro_mmul_341
Mus musculus	retro_mmus_332

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000003863	1 retrocopy	retro_btau_182,
Cavia porcellus	ENSCPOG00000025475	2 retrocopies	retro_cpor_343, retro_cpor_79,
Equus caballus	ENSECAG00000016497	1 retrocopy	retro_ecab_87,
Felis catus	ENSFCAG00000002886	1 retrocopy	retro_fcat_18,
Homo sapiens	ENSG00000132635	2 retrocopies	retro_hsap_2207, retro_hsap_82,
Microcebus murinus	ENSMICG00000016578	2 retrocopies	retro_mmur_163, retro_mmur_278,
Myotis lucifugus	ENSMLUG00000028662	2 retrocopies	retro_mluc_222, retro_mluc_647,
Macaca mulatta	ENSMMUG00000005200	2 retrocopies	retro_mmul_333, retro_mmul_341,
Mus musculus	ENSMUSG00000037773	2 retrocopies	retro_mmus_1001, retro_mmus_332,
Otolemur garnettii	ENSOGAG00000004701	1 retrocopy	retro_ogar_81,
Pongo abelii	ENSPPYG00000010833	2 retrocopies	retro_pabe_192, retro_pabe_2080 ,
Pan troglodytes	ENSPTRG00000013185	1 retrocopy	retro_ptro_105,
Pteropus vampyrus	ENSPVAG00000006834	1 retrocopy	retro_pvam_9,
Sus scrofa	ENSSSCG00000007168	1 retrocopy	retro_sscr_23,
Ictidomys tridecemlineatus	ENSSTOG00000016356	2 retrocopies	retro_itri_1190, retro_itri_783,
Tursiops truncatus	ENSTTRG00000003464	1 retrocopy	retro_ttru_16,