RetrogeneDB ID: retro_ptro_105

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 12:42144668..42145967(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPTRG00000004860
• Aliases: PCED1B, FAM113B
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: PCED1A
• Ensembl ID: ENSPTRG00000013185
• Aliases: PCED1A, FAM113A
• Description: PC-esterase domain containing 1A [Source:HGNC Symbol;Acc:16212]

Sequence

>retro_ptro_105
ATGATCCTTCTGCGGGCCTCCGAAGTGCGGCAGCTGCTTCACAATAAGTTCGTGGTCATCCTGGGGGACTCTGTGCATAG
GGCAGTATACAAGGACCTGGTGCTTCTGCTGCAGAAGGACCGCCTGCTCACTCCCGGGCAGCTTAGAGCAAGGGGGGAGC
TGAACTTCGAACAAGATGAGCTGGTGGACGGAGGCCAGCGGGGCCACATGCACAACGGCCTTAACTACCGTGAGGTCCGC
GAGTTCCGCTCCGACCACCATCTGGTGCGTTTTTACTTCCTCACCCGCGTGTACTCCGATTACCTCCAGACCATCTTGAA
AGAGCTGCAGTCGGGCGAGCACGCCCCCGACCTGGTCATCATGAATTCCTGCCTCTGGGACATCTCCAGGTATGGTCCGA
ACTCCTGGAGAAGCTACCTGGAGAACCTGGAGAACCTGTTCCAGTGCCTGGGCCAGGTGCTGCCCGAGTCTTGCCTCCTG
GTGTGGAACACGGCCATGCCTGTGGGCGAGGAAGTCACCGGGGGTTTTCTTCCGCCCAAGCTCCGGCGGCAGAAGGCCAC
CTTCCTGAAAAACGAAGTGGTCAAAGCCAACTTCCACAGCGCCACCGAGGCACGTAAACATAACTTCGATGTACTGGACT
TGCATTTCCACTTCCGCCACGCGAGGGAGAACCTGCACTGGGACGGGGTGCACTGGAATGGACGTGTGCACCGCTGCCTC
TCCCAGCTGCTGCTGGCCCACGTGGCCGACGCCTGGGGTGTGGAGCTGCCCCACCGCCACCCCGTGGGCGAGTGGATCAA
GAAGAAAAAACCTGGCCCGAGAGTCGAAGGGCCGCCCCAGGCCAACAGAAATCACCCGGCCTTACCTCTGTCTCCACCCT
TACCTTCCCCCACATACCGCCCCCTGCTTGGGTTCCCACCCCAGCGCTTGCCGCTGCTCCCGCTCCTGTCCCCACAGCCT
CCTCCTCCCATTCTCCATCACCAGGGAATGCCCCGGTTCCCACAGGGTCCCCCAGATGCCTGTTTTTCCTCAGACCATAC
TTTCCAGTCGGATCAATTCTATTGCCATTCAGATATCCCCTCATCAGCCCATGCAGGTTTCTTCTTCGAAGACAACTTTA
TGGTTGGTCCTCAGCTGCCTATGCCCTTCTTCCCCACACCCCGTTATCAGCGGCCTGCCCCAGTGGTACATAGGGGTTTT
GGTAGGTATCGTCCCCGTGGCCCCTATGCGCCCTGGGGACAGCGGCCTCGACCTTCAAAGAGAAGGGCCCCAGCCAATCC
TGAGCCAAGGCCTCAATAG

Alignment

ORF - retro_ptro_105 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.04 %
• Parental protein coverage: 59.03 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MVHFQASEVQQLLHNKFVVILGDSIQRAVYKDLVLLLQKDSLLTAAQLKAKGELSFEQDQLVAGGQLGEL
          M....ASEV.QLLHNKFVVILGDS..RAVYKDLVLLLQKD.LLT..QL.A.GEL.FEQD.LV.GGQ.G..
Retrocopy MILLRASEVRQLLHNKFVVILGDSVHRAVYKDLVLLLQKDRLLTPGQLRARGELNFEQDELVDGGQRGHM

Parental  HNGTQYREVRQFCSGSGHHLVRFYFLTRVYSEYLEDVLEELTYGP-APDLVIINSCLWDLSRYGRCSMES
          HNG..YREVR.F...S.HHLVRFYFLTRVYS.YL...L.EL..G..APDLVI.NSCLWD.SRYG..S..S
Retrocopy HNGLNYREVREF--RSDHHLVRFYFLTRVYSDYLQTILKELQSGEHAPDLVIMNSCLWDISRYGPNSWRS

Parental  YRENLERVFVRMDQVLPDSCLLVWNMAMPLGERITGGFLLPEL-QPLAGSLRRDVVEGNFYSATLAGDHC
          Y.ENLE..F....QVLP.SCLLVWN.AMP.GE..TGGFL.P.L....A..L...VV..NF.SAT.A..H.
Retrocopy YLENLENLFQCLGQVLPESCLLVWNTAMPVGEEVTGGFLPPKLRRQKATFLKNEVVKANFHSATEARKHN

Parental  FDVLDLHFHFRHAVQHRHRDGVHWDQHAHRHLSHLLLTHVADAWGVELPKRGYPPDPWIE
          FDVLDLHFHFRHA....H.DGVHW....HR.LS.LLL.HVADAWGVELP.R..P...WI.
Retrocopy FDVLDLHFHFRHARENLHWDGVHWNGRVHRCLSQLLLAHVADAWGVELPHR-HPVGEWIK

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	1.89 RPM	36.09 RPM
SRP007412_cerebellum	0.54 RPM	20.94 RPM
SRP007412_heart	0.52 RPM	2.59 RPM
SRP007412_kidney	4.37 RPM	28.95 RPM
SRP007412_liver	0.95 RPM	17.35 RPM
SRP007412_testis	3.58 RPM	7.80 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_105 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_105 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_105 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_82
Pongo abelii	retro_pabe_192

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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,