RetrogeneDB ID: retro_hsap_82

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 12:47628846..47630145(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000179715
• Aliases: PCED1B, FAM113B
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: PCED1A
• Ensembl ID: ENSG00000132635
• Aliases: PCED1A, C20orf81, FAM113A, bA12M19.1
• Description: PC-esterase domain containing 1A [Source:HGNC Symbol;Acc:16212]

Sequence

>retro_hsap_82
ATGATCCTTCTGCGGGCCTCCGAAGTGCGGCAGCTGCTTCACAATAAGTTCGTGGTCATCCTGGGGGACTCTGTGCATAG
GGCAGTATACAAGGACCTGGTGCTTCTGCTGCAGAAGGACCGCCTGCTCACTCCCGGGCAGCTTAGAGCAAGGGGGGAGC
TGAACTTCGAACAAGATGAGCTGGTGGACGGAGGCCAGCGGGGCCACATGCACAACGGCCTTAACTACCGTGAGGTCCGC
GAGTTCCGCTCCGACCACCATCTGGTACGTTTTTACTTCCTCACCCGCGTGTACTCCGATTACCTCCAGACCATCTTGAA
AGAGCTGCAGTCGGGCGAGCACGCCCCCGACCTGGTCATCATGAATTCCTGCCTCTGGGACATCTCCAGGTATGGTCCGA
ACTCCTGGAGAAGCTACCTGGAGAACCTGGAGAACCTGTTCCAGTGCCTGGGCCAGGTGCTGCCCGAGTCTTGCCTCCTG
GTGTGGAACACGGCCATGCCTGTGGGCGAGGAAGTCACCGGGGGTTTTCTTCCGCCCAAGCTCCGGCGGCAGAAGGCCAC
CTTCCTGAAAAACGAAGTGGTCAAAGCCAACTTCCACAGCGCCACCGAGGCACGTAAACATAACTTCGATGTACTGGACT
TGCATTTCCACTTCCGCCACGCGAGGGAGAACCTGCACTGGGACGGGGTGCACTGGAATGGACGTGTGCACCGCTGCCTC
TCCCAGCTGCTGCTGGCCCACGTGGCCGACGCCTGGGGTGTGGAGCTGCCCCACCGCCACCCCGTGGGCGAGTGGATCAA
GAAGAAAAAACCTGGCCCGAGAGTCGAAGGGCCGCCCCAGGCCAACAGAAATCACCCGGCCTTACCTCTGTCCCCACCCT
TACCTTCCCCCACATACCGCCCCCTGCTTGGGTTCCCACCCCAGCGCTTGCCGCTGCTCCCGCTCCTGTCCCCACAGCCT
CCTCCTCCCATTCTCCATCACCAGGGAATGCCCCGGTTCCCACAGGGTCCCCCAGATGCCTGTTTTTCCTCAGACCATAC
TTTCCAGTCGGATCAATTCTATTGCCATTCAGATGTCCCCTCATCAGCCCATGCAGGTTTCTTCGTCGAAGACAATTTTA
TGGTTGGTCCTCAGCTGCCTATGCCCTTCTTCCCCACACCCCGTTATCAGCGGCCTGCCCCAGTGGTACATAGGGGTTTT
GGCAGGTATCGTCCCCGTGGCCCCTATACGCCCTGGGGACAGCGGCCTCGACCTTCAAAGAGAAGGGCCCCAGCCAATCC
TGAGCCAAGGCCTCAATAG

Alignment

ORF - retro_hsap_82 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
bodymap2_adipose	3.60 RPM	10.63 RPM
bodymap2_adrenal	12.92 RPM	21.68 RPM
bodymap2_brain	0.42 RPM	9.26 RPM
bodymap2_breast	3.83 RPM	10.19 RPM
bodymap2_colon	1.64 RPM	6.34 RPM
bodymap2_heart	0.46 RPM	2.95 RPM
bodymap2_kidney	0.60 RPM	10.48 RPM
bodymap2_liver	0.42 RPM	5.17 RPM
bodymap2_lung	4.10 RPM	12.03 RPM
bodymap2_lymph_node	20.38 RPM	27.65 RPM
bodymap2_ovary	10.74 RPM	17.68 RPM
bodymap2_prostate	3.85 RPM	14.06 RPM
bodymap2_skeletal_muscle	0.33 RPM	1.93 RPM
bodymap2_testis	3.94 RPM	9.58 RPM
bodymap2_thyroid	0.85 RPM	34.63 RPM
bodymap2_white_blood_cells	22.56 RPM	7.42 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_hsap_82 was not detected

EST

8 EST(s) were mapped to retro_hsap_82 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
BF798708	47629601	47629742	98.6	139	0	135
BF798709	47629602	47629742	95.7	136	1	129
CD636379	47628942	47629509	99.9	566	1	565
CD636381	47629222	47629716	99.4	490	2	486
CD636382	47628945	47629571	98.6	599	6	574
CD636383	47629274	47629721	99.1	438	3	430
CD636384	47628942	47629538	96.5	585	4	567
CV027149	47628846	47629433	99.5	577	2	573

TSS

TSS No.	TSS Name	TSS expression level (Expr) in TPM range:
		no expression	0 < Expr ≤ 1	1 < Expr ≤ 5	5 < Expr ≤ 10	Expr > 10
TSS #1	TSS_25348	1699 libraries	88 libraries	25 libraries	12 libraries	5 libraries
TSS #2	TSS_25349	1775 libraries	47 libraries	6 libraries	0 libraries	1 library

The graphical summary, for retro_hsap_82 TSS expression levels > 0 TPM .
TSS expression levels were studied across 1829 TSS-CAGE libraries, based on FANTOM5 data.
The expression values were visualized using beanplot. If you have any doubts, how to read it, read more in Kampstra P (2008)

Lab

retro_hsap_82 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_82 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_105
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,