RetrogeneDB ID: retro_ptro_2493

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 6:150892500..150892845(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FABP12
• Ensembl ID: ENSPTRG00000022654
• Aliases: None
• Description: fatty acid binding protein 12 [Source:HGNC Symbol;Acc:34524]

Sequence

>retro_ptro_2493
GGAATAGGGAGAGCCAGCAGGAAACTGGGCTGCCTGGCAAAACCCATGGTGACCATCGGTAGAAATGGAGATGTGATCAC
TATAAAAATGAAAAGCATCTTTAAAAATAATGAGATTGCTTTTAAACCTAGAAAAGTGTGAGGAAACCACACCAGGTGGC
CATAAAATCAAGAGTACCATAACCTTAGATAATGACCCCCTGATTCAGGTTCAGGACTGGGATCACAAGGAGACCTCATT
GGGAGAAAGTTGGTGGGTGAGAAGATGGGGGTGGAAAGTGCCATGAGCAATATTACCTGTGCTCAGATATAGGGGAGAGA
ATGAACAAATTCAGTCTCAAACTCC

Alignment

ORF - retro_ptro_2493 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.47 %
• Parental protein coverage: 82.86 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  GIGRASRKLGRLAKPTVTISTDGDVITI-KTKSIFKNNEISFKLGEEFEEITPGGHKTKSKVTLDKESLI
          GIGRASRKLG.LAKP.VTI...GDVITI.K.K...K.......L.E..EE.TPGGHK.KS..TLD...LI
Retrocopy GIGRASRKLGCLAKPMVTIGRNGDVITI>K*KASLKIMRLLLNL-EKCEETTPGGHKIKSTITLDNDPLI

Parental  QVQDWDGKETT-ITRKLVDGKMVVESTVNSVICTRTYEKVSSNSVSNS
          QVQDWD.KET..I.RKLV..KM.VES......C.........NSVSNS
Retrocopy QVQDWDHKETS<IGRKLVGEKMGVESAMSNITCAQI*GRE*TNSVSNS

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	0.02 RPM
SRP007412_cerebellum	0.00 RPM	0.07 RPM
SRP007412_heart	0.00 RPM	0.00 RPM
SRP007412_kidney	0.00 RPM	0.03 RPM
SRP007412_liver	0.00 RPM	0.00 RPM
SRP007412_testis	0.00 RPM	9.48 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2493 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2493 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2493 has 6 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3679
Gorilla gorilla	retro_ggor_2488
Pongo abelii	retro_pabe_3016
Macaca mulatta	retro_mmul_1787
Callithrix jacchus	retro_cjac_2486
Equus caballus	retro_ecab_761

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 28 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000014554	1 retrocopy	retro_amel_945,
Callithrix jacchus	ENSCJAG00000000433	1 retrocopy	retro_cjac_2486,
Equus caballus	ENSECAG00000023552	1 retrocopy	retro_ecab_761,
Homo sapiens	ENSG00000197416	1 retrocopy	retro_hsap_3679,
Gorilla gorilla	ENSGGOG00000016835	1 retrocopy	retro_ggor_2488,
Latimeria chalumnae	ENSLACG00000008511	3 retrocopies	retro_lcha_37, retro_lcha_45, retro_lcha_57,
Microcebus murinus	ENSMICG00000005319	1 retrocopy	retro_mmur_1131,
Macaca mulatta	ENSMMUG00000019337	1 retrocopy	retro_mmul_1787,
Nomascus leucogenys	ENSNLEG00000002515	1 retrocopy	retro_nleu_528,
Oryzias latipes	ENSORLG00000008282	1 retrocopy	retro_olat_7,
Pongo abelii	ENSPPYG00000018703	1 retrocopy	retro_pabe_3016,
Pan troglodytes	ENSPTRG00000000457	1 retrocopy	retro_ptro_3047,
Pan troglodytes	ENSPTRG00000018564	1 retrocopy	retro_ptro_402,
Pan troglodytes	ENSPTRG00000020373	12 retrocopies	retro_ptro_1029, retro_ptro_1030, retro_ptro_1498, retro_ptro_1654, retro_ptro_2029, retro_ptro_2131, retro_ptro_2265, retro_ptro_2295, retro_ptro_2664, retro_ptro_3135, retro_ptro_823, retro_ptro_875,
Pan troglodytes	ENSPTRG00000022654	1 retrocopy	retro_ptro_2493 ,