RetrogeneDB ID: retro_pabe_3016

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 6:152404278..152404584(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FABP12
• Ensembl ID: ENSPPYG00000018703
• Aliases: None
• Description: fatty acid binding protein 12 [Source:HGNC Symbol;Acc:34524]

Sequence

>retro_pabe_3016
GGAATAGGGAGAGCCAGCAGGAAACTGGGCTGCCTGGCAAAACCCATGGTGACCATCAGTAGAAATGGAGATGTGATCAC
TATAAAAATGAAAAGCATCTTTAAAAATAATGAGATTGCTTTTAAACCTAGAAAAGTGTGAGGAAACCACACCAGGTGGC
CATAAAATCAAGAGTACTGTAACCTTAGATAATGACTCCCTGATTCAGGTTCAGGACTGGGATCACAAGGAGATCTCATT
GGGAGAAAGTTGGTGGGTGAGAAGATGGGGGTGGAAAGTGCCGTGAGCAATATTACCTGTGCTCAG

Alignment

ORF - retro_pabe_3016 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.81 %
• Parental protein coverage: 78.03 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  GIGRASRKLGRLAKPTVTISTDGDVITI-KTKSIFKNNEISFKLGEEFEEITPGGHKTKSKVTLDKESLI
          GIGRASRKLG.LAKP.VTIS..GDVITI.K.K...K.......L.E..EE.TPGGHK.KS.VTLD..SLI
Retrocopy GIGRASRKLGCLAKPMVTISRNGDVITI>K*KASLKIMRLLLNL-EKCEETTPGGHKIKSTVTLDNDSLI

Parental  QVQDWDGKETT-ITRKLVDGKMVVESAVNSVICTR
          QVQDWD.KE...I.RKLV..KM.VESAV....C..
Retrocopy QVQDWDHKEIS<IGRKLVGEKMGVESAVSNITCAQ

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	0.00 RPM
SRP007412_cerebellum	0.00 RPM	0.00 RPM
SRP007412_heart	0.00 RPM	0.00 RPM
SRP007412_kidney	0.00 RPM	0.00 RPM
SRP007412_liver	0.00 RPM	0.00 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3016 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3016 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3016 has 6 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3679
Pan troglodytes	retro_ptro_2493
Gorilla gorilla	retro_ggor_2488
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 17 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	ENSPPYG00000001616	1 retrocopy	retro_pabe_1048,
Pongo abelii	ENSPPYG00000016979	1 retrocopy	retro_pabe_213,
Pongo abelii	ENSPPYG00000018699	1 retrocopy	retro_pabe_27,
Pongo abelii	ENSPPYG00000018703	1 retrocopy	retro_pabe_3016 ,
Pan troglodytes	ENSPTRG00000022654	1 retrocopy	retro_ptro_2493,