RetrogeneDB ID: retro_pabe_213

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 1:5596981..5597201(+)
• Located in intron of: ENSPPYG00000000060

Retrocopy information

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

Parental gene information

• Parental gene symbol: FABP7
• Ensembl ID: ENSPPYG00000016979
• Aliases: None
• Description: fatty acid binding protein 7, brain [Source:HGNC Symbol;Acc:3562]

Sequence

>retro_pabe_213
AACACAGTGGTTAGTTTCCATCTGGGAGAAGAGTTTGATGAAACCGCTACAGATGATAGAAACTGCAAGTTTGTTGTTAG
TCTGGATAGAGACAAACTCATTCACATACAGAAATGGGATGACAAAGAAACATATTTTATAAGAGAAATTAAGTATGGTG
AAATGGTTATGACTTACTTTTGGTGATGATGTGGTTGCCGTTCACCACTATAAGAAGGCA

Alignment

ORF - retro_pabe_213 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.32 %
• Parental protein coverage: 55.3 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  NTEISFHLGEEFDETTADDRNCKSVVSLDGDKLVHIQKWDGKETNFVREIKDGKMVMTLTF-GDVVAVRH
          NT..SFHLGEEFDET..DDRNCK.VVSLD.DKL.HIQKWD.KET.F.REIK.G.MVMT.....DVVAV.H
Retrocopy NTVVSFHLGEEFDETATDDRNCKFVVSLDRDKLIHIQKWDDKETYFIREIKYGEMVMTYFW>DDVVAVHH

Parental  YEKA
          Y.KA
Retrocopy YKKA

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	0.11 RPM	10.51 RPM
SRP007412_cerebellum	0.36 RPM	46.82 RPM
SRP007412_heart	0.00 RPM	0.12 RPM
SRP007412_kidney	0.00 RPM	0.27 RPM
SRP007412_liver	0.00 RPM	0.06 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_213 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_213 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_213 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_536
Pan troglodytes	retro_ptro_402
Gorilla gorilla	retro_ggor_489
Macaca mulatta	retro_mmul_458

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000014056	1 retrocopy	retro_cpor_34,
Homo sapiens	ENSG00000164434	1 retrocopy	retro_hsap_536,
Gorilla gorilla	ENSGGOG00000025475	1 retrocopy	retro_ggor_489,
Macaca mulatta	ENSMMUG00000021907	1 retrocopy	retro_mmul_458,
Oryctolagus cuniculus	ENSOCUG00000001497	1 retrocopy	retro_ocun_1874,
Otolemur garnettii	ENSOGAG00000031110	1 retrocopy	retro_ogar_2821,
Ochotona princeps	ENSOPRG00000000992	1 retrocopy	retro_opri_840,
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	ENSPTRG00000018564	1 retrocopy	retro_ptro_402,
Sarcophilus harrisii	ENSSHAG00000003313	1 retrocopy	retro_shar_521,