RetrogeneDB ID: retro_ptro_402

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 1:223021870..223022123(-)
• Located in intron of: ENSPTRG00000002174

Retrocopy information

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

Parental gene information

• Parental gene symbol: FABP7
• Ensembl ID: ENSPTRG00000018564
• Aliases: None
• Description: fatty acid binding protein 7, brain [Source:HGNC Symbol;Acc:3562]

Sequence

>retro_ptro_402
AAGGTGGTGATGAGGATTCAAAGTATGTTCAAGAACACAGAGGTTAGTTTCCATCTGGGAGAAGAGTTTGATGAAACCAC
TACAGATGACAGAAACTGCAAGTTTGTTGTTAGTCTGGACAGAGACAAACTCATTCACATACAGAAATGGGATGACAAAG
AAACATATTTTATAAGAGAAATTAAGTATGGTGAAGTGGTTATGACTTACTTTTGGTGATGATGTGGTTGCCGTTTACCA
CTATAAGAAGTCA

Alignment

ORF - retro_ptro_402 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.76 %
• Parental protein coverage: 63.64 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KVVIRTLSTFKNTEISFQLGEEFDETTADDRNCKSVVSLDGDKLVHIQKWDGKETNFVREIKDGKMVMTL
          KVV.R..S.FKNTE.SF.LGEEFDETT.DDRNCK.VVSLD.DKL.HIQKWD.KET.F.REIK.G..VMT.
Retrocopy KVVMRIQSMFKNTEVSFHLGEEFDETTTDDRNCKFVVSLDRDKLIHIQKWDDKETYFIREIKYGEVVMTY

Parental  TF-GDVVAVRHYEKA
          ....DVVAV.HY.K.
Retrocopy FW>DDVVAVYHYKKS

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	0.32 RPM	19.36 RPM
SRP007412_cerebellum	0.14 RPM	31.69 RPM
SRP007412_heart	0.06 RPM	0.06 RPM
SRP007412_kidney	0.00 RPM	0.42 RPM
SRP007412_liver	0.00 RPM	0.88 RPM
SRP007412_testis	0.11 RPM	0.53 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_402 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_402 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_402 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_536
Gorilla gorilla	retro_ggor_489
Pongo abelii	retro_pabe_213
Macaca mulatta	retro_mmul_458

---

Parental genes homology:

Parental genes homology involve 13 parental genes, and 24 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	ENSPPYG00000016979	1 retrocopy	retro_pabe_213,
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,
Sarcophilus harrisii	ENSSHAG00000003313	1 retrocopy	retro_shar_521,