RetrogeneDB ID: retro_pabe_936

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 12:67449864..67450098(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSPPYG00000019565
• Aliases: None
• Description: None

Sequence

>retro_pabe_936
TCTGGGGTGAAAGAAGCAGATGATAAGGAGAAAATAATGAATGTCAAAGGAAACGTAATTCCTCCAATGCTGGTTGTCTC
AGCTGCGATTGTTGTGGTTTGGAAATGTATCAACACCCAAGAAGGCTCTCTCTTGTGGATGTATCACTTAAAACACCCGG
AAGTTGTTGAGGGCGGCGGGCAGAAGGGCCGGTGGTTTCCAAGCTGCTTCAACAGTGGGACCCACAATCCTCAA

Alignment

ORF - retro_pabe_936 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.69 %
• Parental protein coverage: 53.79 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  AGCRLRDFTEKIMNVKGKVILSMLVVSTVIVVFWEYINSPEASFLWIYHSKNPEVDDSSAQKGWWFLSWF
          .G....D..EKIMNVKG.VI..MLVVS..IVV.W..IN..E.S.LW.YH.K.PEV.....QKG.WF.S.F
Retrocopy SGVKEADDKEKIMNVKGNVIPPMLVVSAAIVVVWKCINTQEGSLLWMYHLKHPEVVEGGGQKGRWFPSCF

Parental  NNGIHNYQ
          N.G.HN.Q
Retrocopy NSGTHNPQ

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	0.28 RPM
SRP007412_cerebellum	0.00 RPM	0.00 RPM
SRP007412_heart	0.00 RPM	0.60 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_936 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_936 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_936 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Gorilla gorilla	retro_ggor_883

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000012094	2 retrocopies	retro_chof_1206, retro_chof_642,
Gorilla gorilla	ENSGGOG00000009067	1 retrocopy	retro_ggor_883,
Pongo abelii	ENSPPYG00000019565	1 retrocopy	retro_pabe_936 ,