RetrogeneDB ID: retro_pabe_1495

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 17:30175313..30175694(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RAB38
• Ensembl ID: ENSPPYG00000003752
• Aliases: None
• Description: RAB38, member RAS oncogene family [Source:HGNC Symbol;Acc:9776]

Sequence

>retro_pabe_1495
GTGAACTGTGCACTGAAGGAGCTCCACTGGGACTCAGAGGCCTTGGCACACCTGCAGCTGTGGAATATTGCGATGAGGAA
AGATTGGGAAAATGACAAGAGCCCACTGTCTGGAATTTATAGGTGCATTGATTGTCTTCAGTATCACCAGCCCAGCCCCA
TTTGAAGCAGAGCCAAAGTGGAAAAATGATTTGGACTAAACGTTAACTCATGGCAGACCAGTTTCTGTGGTTCTGTTGGC
CAAGAAACATGACCATGGGAGGATGAACGCAGGAACAATAGCCTCAAGATGGGCCAGATCTACATGGAACATAGTTTTGT
AGGATGAGTTGAAGCATCAGCAAAGGAAAATGTAAACTTTGATGAAGCCTCCAGGTGCCTG

Alignment

ORF - retro_pabe_1495 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.89 %
• Parental protein coverage: 61.61 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  VDFALKVLHWDPETVVRLQLW-DIAGQERFGN-MTRVYYREAMGAFIVFDVTRPATFEAVAKWKNDLDSK
          V..ALK.LHWD.E....LQLW......ER.G..MTR....E..GA.IVF..T.PA.FEA..KWKNDLD..
Retrocopy VNCALKELHWDSEALAHLQLW<EYCDEERLGK<MTRAHCLEFIGALIVFSITSPAPFEAEPKWKNDLD*T

Parental  LSLPNGKPVSVVLLANKCDQGK-DVLMNNGLKMDQFCKEHGFVGWFETSAKENINIDEASRCL
          L....G.PVSVVLLA.K.D.G..D...NN.LKM.Q...EH.FVG..E.SAKEN.N.DEASRCL
Retrocopy LT--HGRPVSVVLLAKKHDHGR<DERRNNSLKMGQIYMEHSFVG*VEASAKENVNFDEASRCL

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	0.28 RPM	0.17 RPM
SRP007412_cerebellum	0.00 RPM	0.00 RPM
SRP007412_heart	0.69 RPM	0.12 RPM
SRP007412_kidney	0.83 RPM	0.53 RPM
SRP007412_liver	0.46 RPM	0.15 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1495 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1495 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1495 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Macaca mulatta	ENSMMUG00000016006	1 retrocopy	retro_mmul_1254,
Pongo abelii	ENSPPYG00000003752	1 retrocopy	retro_pabe_1495 ,
Pongo abelii	ENSPPYG00000013431	1 retrocopy	retro_pabe_90,