RetrogeneDB ID: retro_pabe_3246

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 8:26189569..26189844(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSPPYG00000014851
• Aliases: None
• Description: None

Sequence

>retro_pabe_3246
ATGGAAAACTTTCTGGGAAGTTACTTCATTCTTTTTCTCTTTTTCAAAAGGCATCTCGCAGCGCCAACTGTTTTTCTCGG
AAGGAACGCTTATTTTTTGACCAGACATTCTGGCTATACCACATCATCATAAAGTTCTTCTGTTTTTTCCACTCTTTATT
TTTTGAACTGGAAAATGGATTCACTTTGGTTTCCTTCCTCGCAAATTCTTTTCGATCTGTCTTTCCAGCCATTGCAGTTG
CTAATCTTGTCTCTTTGTCAGACTTTGTCTTTTTA

Alignment

ORF - retro_pabe_3246 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.11 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MENLPGSYFILFLFFK-SASRSANSCFSRKERLFFDRTFWLYRIIIKFFCFFFSLFVELENGFVLVFFLI
          MEN..GSYFILFLFFK..ASRSAN.CFSRKERLFFD.TFWLY.IIIKFFCFF.SLF.ELENGF.LV.FL.
Retrocopy MENFLGSYFILFLFFK<KASRSAN-CFSRKERLFFDQTFWLYHIIIKFFCFFHSLFFELENGFTLVSFLA

Parental  NSFRSVFPAIAVASLVSLSDFGFL
          NSFRSVFPAIAVA.LVSLSDF.FL
Retrocopy NSFRSVFPAIAVANLVSLSDFVFL

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	0.39 RPM	0.00 RPM
SRP007412_cerebellum	0.00 RPM	0.00 RPM
SRP007412_heart	0.15 RPM	0.00 RPM
SRP007412_kidney	0.13 RPM	0.00 RPM
SRP007412_liver	0.06 RPM	0.00 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3246 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3246 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3246 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000268788	2 retrocopies	retro_hsap_2447, retro_hsap_3938,
Gorilla gorilla	ENSGGOG00000027929	1 retrocopy	retro_ggor_1523,
Microcebus murinus	ENSMICG00000006676	1 retrocopy	retro_mmur_1203,
Pongo abelii	ENSPPYG00000014851	2 retrocopies	retro_pabe_1798, retro_pabe_3246 ,