RetrogeneDB ID: retro_pabe_167

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 20:320771..321383(-)
• Located in intron of: ENSPPYG00000010688

Retrocopy information

• Ensembl ID: ENSPPYG00000010689
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSPPYG00000011872
• Aliases: None
• Description: None

Sequence

>retro_pabe_167
ATGTTCGTCCTGGTGGAGATGGTGGACACCGTGCGGATCCCCCCTTGGCAGTTTCAGAGGAAGCTCAACGACTCCATTGC
CGAGGAGCTGAACAAGAAGTTGGCCAACAAGGTCGTGTACAACGTGGGACTCTGCATTTGTTTGTTTGATATCACCAAAC
TGGAGGATGCCTACGTATTCCCTGGGGATGGCACATCACACACCAAAGTCCATTTTCCCTACGTGGTGTTTCATCCATTC
CTAGACGAGATTCTGATTGGGAAGATCAAAGGCTGCAGCCCGGAAGGAGTGCATGTCTCTCTAGGCTTCTTCCATGACAT
TCTCATCCCCCCAGAGTCACTGCAGCAGCCAGCCAAGTTCGACGAAGCGGAGCAGGTGTGGGTGTGGGAGTACGAGACGG
AGGAAGGAGCGCACGACCTCTACATGGACACCGGAGAGGAGATCCGCTTCCGCGTGGTGGACGAGAGCTTTGTTGACACG
TCCCCCACAGGGCCCAGCTCAGCAGATGCCACTGCTTCCAGTGAGGAGCTGCCAAAGAAGGAGGCTCCGTACACGCTTGT
GGGATCCATCAGTGAGCCAGGCCTGGGCCTTCTCTCCTGGTGGACCAGCAAC

Alignment

ORF - retro_pabe_167 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.08 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MFVLVEMVDTVRIPPWQFERKLNDSIAEELNKKLANKVVYNVGLCICLFDITKLEDAYVFPGDGASHTKV
          MFVLVEMVDTVRIPPWQF.RKLNDSIAEELNKKLANKVVYNVGLCICLFDITKLEDAYVFPGDG.SHTKV
Retrocopy MFVLVEMVDTVRIPPWQFQRKLNDSIAEELNKKLANKVVYNVGLCICLFDITKLEDAYVFPGDGTSHTKV

Parental  HFRYVVFHPFLDEILIGKIKGCSPE---VSLGFFDDILIPPESLQQPAKFDEAEQVWVWEYETEEGAHDL
          HF.YVVFHPFLDEILIGKIKGCSPE...VSLGFF.DILIPPESLQQPAKFDEAEQVWVWEYETEEGAHDL
Retrocopy HFPYVVFHPFLDEILIGKIKGCSPEGVHVSLGFFHDILIPPESLQQPAKFDEAEQVWVWEYETEEGAHDL

Parental  YMDTGEEIRFRVVDESFVDTSPTGPSSADATTSSEELPKKEAPYTLVGSISEPGLGLLSWWTSN
          YMDTGEEIRFRVVDESFVDTSPTGPSSADAT.SSEELPKKEAPYTLVGSISEPGLGLLSWWTSN
Retrocopy YMDTGEEIRFRVVDESFVDTSPTGPSSADATASSEELPKKEAPYTLVGSISEPGLGLLSWWTSN

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	2.76 RPM	7.74 RPM
SRP007412_cerebellum	2.80 RPM	9.12 RPM
SRP007412_heart	0.42 RPM	0.81 RPM
SRP007412_kidney	1.86 RPM	3.85 RPM
SRP007412_liver	0.70 RPM	2.33 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_167 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_167 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_167 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
Erinaceus europaeus	ENSEEUG00000010464	1 retrocopy	retro_eeur_538,
Otolemur garnettii	ENSOGAG00000002850	1 retrocopy	retro_ogar_243,
Pongo abelii	ENSPPYG00000011872	1 retrocopy	retro_pabe_167 ,