RetrogeneDB ID: retro_pabe_426

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 1:107333249..107334216(-)
• Located in intron of: ENSPPYG00000000952

Retrocopy information

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

Parental gene information

• Parental gene symbol: NUDT18
• Ensembl ID: ENSPPYG00000018412
• Aliases: None
• Description: nudix (nucleoside diphosphate linked moiety X)-type motif 18 [Source:HGNC Symbol;Acc:26194]

Sequence

>retro_pabe_426
ATGGCCTCGGAGGGCCTGGCGGGGGCTCTGGCTTCCGTGCTGGCTGGCCAGGGGTCGAGCGTGCAGAGCTGCGACTTGGC
GCCTGCAGGGGAGCCGCGGGTGCCCGTGCGGCTGCGGAAGAACCTGTGCTACATGGTGCTGGCCGTGTTCCTCAGCGAGC
AGGATGAGGTGCTACTGATCCAGGAGGCCAAGAGGGAGTGCCGGGGATCGTGGTACCTGCCTGCGGGGAGAATGGAGCCG
GGGGAGACCATCGTGGAGACGCTGCAGCTGGAGGTGAAGGAGGAGGCGGGACTGCACTGTGAGCCCAAGACACTGCTGTC
CGTGGAGGAGCGGGGCCCCTCCTGGGTCCGCTTCATGTTCTTCGCTTGCCCCACAGGTGGAATTCTCAAGACTTCCAAGG
AGGCCGATGTGGAGTCCCTGCAGGCTGCCTGGTACCCACGGACCTCCCTGCCCACTCCGCTGCGAGCCCATGACATCCTG
CACCTGGTTGAGCTAGCCACCCAGTATCGCCAGCAAGCCAAGCACCGTCATTCTGCCCCAAGAGCTACCCTGTGATCTGG
TCTGCCAGCGGCTCGTGGCCACCTTTACCAGTGCCCAGACAGTGTGGGTGTTGGTGGGCACAGTGGGAATGCCTCACTTG
CCTGTCACTGCCTGTGGCCTCGACCCTATGGAGCAGAGGGGTGGCATGAAGATGGCTGTCCTGTGGCTGCTGCAGGAGTG
TCTGACCCTGCACCACTTGGTGGTGGAGATCAAGGGGTTGCTTGGACTGCAGCACCTGGGCCGAGATCACAGTGATGGCA
TCTGTCTGAATGTGCTGGTGACTGTGGCTTTTCGGAGCCCAGGGATCCAGGATGAACCCCCGAGAGTTTGGGGTGAGAAC
TTCTTTTGGTGGAAGGTGATGGAGGAAGACCTGCAAAGTCAGCTCCTCCAGTGGCTTCAGGGATCCTCTGTTGTCCCAGT
GAACAGA

Alignment

ORF - retro_pabe_426 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.92 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MASEGLAGALASVLAGQGSSVQSCDSAPAGEPPAPVRLRKNVCYVVLAVFLSEQDEVLLIQEAKRECRGS
          MASEGLAGALASVLAGQGSSVQSCD.APAGEP..PVRLRKN.CY.VLAVFLSEQDEVLLIQEAKRECRGS
Retrocopy MASEGLAGALASVLAGQGSSVQSCDLAPAGEPRVPVRLRKNLCYMVLAVFLSEQDEVLLIQEAKRECRGS

Parental  WYLPAGRMEPGETIVEALQREVKEEAGLHCEPETLLSVEERGPSWVRFVFLARPTGGILKTSKEADVESL
          WYLPAGRMEPGETIVE.LQ.EVKEEAGLHCEP.TLLSVEERGPSWVRF.F.A.PTGGILKTSKEADVESL
Retrocopy WYLPAGRMEPGETIVETLQLEVKEEAGLHCEPKTLLSVEERGPSWVRFMFFACPTGGILKTSKEADVESL

Parental  QAAWYPRTSLPTPLRAHDILHLVELAAQYRQQARH-PLILP-QELPCDLVCQRLVATFTSAQTVWVLVGT
          QAAWYPRTSLPTPLRAHDILHLVELA.QYRQQA.H.P...P.QELPCDLVCQRLVATFTSAQTVWVLVGT
Retrocopy QAAWYPRTSLPTPLRAHDILHLVELATQYRQQAKH<PSFCP<QELPCDLVCQRLVATFTSAQTVWVLVGT

Parental  VGMPHLPVTACGLDPMEQRGGMKMAVLRLLQECLTLHHLVVEIKGLLGLQHLGRDHSDGICLNVLVTVAF
          VGMPHLPVTACGLDPMEQRGGMKMAVL.LLQECLTLHHLVVEIKGLLGLQHLGRDHSDGICLNVLVTVAF
Retrocopy VGMPHLPVTACGLDPMEQRGGMKMAVLWLLQECLTLHHLVVEIKGLLGLQHLGRDHSDGICLNVLVTVAF

Parental  RSPGIQDEPPKVRGENFSWWKVMEEDLQSQLLQRLQGSSVVPVNR
          RSPGIQDEPP.V.GENF.WWKVMEEDLQSQLLQ.LQGSSVVPVNR
Retrocopy RSPGIQDEPPRVWGENFFWWKVMEEDLQSQLLQWLQGSSVVPVNR

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	0.17 RPM	5.20 RPM
SRP007412_cerebellum	0.24 RPM	3.40 RPM
SRP007412_heart	0.00 RPM	0.93 RPM
SRP007412_kidney	0.10 RPM	7.23 RPM
SRP007412_liver	0.06 RPM	3.86 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_426 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_426 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_426 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Pongo abelii	ENSPPYG00000018412	1 retrocopy	retro_pabe_426 ,