RetrogeneDB ID: retro_pabe_3535

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: Un:8313030..8313537(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NOC2L
• Ensembl ID: ENSPPYG00000029645
• Aliases: None
• Description: nucleolar complex associated 2 homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:24517]

Sequence

>retro_pabe_3535
CTGGCGCTGCCTGTGGTCCTGAAGCTGAAGTCGTTCCTCCGGGAGTGCAAGGTGGTCAACTAGTGCCGGCAGGTGCAGCA
GCTGCTTGGGAAGGTTCAGGAGAACTCGGAACACATCTGCAGCCGCTGCCAGAGAGTTTCCTTCGGCGTCTCTGACCAGC
AGGCAGTGGAAGCCTGGGAGAAGCTGACCCGGGAAGAGGGGACCCCCCTGACCTTGTACTACAGCCACTGGCGCAAGCTG
CATGACCGGGAGATCCAGCTGGAGATCAGTGGCAAAGAGCGGCTGGAAGACCTGAACTTCCGTGAGGTCAAACGAAGGAA
GGTGGCTGACAGGAAGGATGAGGACAGGAAGCAATTTAAAGACCTTTTTGACCTGAACAGCTCTGAAGAGGATGACACGG
AGGGATTCTTGGAGAGAGGGATACTGGGGCCCATGAGCACTCGGCATGGGGTGGAAGAGGATGAAGAGGACGAGGAGGAG
GGCGAGGAGGACAGCAGCAAGTCGGAG

Alignment

ORF - retro_pabe_3535 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.35 %
• Parental protein coverage: 82.44 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VADPSLPQLKSFLRECKVANYCRQVQQLLGKVQENSAHICSRRQRVSFGVSDQQAVEAWEKLTREEGTPL
          .A.P....LKSFLRECKV.N.CRQVQQLLGKVQENS.HICSR.QRVSFGVSDQQAVEAWEKLTREEGTPL
Retrocopy LALPVVLKLKSFLRECKVVN*CRQVQQLLGKVQENSEHICSRCQRVSFGVSDQQAVEAWEKLTREEGTPL

Parental  TLYYSHWRKLRDREIQLEISGKERLEDLNFPEIKRRKVADRKDEDRKQFKDLFDLNSSEEDDTEGFSERG
          TLYYSHWRKL.DREIQLEISGKERLEDLNF.E.KRRKVADRKDEDRKQFKDLFDLNSSEEDDTEGF.ERG
Retrocopy TLYYSHWRKLHDREIQLEISGKERLEDLNFREVKRRKVADRKDEDRKQFKDLFDLNSSEEDDTEGFLERG

Parental  ILRPLSTWHGVEEDEEDEEEGEEDSSNSE
          IL.P.ST.HGVEEDEEDEEEGEEDSS.SE
Retrocopy ILGPMSTRHGVEEDEEDEEEGEEDSSKSE

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	15.81 RPM
SRP007412_cerebellum	0.00 RPM	12.16 RPM
SRP007412_heart	0.00 RPM	4.40 RPM
SRP007412_kidney	0.00 RPM	8.82 RPM
SRP007412_liver	0.00 RPM	4.07 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3535 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3535 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3535 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000188976	1 retrocopy	retro_hsap_2320,
Pongo abelii	ENSPPYG00000029645	2 retrocopies	retro_pabe_2173, retro_pabe_3535 ,