RetrogeneDB ID: retro_pabe_1637

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 19:35528139..35528646(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ZNF396
• Ensembl ID: ENSPPYG00000009107
• Aliases: None
• Description: zinc finger protein 396 [Source:HGNC Symbol;Acc:18824]

Sequence

>retro_pabe_1637
GAGCTCCACCTTCTCTGACTGAGGCCGGAGGTGCACACAAAGGAGCAGATCCTGGAGCTGCTGGTGCTGGAACAGTTCCT
AGCCATCCTCCCAGAAAAGCTGCAGCCCTGGGTGCAGAGGCATCATCCAGAAAATGGAGAGGAAGCTGTGACTGTGCTAG
AGGATGTGCAGAGAGAGCTTGATGGACCAGAGCAGGTCTTCTTTTTTGGACGAAGAAGGGACATGGTTGCAGAGAAGCTA
GCACCTTCAGAAATCACTGAGCAATTGCCAACTAGCCAGCGCACGCCCGTGAAGAAGCAGCTCCAGCGAGCATCATGGGA
GCTGCAGTCCTTAAGACCACATGATGAAAACATCAAAACTATAAATGTGAAATCCGCTTCAAGGCAAAAGACTTCTTCAG
GCATAGAACTGCATTGCGATGTTTCCAACATCCTTGGTATAAATGCCTCCCAGAGTTCCACATATAGAGGAATCTATGAA
CAAGATGATTCAAAATATGAACATAGG

Alignment

ORF - retro_pabe_1637 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.7 %
• Parental protein coverage: 50.3 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ELCHLWLRPEVHTKEQILELLVLEQFLAILPNELQASVQKHHLENGEETVTMLEDVEREFDGPEQIFF-G
          EL..L.LRPEVHTKEQILELLVLEQFLAILP..LQ..VQ.HH.ENGEE.VT.LEDV.RE.DGPEQ.FF.G
Retrocopy ELHLL*LRPEVHTKEQILELLVLEQFLAILPEKLQPWVQRHHPENGEEAVTVLEDVQRELDGPEQVFFFG

Parental  RRKDMIAEKLAPSEITEELPSSQLMPVKKQPQGASWELQSLRPHDEDIKTTNVKSASRQKTSLGIELHCH
          RR.DM.AEKLAPSEITE.LP.SQ..PVKKQ.Q.ASWELQSLRPHDE.IKT.NVKSASRQKTS.GIELHC.
Retrocopy RRRDMVAEKLAPSEITEQLPTSQRTPVKKQLQRASWELQSLRPHDENIKTINVKSASRQKTSSGIELHCD

Parental  VSNIFHMNASQSSTYRGTYEQ-DGRFERR
          VSNI...NASQSSTYRG.YEQ.D...E.R
Retrocopy VSNILGINASQSSTYRGIYEQDDSKYEHR

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	0.22 RPM
SRP007412_cerebellum	0.00 RPM	0.61 RPM
SRP007412_heart	0.00 RPM	0.15 RPM
SRP007412_kidney	0.00 RPM	1.89 RPM
SRP007412_liver	0.00 RPM	0.73 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1637 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1637 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1637 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000186496	1 retrocopy	retro_hsap_1996,
Gorilla gorilla	ENSGGOG00000023692	1 retrocopy	retro_ggor_1443,
Pongo abelii	ENSPPYG00000009107	1 retrocopy	retro_pabe_1637 ,
Pan troglodytes	ENSPTRG00000009970	1 retrocopy	retro_ptro_1332,