RetrogeneDB ID: retro_pabe_476

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 1:189979843..189980225(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: OAZ1
• Ensembl ID: ENSPPYG00000009345
• Aliases: None
• Description: ornithine decarboxylase antizyme 1 [Source:HGNC Symbol;Acc:8095]

Sequence

>retro_pabe_476
ATTCCGGGTGGGCGAGGGAATCGTCAGAGGGATCACAATCTTTCAGCTAACTTACTCTACTCCTACGATCGGCTGAATGT
GACAGAGATTCTAACGTCCAACGGCAAGACGAGGATTCTCAACGTCCATTCCAGGCTCACAGATGCCAAACGCATTAACT
GGCGAGCCGTGCTGAGCGGCGGCAGCCTCTGCATCGGAGATCCCTGGTGGTGCGCTGCCCCAGGGGAGCGAGTATAGCTT
TGCAGTTCTCCAGCAGCTCGCCGAGGAGCAGCTGAGCGCCGACCACGTCTTCATTTGCTTCCACAAGAACCACGAGGACA
GAGCCGCCTTGCTCTGGACCTTCAGCTTTTGGGGCTTTGAGATTGTGAGACCGGGGCATCCC

Alignment

ORF - retro_pabe_476 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.16 %
• Parental protein coverage: 55.95 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  IPGGRGNSQRDHNLSANLFYSDDRLNVTEELTSNDKTRILNVQSRLTDAKRINWRTVLSGGSLYI-EIPG
          IPGGRGN.QRDHNLSANL.YS.DRLNVTE.LTSN.KTRILNV.SRLTDAKRINWR.VLSGGSL.I.EIPG
Retrocopy IPGGRGNRQRDHNLSANLLYSYDRLNVTEILTSNGKTRILNVHSRLTDAKRINWRAVLSGGSLCI>EIPG

Parental  GALPEGSKDSFAVLLEFAEEQLRADHVFICFHKNREDRAALLRTFSFLGFEIVRPGHP
          GALP.GS..SFAVL...AEEQL.ADHVFICFHKN.EDRAALL.TFSF.GFEIVRPGHP
Retrocopy GALPQGSEYSFAVLQQLAEEQLSADHVFICFHKNHEDRAALLWTFSFWGFEIVRPGHP

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	200.32 RPM
SRP007412_cerebellum	0.00 RPM	99.59 RPM
SRP007412_heart	0.00 RPM	67.07 RPM
SRP007412_kidney	0.00 RPM	130.07 RPM
SRP007412_liver	0.03 RPM	103.56 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_476 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_476 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_476 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Dipodomys ordii	ENSDORG00000016529	2 retrocopies	retro_dord_558, retro_dord_654,
Echinops telfairi	ENSETEG00000017945	2 retrocopies	retro_etel_2073, retro_etel_452,
Myotis lucifugus	ENSMLUG00000004446	2 retrocopies	retro_mluc_1524, retro_mluc_2157,
Mus musculus	ENSMUSG00000035242	1 retrocopy	retro_mmus_1622,
Nomascus leucogenys	ENSNLEG00000002179	1 retrocopy	retro_nleu_2435,
Pongo abelii	ENSPPYG00000009345	1 retrocopy	retro_pabe_476 ,