RetrogeneDB ID: retro_pabe_2422

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 4:3372700..3373027(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: XAGE3
• Ensembl ID: ENSPPYG00000020369
• Aliases: None
• Description: X antigen family, member 3 [Source:HGNC Symbol;Acc:14618]

Sequence

>retro_pabe_2422
ATGAGTTGGCAAGGAAGATCAGCATGTAGGCTTAGACCAAGACGGTATCTGCAGCCCCTGAGCTAACTGGGTCTGTGCTT
GAGCCCAGTGATGAGAAGCCTCAACTAGAGGAACCACCACCTGAAAGTCGGGGTCCTACACCTGGCCAGGAGAGAGAGGA
TGATCACGGTGCCGCTGAGATTCTTGTGCTTGACCAGGAAGCTGATCTCTGGGAGCTGTCTCAAAAGACTGGGATGAATG
TGGAGATGGTCCTGATGTCCGGGGAAGATTCTGCCGAAATCAGAGCAATTTAAATTGCCAGAAGGAGGTGAAGGGCAACC
ACAGGTT

Alignment

ORF - retro_pabe_2422 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.05 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MIWRGRSTYRPRPRRSVPP-PELIGPMLEPSDEEPQQEEPPTESQDPAPGQEREEDQGAAEIQVPDLEAD
          M.W.GRS..R.RPRR...P.PEL.G..LEPSDE.PQ.EEPP.ES..P.PGQERE.D.GAAEI.V.D.EAD
Retrocopy MSWQGRSACRLRPRRYLQP<PELTGSVLEPSDEKPQLEEPPPESRGPTPGQEREDDHGAAEILVLDQEAD

Parental  LQELSQSKTG-DECGNGPDDQ-GKILPKSEQFKMPEGGDRQPQV
          L.ELSQ.KTG.DECG.GPD...GKILPKSEQFK.PEGG..QPQV
Retrocopy LWELSQ-KTG<DECGDGPDVR<GKILPKSEQFKLPEGGEGQPQV

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	0.00 RPM
SRP007412_cerebellum	0.24 RPM	0.00 RPM
SRP007412_heart	0.03 RPM	0.09 RPM
SRP007412_kidney	0.00 RPM	0.00 RPM
SRP007412_liver	0.00 RPM	0.03 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2422 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2422 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2422 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Callithrix jacchus	retro_cjac_2302

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Gorilla gorilla	ENSGGOG00000027404	1 retrocopy	retro_ggor_2013,
Pongo abelii	ENSPPYG00000020345	1 retrocopy	retro_pabe_2503,
Pongo abelii	ENSPPYG00000020369	1 retrocopy	retro_pabe_2422 ,
Pan troglodytes	ENSPTRG00000021922	1 retrocopy	retro_ptro_1965,