RetrogeneDB ID: retro_ptro_1965

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 4:3389068..3389293(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: XAGE3
• Ensembl ID: ENSPTRG00000021922
• Aliases: None
• Description: X antigen family, member 3 [Source:HGNC Symbol;Acc:14618]

Sequence

>retro_ptro_1965
ATGAGTTGGCAAGGAAGATCAGCATGTAGGCTTAGACCAAGACGGTATCTGCAGCCTCCTGAGCTAACTGGGCCTGTGCT
TGAGCCCAGTGATGAGCAGCCTCAGCAAGAGGCACCACCACCTGAAAGTCGGGGTCCTACACCTGGCCAGGAGAGAGAGG
AAGATCACGGTGCTGCTGAGATTCTTGTGCTTGACCAGGAAGCTGATCTCCGGGAGCTGTCTCAA

Alignment

ORF - retro_ptro_1965 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72. %
• Parental protein coverage: 67.57 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MIWRGRSTYRPRPRRSVPPPELIGPMLEPGDEEPQQEEPPTESRDPAPGQEREEDQGAAEIQVPDLEADL
          M.W.GRS..R.RPRR...PPEL.GP.LEP.DE.PQQE.PP.ESR.P.PGQEREED.GAAEI.V.D.EADL
Retrocopy MSWQGRSACRLRPRRYLQPPELTGPVLEPSDEQPQQEAPPPESRGPTPGQEREEDHGAAEILVLDQEADL

Parental  QELSQ
          .ELSQ
Retrocopy RELSQ

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	0.11 RPM	0.00 RPM
SRP007412_heart	0.00 RPM	0.00 RPM
SRP007412_kidney	0.00 RPM	0.03 RPM
SRP007412_liver	0.03 RPM	0.00 RPM
SRP007412_testis	0.00 RPM	0.53 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1965 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1965 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1965 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Gorilla gorilla	retro_ggor_2013

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Parental genes homology:

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

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