RetrogeneDB ID: retro_ptro_2521

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 7:38436398..38436705(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: VMA21
• Ensembl ID: ENSPTRG00000022372
• Aliases: None
• Description: None

Sequence

>retro_ptro_2521
GTGGAGCGCCCAGATAAAGTGGCGCTGAACGCACTGCAGCCTCCTAAGTTCGGAAAAGAAAGCTCATTAGCATCTACACT
GAAGACGCTCCTGTTCTTCACAGCTTTAATGATCACTGTTCCTATCGGGTTATTTATATTTCACAACTAAATCTTATATA
TCTGGAGGCGCCCTTGGGATGTCCAATAAGGACAGCTGTTTTTATGCTGCTATTGTTGCCGTGGTCACCGGCCATGTGGT
GCTGGCCCTCTTTATGTATGTGGTCTGGAATGAAGGCTCATGACAGTGACATGAAGGCAAACAGGAT

Alignment

ORF - retro_ptro_2521 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.73 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MERPDKAALNALQPPEFRNESSLASTLKTLLFFTALMITVPIGLY-FTTKSYIFEG-ALGMSNRDSYFYA
          .ERPDK.ALNALQPP.F..ESSLASTLKTLLFFTALMITVPIGL....T......G.ALGMSN.DS.FYA
Retrocopy VERPDKVALNALQPPKFGKESSLASTLKTLLFFTALMITVPIGLF>YFTTKSYISGGALGMSNKDSCFYA

Parental  AIVAVVAVHVVLALFVYVAWNEGSRQWREGKQD
          AIVAVV..HVVLALF.YV.WNEGS.Q..EGKQD
Retrocopy AIVAVVTGHVVLALFMYVVWNEGS*Q*HEGKQD

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	3.16 RPM
SRP007412_cerebellum	0.00 RPM	4.37 RPM
SRP007412_heart	0.00 RPM	1.87 RPM
SRP007412_kidney	0.00 RPM	3.43 RPM
SRP007412_liver	0.00 RPM	1.37 RPM
SRP007412_testis	0.00 RPM	1.48 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2521 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2521 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2521 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000003916	1 retrocopy	retro_cjac_150,
Dasypus novemcinctus	ENSDNOG00000008426	1 retrocopy	retro_dnov_504,
Mus musculus	ENSMUSG00000073131	2 retrocopies	retro_mmus_116, retro_mmus_3675,
Pan troglodytes	ENSPTRG00000022372	1 retrocopy	retro_ptro_2521 ,
Rattus norvegicus	ENSRNOG00000049744	1 retrocopy	retro_rnor_2843,