RetrogeneDB ID: retro_ptro_77

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 4:93132490..93132700(-)
• Located in intron of: ENSPTRG00000016285

Retrocopy information

• Ensembl ID: ENSPTRG00000000612
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSPTRG00000028317
• Aliases: None
• Description: None

Sequence

>retro_ptro_77
AACTCGGTGGTGGCCACTGCGCAGACCAGACTTCGCTCGTACTCGCGCGCCTGGCTCCGCTTTTCCTCCGCAACCATGTC
TGACAAACCCGATATGGCTGAGATCGAGAAATTCGATAAGTCGAAACTGAAGAAGACAGAGACGCAAGAGAAAAATCCAC
TGCCTTCCAAAGAAACGATTGAACAGGAGAAGCAAGCAGGCGAATCGTAA

Alignment

ORF - retro_ptro_77 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.55 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  NSVVATAQTRLRSYSRASLRFSSATMSDKPDMAEIEKFDKSKLKKTETQEKNPLPSKETIEQEKQAGES
          NSVVATAQTRLRSYSRA.LRFSSATMSDKPDMAEIEKFDKSKLKKTETQEKNPLPSKETIEQEKQAGES
Retrocopy NSVVATAQTRLRSYSRAWLRFSSATMSDKPDMAEIEKFDKSKLKKTETQEKNPLPSKETIEQEKQAGES

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	4.16 RPM	302.67 RPM
SRP007412_cerebellum	1.18 RPM	63.56 RPM
SRP007412_heart	0.90 RPM	53.28 RPM
SRP007412_kidney	0.52 RPM	105.68 RPM
SRP007412_liver	1.51 RPM	82.39 RPM
SRP007412_testis	0.21 RPM	8.01 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_77 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_77 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_77 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000038488	2 retrocopies	retro_btau_1731, retro_btau_599,
Gorilla gorilla	ENSGGOG00000006450	1 retrocopy	retro_ggor_200,
Macaca mulatta	ENSMMUG00000014256	2 retrocopies	retro_mmul_1274, retro_mmul_1890,
Pan troglodytes	ENSPTRG00000028317	4 retrocopies	retro_ptro_1440, retro_ptro_1572, retro_ptro_2864, retro_ptro_77 ,