RetrogeneDB ID: retro_ptro_2864

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 9:127504167..127504374(+)
• Located in intron of: ENSPTRG00000021425

Retrocopy information

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

Parental gene information

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

Sequence

>retro_ptro_2864
AACTCGGTGGTGGCCACTGCGCAGACCAGACTTCGCTCGTTCTCGCACGCCTCGCTCCGCTTTTCCTCCGCAACCATGTC
TGACAAACCCGATATGGCTGAGATTGAGAAATTCGGTAAGTCGAAACTGAAGAAGACAGAGACGCAAGAGAAAAATCCAC
TGCCTTCCAAAGAAACGATTGAACAGGAGAAGCAAGCAGGCGAATCG

Alignment

ORF - retro_ptro_2864 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.65 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  NSVVATAQTRLRSYSRASLRFSSATMSDKPDMAEIEKFDKSKLKKTETQEKNPLPSKETIEQEKQAGES
          NSVVATAQTRLRS.S.ASLRFSSATMSDKPDMAEIEKF.KSKLKKTETQEKNPLPSKETIEQEKQAGES
Retrocopy NSVVATAQTRLRSFSHASLRFSSATMSDKPDMAEIEKFGKSKLKKTETQEKNPLPSKETIEQEKQAGES

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	0.84 RPM	302.67 RPM
SRP007412_cerebellum	0.43 RPM	63.56 RPM
SRP007412_heart	0.12 RPM	53.28 RPM
SRP007412_kidney	0.24 RPM	105.68 RPM
SRP007412_liver	0.10 RPM	82.39 RPM
SRP007412_testis	0.11 RPM	8.01 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2864 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2864 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2864 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,