RetrogeneDB ID: retro_ptro_2826

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 9:38343868..38344225(+)
• Located in intron of: ENSPTRG00000020953

Retrocopy information

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

Parental gene information

• Parental gene symbol: MRPS10
• Ensembl ID: ENSPTRG00000018169
• Aliases: None
• Description: None

Sequence

>retro_ptro_2826
CACGGTAAGGCTGTATTGGACAGTTATGAATATTTTGCTGTGCTTGATGCTAAAGAACTTGGTATCTCTATTAAAGTACA
CGAACCTCCAAGGAAAATAGAGCGATTTACTCTTCTCATATCAGTGCATATTTACAAGAAGCACGGAGTTCAGTATGAAA
TGAGAACACTTTACAGATGTTTAGAGTTAGAACATCTAACTGGAAGCACAGCAGATGTCTACTTGGAATATATTCAGCGA
AACTTACCTGAAAGGGTTGCCATGGAAGTAACAAAGACACAATTAGAACAGTTACCAGAACACATCAAGGAGCCAATCTG
GGAAACACTATCAGAAGAAAAAGAAGAAAGCAAGTCT

Alignment

ORF - retro_ptro_2826 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.96 %
• Parental protein coverage: 59.2 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  HDKAVLDSYEYFAVLAAKELGISIKVHEPPRKIERFTLLQSVHIYKKHRVQYEMRTLYRCLELEHLTGST
          H.KAVLDSYEYFAVL.AKELGISIKVHEPPRKIERFTLL.SVHIYKKH.VQYEMRTLYRCLELEHLTGST
Retrocopy HGKAVLDSYEYFAVLDAKELGISIKVHEPPRKIERFTLLISVHIYKKHGVQYEMRTLYRCLELEHLTGST

Parental  ADVYLEYIQRNLPEGVAMEVTKTQLEQLPEHIKEPIWETLSEEKEASKS
          ADVYLEYIQRNLPE.VAMEVTKTQLEQLPEHIKEPIWETLSEEKE.SKS
Retrocopy ADVYLEYIQRNLPERVAMEVTKTQLEQLPEHIKEPIWETLSEEKEESKS

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	0.21 RPM	21.61 RPM
SRP007412_cerebellum	0.29 RPM	11.15 RPM
SRP007412_heart	0.26 RPM	20.99 RPM
SRP007412_kidney	0.10 RPM	17.47 RPM
SRP007412_liver	0.26 RPM	13.81 RPM
SRP007412_testis	0.11 RPM	12.33 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2826 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2826 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2826 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4157
Pongo abelii	retro_pabe_3456

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Dipodomys ordii	ENSDORG00000002081	1 retrocopy	retro_dord_412,
Homo sapiens	ENSG00000048544	1 retrocopy	retro_hsap_4157,
Gorilla gorilla	ENSGGOG00000012808	1 retrocopy	retro_ggor_2532,
Microcebus murinus	ENSMICG00000011379	1 retrocopy	retro_mmur_321,
Macaca mulatta	ENSMMUG00000014661	1 retrocopy	retro_mmul_48,
Mus musculus	ENSMUSG00000034729	1 retrocopy	retro_mmus_1654,
Nomascus leucogenys	ENSNLEG00000004800	1 retrocopy	retro_nleu_1385,
Oryctolagus cuniculus	ENSOCUG00000016697	1 retrocopy	retro_ocun_1141,
Pongo abelii	ENSPPYG00000016613	1 retrocopy	retro_pabe_3456,
Pan troglodytes	ENSPTRG00000018169	1 retrocopy	retro_ptro_2826 ,
Rattus norvegicus	ENSRNOG00000022609	1 retrocopy	retro_rnor_2284,
Ictidomys tridecemlineatus	ENSSTOG00000027016	1 retrocopy	retro_itri_1183,