RetrogeneDB ID: retro_ptro_2305

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 5:142797256..142797568(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MRPL11
• Ensembl ID: ENSPTRG00000003924
• Aliases: None
• Description: None

Sequence

>retro_ptro_2305
ATGTCAAAGCTCGGCCGGGCCACCCGGGGCCTCAGGAAGCTCGAGGTCGGCGATGTGATCCGGACCATCGTGCGGGCAGG
CCTGGCCATGCCCGGGCCCCCACTAGGCCCAGTGCTGGGTCAGAGAAGGGCTTCCATCAACCAATTTTGCAAGGAGTTCA
ATGAGAGGACAAAGGACATCAAGGAAGGCATTCCTCTGCTTACCAAGATTTTTGTGAAGCCTGACGGGACATTTGAAATC
AAGATTGGACAACCCACTGTTTCCTACTTCGTGAAGGCAGCAGCTGGGATTGAAAAGGGGGCCCGGCCAACA

Alignment

ORF - retro_ptro_2305 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.42 %
• Parental protein coverage: 54.17 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSKLGRAARGLRKPEVGGVIRAIVRAGLAMPGPPLGPVLGQRGVSINQFCKEFNERTKDIKEGIPLPTKI
          MSKLGRA.RGLRK.EVG.VIR.IVRAGLAMPGPPLGPVLGQR..SINQFCKEFNERTKDIKEGIPL.TKI
Retrocopy MSKLGRATRGLRKLEVGDVIRTIVRAGLAMPGPPLGPVLGQRRASINQFCKEFNERTKDIKEGIPLLTKI

Parental  LVKPDRTFEIKIGQPTVSYFLKAAAGIEKGARQT
          .VKPD.TFEIKIGQPTVSYF.KAAAGIEKGAR.T
Retrocopy FVKPDGTFEIKIGQPTVSYFVKAAAGIEKGARPT

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	13.83 RPM
SRP007412_cerebellum	0.00 RPM	11.72 RPM
SRP007412_heart	0.03 RPM	16.26 RPM
SRP007412_kidney	0.00 RPM	23.64 RPM
SRP007412_liver	0.00 RPM	15.48 RPM
SRP007412_testis	0.00 RPM	15.07 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2305 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2305 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2305 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3390
Gorilla gorilla	retro_ggor_2296
Pongo abelii	retro_pabe_2786

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000012706	1 retrocopy	retro_cfam_761,
Callithrix jacchus	ENSCJAG00000001470	1 retrocopy	retro_cjac_803,
Dasypus novemcinctus	ENSDNOG00000004111	2 retrocopies	retro_dnov_1607, retro_dnov_566,
Echinops telfairi	ENSETEG00000015216	2 retrocopies	retro_etel_1754, retro_etel_333,
Homo sapiens	ENSG00000174547	1 retrocopy	retro_hsap_3390,
Gorilla gorilla	ENSGGOG00000001300	1 retrocopy	retro_ggor_2296,
Myotis lucifugus	ENSMLUG00000004047	1 retrocopy	retro_mluc_2131,
Mus musculus	ENSMUSG00000024902	1 retrocopy	retro_mmus_2118,
Nomascus leucogenys	ENSNLEG00000006111	1 retrocopy	retro_nleu_1705,
Otolemur garnettii	ENSOGAG00000010448	2 retrocopies	retro_ogar_1143, retro_ogar_3159,
Pongo abelii	ENSPPYG00000003025	1 retrocopy	retro_pabe_2786,
Pan troglodytes	ENSPTRG00000003924	1 retrocopy	retro_ptro_2305 ,
Ictidomys tridecemlineatus	ENSSTOG00000025971	1 retrocopy	retro_itri_941,
Tarsius syrichta	ENSTSYG00000008712	1 retrocopy	retro_tsyr_1095,
Tursiops truncatus	ENSTTRG00000002678	1 retrocopy	retro_ttru_431,