RetrogeneDB ID: retro_ptro_1128

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 16:11549846..11550195(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MRPL18
• Ensembl ID: ENSPTRG00000018761
• Aliases: None
• Description: None

Sequence

>retro_ptro_1128
GCTGCAGAGAAACAAGGTAGTGCCACACACCTGAGCTCCAGTGAGTTCCGGCACGGGTGGTGAGTTCCAAGGACTCAGCA
GCGTAAAGCATTGGTTGAACATCCAAATGGCCAGGTTGTGATTTCAGCGTCCAGTTATGAGTGCACTATAAAAAGCACCG
TTCTAGTACCAAAAATGTGACTGGTGAGAATATAGGACAACTGCTTGCAGAGCCAGGCTTAAGGCAGGAATCAACTTCAT
GGTCTACCAACCAGACCCTTGGGAGGCAGCCTTGGACTTGATGAGACAACTATGAAGTGCCAAGATGGGAGGTGCTGTGG
CTCCACAGGAACCTCGGAGAATCTGTGAA

Alignment

ORF - retro_ptro_1128 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 53.72 %
• Parental protein coverage: 66.11 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  ARKERGWRTVFPSREFWHRLRVIRTQHHVEALVEHQNGKVVVSASTREWAIK-KHLYSTRNVVACESIGR
          A....G..T...S.EF.H...V.RTQ....ALVEH.NG.VV.SAS..E..IK.KH..ST.NV...E.IG.
Retrocopy AAEKQGSATHLSSSEFRHGW*VPRTQQR-KALVEHPNGQVVISASSYECTIK<KHRSSTKNVTG-ENIGQ

Parental  VLAQ-RCLEAGINFMVYQPTPWEAASDSMKRLQSAMTEGGVVLREPQRIYE
          .LA....L.AGINFMVYQP.PWEAA.D.M..L.SA...G.V...EP.RI.E
Retrocopy LLAE<ARLKAGINFMVYQPDPWEAALDLMRQL*SAKMGGAVAPQEPRRICE

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	0.02 RPM	20.97 RPM
SRP007412_cerebellum	0.00 RPM	19.82 RPM
SRP007412_heart	0.00 RPM	15.59 RPM
SRP007412_kidney	0.00 RPM	24.61 RPM
SRP007412_liver	0.00 RPM	26.97 RPM
SRP007412_testis	0.21 RPM	22.66 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1128 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1128 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1128 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1664
Gorilla gorilla	retro_ggor_1255

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000015398	1 retrocopy	retro_amel_1445,
Dipodomys ordii	ENSDORG00000011514	1 retrocopy	retro_dord_741,
Echinops telfairi	ENSETEG00000007591	1 retrocopy	retro_etel_438,
Homo sapiens	ENSG00000112110	1 retrocopy	retro_hsap_1664,
Gorilla gorilla	ENSGGOG00000014075	1 retrocopy	retro_ggor_1255,
Macaca mulatta	ENSMMUG00000017037	1 retrocopy	retro_mmul_61,
Mus musculus	ENSMUSG00000057388	1 retrocopy	retro_mmus_1940,
Otolemur garnettii	ENSOGAG00000007327	1 retrocopy	retro_ogar_1660,
Pongo abelii	ENSPPYG00000017147	3 retrocopies	retro_pabe_1416, retro_pabe_1418, retro_pabe_1421,
Pan troglodytes	ENSPTRG00000018761	1 retrocopy	retro_ptro_1128 ,
Pteropus vampyrus	ENSPVAG00000005322	2 retrocopies	retro_pvam_1480, retro_pvam_252,
Tarsius syrichta	ENSTSYG00000005598	1 retrocopy	retro_tsyr_1847,