RetrogeneDB ID: retro_pabe_1418

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 16_random:1739798..1740147(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MRPL18
• Ensembl ID: ENSPPYG00000017147
• Aliases: None
• Description: mitochondrial ribosomal protein L18 [Source:HGNC Symbol;Acc:14477]

Sequence

>retro_pabe_1418
GCCGCAGAGAAACAAGGTAGCGCCACACACCTCAGCTCCAGTGAGTTCTGGCACGGGTGGTGAGTTCCAAGGACTCAGCA
GCATAAAGCATTGGTTGAACATCCAAATGGCCAGGTTGTGATTTCAGCGTCCACTTATGAGTGCACCATAAAACGCGCCG
TTCTAGTACCAAAAATGTGACTGGTGAGAATATAGGACAACTGCTTGCAAAGCTAGGCTTAAGGCAGGAATCAACTTCAC
GGTGTACCAAGCAGACCCTTGGGAGGCAGCCTTGGACTCGATGAGACGACTACGAAGTGCCAAGACAGGAGGTGGTGTGG
CTCCACGGGAACCTCGGAGAACCTGTGAA

Alignment

ORF - retro_pabe_1418 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.02 %
• Parental protein coverage: 66.11 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  ARKERGWRTVFPSREFWHRLRVIRTQHHVEALVEHQNGKVVVSASTREWAIKKHLY-STRNVVACESIGR
          A....G..T...S.EFWH...V.RTQ.H..ALVEH.NG.VV.SAST.E..IK.....ST.NV...E.IG.
Retrocopy AAEKQGSATHLSSSEFWHGW*VPRTQQH-KALVEHPNGQVVISASTYECTIKRAVL<STKNVTG-ENIGQ

Parental  VLAQ-RCLEAGINFMVYQPTPWEAASDSMKRLRSAMTEGGVVLREPQRIYE
          .LA....L.AGINF.VYQ..PWEAA.DSM.RLRSA.T.GGV..REP.R..E
Retrocopy LLAK<ARLKAGINFTVYQADPWEAALDSMRRLRSAKTGGGVAPREPRRTCE

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	25.05 RPM
SRP007412_cerebellum	0.00 RPM	19.46 RPM
SRP007412_heart	0.00 RPM	13.49 RPM
SRP007412_kidney	0.00 RPM	26.35 RPM
SRP007412_liver	0.00 RPM	20.50 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1418 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1418 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1418 has 0 orthologous retrocopies within eutheria group .

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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,