RetrogeneDB ID: retro_ptro_1108

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 16:50273049..50273650(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: UNG
• Ensembl ID: ENSPTRG00000005419
• Aliases: None
• Description: Pan troglodytes uracil-DNA glycosylase (UNG), nuclear gene encoding mitochondrial protein, mRNA. [Source:RefSeq mRNA;Acc:NM_001246523]

Sequence

>retro_ptro_1108
CTACCCATGGGTTTTAGTGAGAGCTGGAAGAAGTACCTCAGTGCAGTTCAGGGAAAAGTATTTTATAAAAGTAATGAGAT
TTGTGCAGAATAAAGCAGACATTACATTGTTTATTCACCCCCACACCAAGTTTTCACCTAGACCCATATGTGTGACATGA
GAGATGGGAAGGTTCTAATTCCCAGACAGGATCCATATCATGGACCCAGTCAAGCTCACAGGCTCTGCTTTCACGTACAA
AGACATGTTCCACCTCCACCCAGCTCAGAAAGTGTTTAAAAATTGTTGTCTGCAGACATAGATGGTTTTGCTCACCTTCA
GCATGGAGATTTATCTGGGTGGGCCAAACAAGGGGTTCTTTTACTCAATGCTGTCTCACTATTCTGGCCCATCAAGCCAG
TTCTCATAAGGAGAGAGGCTGGGAGCAACTCACTGACGCAGTTGTGTCCTGGCTAAATCAGAACTCGATCTGGCTTGTCT
TCTTGCTCTGGGGCTCTTATGCTCAGAAGAAGGGCAGTGCCATGGATAGGAAACAGCACCACATTCTGCAGCTGGCTCAT
CCCTCCCTGTTGTCTGCATATAGAGGTTCTTTGGATGTAGA

Alignment

ORF - retro_ptro_1108 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.06 %
• Parental protein coverage: 64.54 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  VPVGFGESWKKHLSGEFGKPYFIKLMGFVAEERKHYTVYPPPHQVFTWTQMCDIKDVKVVILGQDPYHGP
          .P.GF.ESWKK.LS...GK..F.K.....AE...HY.VY.PPHQVFT.T.MCD..D.KV.I..QDPYHGP
Retrocopy LPMGFSESWKKYLSAVQGK-VFYKSNEICAE*SRHYIVYSPPHQVFT*THMCDMRDGKVLIPRQDPYHGP

Parental  NQAHGLCFSVQRPVPPPPSLENIYKELSTDIEDFVHPGHGDLSGWAKQGVLLLNAV-LTVRAHQANSHKE
          .QAH.LCF.VQR.VPPPPS.E...K.LS.DI..F.H..HGDLSGWAKQGVLLLNAV.LT..AHQA.SHKE
Retrocopy SQAHRLCFHVQRHVPPPPSSESV*KLLSADIDGFAHLQHGDLSGWAKQGVLLLNAV<LTILAHQASSHKE

Parental  RGWEQFTDAVVSWLNQNSNGLVFLLWGSYAQKKGSAIDRKRHHVLQTAHPSPLSVYRG-FFGCR
          RGWEQ.TDAVVSWLNQNS..LVFLLWGSYAQKKGSA.DRK.HH.LQ.AHPS.LS.YRG.FFGCR
Retrocopy RGWEQLTDAVVSWLNQNSIWLVFLLWGSYAQKKGSAMDRKQHHILQLAHPSLLSAYRG<FFGCR

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	9.97 RPM
SRP007412_cerebellum	0.00 RPM	6.56 RPM
SRP007412_heart	0.00 RPM	12.94 RPM
SRP007412_kidney	0.03 RPM	16.11 RPM
SRP007412_liver	0.00 RPM	12.90 RPM
SRP007412_testis	0.00 RPM	22.97 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1108 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1108 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1108 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Macaca mulatta	retro_mmul_1564

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Parental genes homology:

Parental genes homology involve 18 parental genes, and 32 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000016525	1 retrocopy	retro_amel_153,
Canis familiaris	ENSCAFG00000011144	1 retrocopy	retro_cfam_1567,
Callithrix jacchus	ENSCJAG00000010134	2 retrocopies	retro_cjac_1467, retro_cjac_520,
Cavia porcellus	ENSCPOG00000004634	3 retrocopies	retro_cpor_1339, retro_cpor_6, retro_cpor_863,
Dasypus novemcinctus	ENSDNOG00000005335	2 retrocopies	retro_dnov_1001, retro_dnov_627,
Equus caballus	ENSECAG00000008080	1 retrocopy	retro_ecab_747,
Felis catus	ENSFCAG00000008349	1 retrocopy	retro_fcat_445,
Macropus eugenii	ENSMEUG00000015792	3 retrocopies	retro_meug_1594, retro_meug_1877, retro_meug_2077,
Myotis lucifugus	ENSMLUG00000010755	3 retrocopies	retro_mluc_1305, retro_mluc_2060, retro_mluc_989,
Macaca mulatta	ENSMMUG00000006957	2 retrocopies	retro_mmul_1564, retro_mmul_2115,
Mustela putorius furo	ENSMPUG00000003463	1 retrocopy	retro_mputfur_1592,
Nomascus leucogenys	ENSNLEG00000001442	3 retrocopies	retro_nleu_1325, retro_nleu_1950, retro_nleu_2802,
Oryctolagus cuniculus	ENSOCUG00000003145	1 retrocopy	retro_ocun_1767,
Otolemur garnettii	ENSOGAG00000007441	2 retrocopies	retro_ogar_1593, retro_ogar_2716,
Pongo abelii	ENSPPYG00000004929	3 retrocopies	retro_pabe_1354, retro_pabe_1355, retro_pabe_2792,
Pan troglodytes	ENSPTRG00000005419	1 retrocopy	retro_ptro_1108 ,
Sus scrofa	ENSSSCG00000009938	1 retrocopy	retro_sscr_1202,
Ictidomys tridecemlineatus	ENSSTOG00000006894	1 retrocopy	retro_itri_661,