RetrogeneDB ID: retro_ptro_2427

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 6:36546600..36546966(-)
• Located in intron of: ENSPTRG00000018097

Retrocopy information

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

Parental gene information

• Parental gene symbol: NUDT5
• Ensembl ID: ENSPTRG00000002294
• Aliases: None
• Description: nudix (nucleoside diphosphate linked moiety X)-type motif 5 [Source:HGNC Symbol;Acc:8052]

Sequence

>retro_ptro_2427
CTCATAGAAGATGGTGAAACCCCAGGAGCAGCTGCTCTTTGGGAGCTTGAGGAAGAAACTGGCTACAAAGGGGACGCTGC
CGAATGTTCTCCAGTGGTCTATATGGACCCAGGTTTGTCAAACTGTACCACACACATCGTGACAGTAATCATTAACGGAG
ATGACGCAGAAAATGTAAGGCCCAAGCCAAAGCCAGGGGATGGAGAATTTGTGGAAGTCATTTCGTTACCCAAGAATGAC
CTGCTGCAGGGACTCGATGCTCTCGTAGCTGAAAAACATCTTACAGTGGATGCCAGAGTCTATTCCCATGCTCTAGCACT
GAAACATGCAAATGTGAAGCCATTTGAAGTGCCTGTCCTGAAATTT

Alignment

ORF - retro_ptro_2427 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.89 %
• Parental protein coverage: 55.71 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LIDDGETPEAAALRELEEETGYKGDVAECSPAVCMDPGLSNCTIHIVTVTINGDDAENARPKPKPGILEF
          LI.DGETP.AAAL.ELEEETGYKGD.AECSP.V.MDPGLSNCT.HIVTV.INGDDAEN.RPKPKPG..EF
Retrocopy LIEDGETPGAAALWELEEETGYKGDAAECSPVVYMDPGLSNCTTHIVTVIINGDDAENVRPKPKPGDGEF

Parental  VEVISLPKNDLLQRLDALVAEEHLTVDARVYSYALALKHANAKPFEVPFLKF
          VEVISLPKNDLLQ.LDALVAE.HLTVDARVYS.ALALKHAN.KPFEVP.LKF
Retrocopy VEVISLPKNDLLQGLDALVAEKHLTVDARVYSHALALKHANVKPFEVPVLKF

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	0.13 RPM	7.35 RPM
SRP007412_cerebellum	0.50 RPM	6.92 RPM
SRP007412_heart	0.12 RPM	2.62 RPM
SRP007412_kidney	0.65 RPM	21.31 RPM
SRP007412_liver	0.59 RPM	21.38 RPM
SRP007412_testis	0.11 RPM	4.64 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2427 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2427 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2427 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3580
Gorilla gorilla	retro_ggor_2415
Pongo abelii	retro_pabe_2949
Macaca mulatta	retro_mmul_1828

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Parental genes homology:

Parental genes homology involve 18 parental genes, and 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000019509	2 retrocopies	retro_btau_1326, retro_btau_1438,
Canis familiaris	ENSCAFG00000004794	2 retrocopies	retro_cfam_435, retro_cfam_612,
Equus caballus	ENSECAG00000023658	1 retrocopy	retro_ecab_647,
Echinops telfairi	ENSETEG00000006403	1 retrocopy	retro_etel_946,
Felis catus	ENSFCAG00000025093	1 retrocopy	retro_fcat_350,
Homo sapiens	ENSG00000165609	1 retrocopy	retro_hsap_3580,
Gorilla gorilla	ENSGGOG00000006325	1 retrocopy	retro_ggor_2415,
Loxodonta africana	ENSLAFG00000012052	1 retrocopy	retro_lafr_226,
Myotis lucifugus	ENSMLUG00000010453	2 retrocopies	retro_mluc_1263, retro_mluc_2073,
Macaca mulatta	ENSMMUG00000017141	1 retrocopy	retro_mmul_1828,
Nomascus leucogenys	ENSNLEG00000012298	1 retrocopy	retro_nleu_2838,
Oryctolagus cuniculus	ENSOCUG00000009308	1 retrocopy	retro_ocun_862,
Otolemur garnettii	ENSOGAG00000005816	2 retrocopies	retro_ogar_2071, retro_ogar_2988,
Pongo abelii	ENSPPYG00000002091	2 retrocopies	retro_pabe_2949, retro_pabe_3040,
Pan troglodytes	ENSPTRG00000002294	1 retrocopy	retro_ptro_2427 ,
Rattus norvegicus	ENSRNOG00000017741	1 retrocopy	retro_rnor_1672,
Sus scrofa	ENSSSCG00000011113	1 retrocopy	retro_sscr_143,
Tursiops truncatus	ENSTTRG00000007394	2 retrocopies	retro_ttru_209, retro_ttru_495,