RetrogeneDB ID: retro_cfam_612

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 14:57931714..57932064(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NUDT5
• Ensembl ID: ENSCAFG00000004794
• Aliases: None
• Description: nudix (nucleoside diphosphate linked moiety X)-type motif 5 [Source:HGNC Symbol;Acc:8052]

Sequence

>retro_cfam_612
GCAGTAGTCTCAGCACTGCAAAGAACCCTTCATGATGAATATGCCTTTTTGGGAAAACAGTTCTGACTGCCAATGGGAGC
CAAAGGCCTCAAACTCCCCATAGATCTCATAAGATGATGGAAACCCAGAAGCAGCCATTCTTCTGGAGCCTGAGAAAGAA
ACTGGCTTTGAAGGTGACATTGAATATTCTCCAGCTGAATGTATGGATGCAGGCTTGTCAGGCTGTACACACGCTCTGTG
ACAGTGACTTAATGAAGATGATGCTAAAAATTGAGACCCAACCCAAAGCTGGGGATGGACAATTTGTGGAAGTGACGTCT
TTACTACCAAAAAATGATCTACTGAAGAGA

Alignment

ORF - retro_cfam_612 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.54 %
• Parental protein coverage: 54.34 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  AVIPVLQRTLHYECIVLVKQFRPPMGGYCLEFPAGLI-DDNESPEAAALRELEEETGYKGDVAECSPAVC
          AV...LQRTLH.E...L.KQF..PMG...L..P..LI.DD...PEAA.L.E.E.ETG..GD..E.SPA.C
Retrocopy AVVSALQRTLHDEYAFLGKQF*LPMGAKGLKLPIDLI>DDG-NPEAAILLEPEKETGFEGDI-EYSPAEC

Parental  MDPGLTNCTTHIVTVTINGDDAEN-VRP-KPKPGDGEFVEVIS-LPKNDLLKR
          MD.GL..C.TH......N.DDA.N..RP..PK.GDG.FVEV.S.LPKNDLLKR
Retrocopy MDAGLSGC-THAL*Q*LNEDDAKN<LRP<QPKAGDGQFVEVTSLLPKNDLLKR

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
SRP012049_cerebellum	0.00 RPM	11.21 RPM
SRP017611_brain	0.00 RPM	13.02 RPM
SRP017611_kidney	0.00 RPM	15.85 RPM
SRP017611_liver	0.00 RPM	11.60 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_612 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_612 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_612 has 0 orthologous retrocopies within eutheria group .

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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,