RetrogeneDB ID: retro_cfam_2113

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: X:94449739..94450312(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RRM2
• Ensembl ID: ENSCAFG00000003409
• Aliases: None
• Description: ribonucleotide reductase M2 [Source:HGNC Symbol;Acc:10452]

Sequence

>retro_cfam_2113
AGCTTGCTGGCTAGGAGGATCTTCCAGCAGCCCGCCAAGCAAAAACTGAGGTATTTGCCCCTAGCATGGAGAATGAGTCA
CTACTCGGAGAAAACCCTTGTCACGTTGTCATTCTCCTTATCGAGTACCATGGTATTTGGCAGATGTATAAGAAAGCTGA
GGCTTCCTTTTGGACAGCTGAAGAGGTGGATCTTTCCAAGGACATTCAGCATTGGGAATCCTCGAAACCTGAGGAGAGAT
ATTTTATACCCCATATTTTGGCTTTCTTTGTGGCAAGTGATGGCATAGTAAAAGGATAACTTGGTGGAGTGGTTTATCCA
AGAAGTTCAGATTATAGAAGCCCTCTGTTTCTATGGATTCCAAATTGTCGTGGAAAACATCAACTCTGAGATGTATAGCC
TCCTCATTGTCACTTTTATTAAAGATTCTAAAGAAAGGGAATTTCTCTTCAATGCCATTGAGACAATGTCTTGTATAAAG
AAGAAAGCAGATCGGACCTTGCATTGGATTGGGGGCAAAGAGGCCACCTATGGAAAATGGATTATAGCCTTTGCTGCCAT
GGAAGCAGTTTTC

Alignment

ORF - retro_cfam_2113 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.65 %
• Parental protein coverage: 50.13 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  SKTARRIFQEPA-EPKTKVLAPSAEEEPLLRENPRRFVIFPIEYHDIWQMYKKAEASFWTAEEVDLSKDI
          S..ARRIFQ.PA...KT.V.APS.E.E.LL.ENP...VI..IEYH.IWQMYKKAEASFWTAEEVDLSKDI
Retrocopy SLLARRIFQQPA<QAKTEVFAPSMENESLLGENPCHVVILLIEYHGIWQMYKKAEASFWTAEEVDLSKDI

Parental  QHWESLKPEERYFISHVLAFFAASDGIVN-ENLVERFSQEVQITEARCFYGFQIAMENIHSEMYSLLIDT
          QHWES.KPEERYFI.H.LAFF.ASDGIV...NLVE.F.QEVQI.EA.CFYGFQI..ENI.SEMYSLLI.T
Retrocopy QHWESSKPEERYFIPHILAFFVASDGIVK>DNLVEWFIQEVQIIEALCFYGFQIVVENINSEMYSLLIVT

Parental  YIKDSKEREFLFNAIETMPCVKKKADWALRWIGDKEATYGERVVAFAAVEGIF
          .IKDSKEREFLFNAIETM.C.KKKAD..L.WIG.KEATYG....AFAA.E..F
Retrocopy FIKDSKEREFLFNAIETMSCIKKKADRTLHWIGGKEATYGKWIIAFAAMEAVF

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	16.42 RPM
SRP017611_brain	0.00 RPM	0.24 RPM
SRP017611_kidney	0.00 RPM	4.69 RPM
SRP017611_liver	0.00 RPM	0.22 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_2113 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_2113 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_2113 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 18 parental genes, and 26 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000003409	1 retrocopy	retro_cfam_2113 ,
Callithrix jacchus	ENSCJAG00000006533	3 retrocopies	retro_cjac_2134, retro_cjac_2950, retro_cjac_3851,
Cavia porcellus	ENSCPOG00000008652	1 retrocopy	retro_cpor_8,
Erinaceus europaeus	ENSEEUG00000009755	2 retrocopies	retro_eeur_421, retro_eeur_585,
Echinops telfairi	ENSETEG00000015797	2 retrocopies	retro_etel_640, retro_etel_691,
Homo sapiens	ENSG00000171848	1 retrocopy	retro_hsap_4815,
Macropus eugenii	ENSMEUG00000000121	3 retrocopies	retro_meug_1450, retro_meug_199, retro_meug_277,
Microcebus murinus	ENSMICG00000012789	1 retrocopy	retro_mmur_1384,
Myotis lucifugus	ENSMLUG00000010596	1 retrocopy	retro_mluc_794,
Macaca mulatta	ENSMMUG00000002057	1 retrocopy	retro_mmul_2568,
Monodelphis domestica	ENSMODG00000014763	1 retrocopy	retro_mdom_775,
Mus musculus	ENSMUSG00000020649	2 retrocopies	retro_mmus_2472, retro_mmus_3073,
Nomascus leucogenys	ENSNLEG00000013733	2 retrocopies	retro_nleu_2190, retro_nleu_3040,
Otolemur garnettii	ENSOGAG00000007075	1 retrocopy	retro_ogar_2665,
Pongo abelii	ENSPPYG00000012656	1 retrocopy	retro_pabe_3743,
Rattus norvegicus	ENSRNOG00000023272	1 retrocopy	retro_rnor_331,
Sus scrofa	ENSSSCG00000021742	1 retrocopy	retro_sscr_901,
Tursiops truncatus	ENSTTRG00000017209	1 retrocopy	retro_ttru_603,