RetrogeneDB ID: retro_cfam_1148

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 24:27714089..27714329(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DNPH1
• Ensembl ID: ENSCAFG00000001837
• Aliases: None
• Description: 2'-deoxynucleoside 5'-phosphate N-hydrolase 1 [Source:HGNC Symbol;Acc:21218]

Sequence

>retro_cfam_1148
GAAGAGGCTGCTGGGGCCCCAGGCTCATCCATCGGGGGGCCTGGCCTGGCTGCGGCAGGCACACCTGGTCATGGCAGCTG
TGACCCTCCATCCCCAGGTACACCAAGGCTGTGAGCTGGGCCAGCCTGTGGCCCTCAGTAAGAGAATCCTGTGCCTATCC
CGCCCCCCACAACAGTCTGGCCAAGTGCTTCAATTAGGCCCCGGGGAACAGCAGGCTGGCCATTCTAGGTGTGAGACTAC

Alignment

ORF - retro_cfam_1148 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.47 %
• Parental protein coverage: 54.48 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  EEAAG-GDRFIYER-DLAWLQQADVVVAEVT-QPSLGVGYELGQAMALNKRILCLFRP--QSGRVL-SAM
          EEAAG.G.R.I.....LAWL.QA..V.A.VT..P....G.ELGQ..AL.KRILCL.RP..QSG.VL.S..
Retrocopy EEAAG<GPRLIHRG<GLAWLRQAHLVMAAVTLHPQVHQGCELGQPVALSKRILCLSRPPQQSGQVL<SIR

Parental  IRGAADGSRFQVLDY
          .RG.A.G..F.V.DY
Retrocopy PRGTA-GWPF*V*DY

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	1.39 RPM
SRP017611_brain	0.00 RPM	0.32 RPM
SRP017611_kidney	0.00 RPM	0.20 RPM
SRP017611_liver	0.00 RPM	0.00 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1148 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1148 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1148 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Equus caballus	retro_ecab_595

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000012390	1 retrocopy	retro_amel_1012,
Bos taurus	ENSBTAG00000019913	1 retrocopy	retro_btau_518,
Canis familiaris	ENSCAFG00000001837	1 retrocopy	retro_cfam_1148 ,
Callithrix jacchus	ENSCJAG00000005337	1 retrocopy	retro_cjac_3948,
Equus caballus	ENSECAG00000006660	1 retrocopy	retro_ecab_595,
Felis catus	ENSFCAG00000009722	1 retrocopy	retro_fcat_365,
Homo sapiens	ENSG00000112667	1 retrocopy	retro_hsap_2562,
Nomascus leucogenys	ENSNLEG00000000516	1 retrocopy	retro_nleu_1515,
Pongo abelii	ENSPPYG00000016635	1 retrocopy	retro_pabe_1888,
Pan troglodytes	ENSPTRG00000029662	1 retrocopy	retro_ptro_1493,
Pteropus vampyrus	ENSPVAG00000008743	1 retrocopy	retro_pvam_1400,
Rattus norvegicus	ENSRNOG00000018397	1 retrocopy	retro_rnor_580,
Tursiops truncatus	ENSTTRG00000007022	1 retrocopy	retro_ttru_1520,