RetrogeneDB ID: retro_cfam_1533

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 33:22000424..22001177(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DCAF13
• Ensembl ID: ENSCAFG00000000663
• Aliases: DCAF13, WDSOF1
• Description: DDB1 and CUL4 associated factor 13 [Source:HGNC Symbol;Acc:24535]

Sequence

>retro_cfam_1533
TGCTTGGCAAAGCATCCAAAGAGTGGGGCTGCTGCCCTTTGTGGGGTAAGCAATGAAGAGGTTAGAATTTGGAACTTGAC
TAAATGAAATGTATCTGTACAAGATATGAGGATTTTGTACAAATAATATGTACTCCCTTTTGTGGGACTTCTTTTTCTAC
TGTCGGTGATGCCAAAACTGGAAAGCAGTGGAAAAATGGACGGACCAGGCTATGGAGAAGAGGAGGAAACATTGCATACA
ATATTAGGAAAGACAATGTTTGCAAGAAATTGATCATCACTGGAGAGAAACTATTTTTGCCTCATGTGGACAGCAAGTAG
ACATTTGGGATGAACAAAGAACAAGTCCTATATATTCAATGACCTGGCGATTCAACAGTATAAATAATGTTAAATTTAAC
ACAATTGAGACATTTTCTTGGAAAGCTGTGCTTCTGACAGGAATATAGTACTAGATGATATGAAGCACACTAGTCCTATA
AAAAAGGTCATCTTAGATATGAGAACAAATGCAATTTATTGGAACCCTGTGAAAGCTTTCATTTTTACTGCAGCAAATGA
AGATTAGAATGTACGTAGTTTTGATATGCGTGTACTAGACATTCCCCTAATGGTACATATGGATCATGCATCTGTGGTGC
TTGATGTGGATTACTTTCCCACTGGGAAAGAGTTTGTGTCTGCTAGTTTTGATAAATCTATTTGAATCTTTTCTGTGGAC
AAAAGTAGAAGCAGGGAAGTCTATCACACAGAA

Alignment

ORF - retro_cfam_1533 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.71 %
• Parental protein coverage: 56.85 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  CLAKHPKSLATVLSGACDGEVRIWNLTK-RKCIRTIQAHEGFVRGICTRFCGTSFFTVGDDKTVKQWK-M
          CLAKHPKS.A..L.G....EVRIWNLTK..KCI.T....E.FV..ICT.FCGTSF.TVGD.KT.KQWK.M
Retrocopy CLAKHPKSGAAALCGVSNEEVRIWNLTK<MKCICT--RYEDFVQIICTPFCGTSFSTVGDAKTGKQWK>M

Parental  DGPGYGEEEEPLHTILGKTVYTG-IDHHWKEAVFATCGQQVDIWDEQRTSPICSMTWGFDSISSVKFNPI
          DGPGYGEEEE.LHTILGKT.....IDHHW.E..FA.CGQQVDIWDEQRTSPI.SMTW.F.SI..VKFN.I
Retrocopy DGPGYGEEEETLHTILGKTMFAR>IDHHWRETIFASCGQQVDIWDEQRTSPIYSMTWRFNSINNVKFNTI

Parental  ETF-LLGSCASDRNIVLYDMRQATPLKKVILDMRTNTICWNPMEAFIFTAANEDYNLYTFDMRALDTPVM
          ETF..L.SCASDRNIVL.DM....P.KKVILDMRTN.I.WNP..AFIFTAANED.N...FDMR.LD.P.M
Retrocopy ETF<FLESCASDRNIVLDDMKHTSPIKKVILDMRTNAIYWNPVKAFIFTAANED*NVRSFDMRVLDIPLM

Parental  VHMDHVSAVLDVDYSPTGKEFVSASFDKSIRIFPVDKSRSREVYHTK
          VHMDH.S.VLDVDY.PTGKEFVSASFDKSI.IF.VDKSRSREVYHT.
Retrocopy VHMDHASVVLDVDYFPTGKEFVSASFDKSI*IFSVDKSRSREVYHTE

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	13.15 RPM
SRP017611_brain	0.00 RPM	9.13 RPM
SRP017611_kidney	0.00 RPM	24.90 RPM
SRP017611_liver	0.00 RPM	6.24 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1533 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1533 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1533 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000001595	3 retrocopies	retro_amel_1453, retro_amel_1723, retro_amel_399,
Canis familiaris	ENSCAFG00000000663	3 retrocopies	retro_cfam_1309, retro_cfam_1533 , retro_cfam_305,
Callithrix jacchus	ENSCJAG00000016181	2 retrocopies	retro_cjac_3083, retro_cjac_612,
Felis catus	ENSFCAG00000027256	1 retrocopy	retro_fcat_1840,
Homo sapiens	ENSG00000164934	1 retrocopy	retro_hsap_1498,
Gorilla gorilla	ENSGGOG00000015124	1 retrocopy	retro_ggor_1150,
Myotis lucifugus	ENSMLUG00000007375	1 retrocopy	retro_mluc_2048,
Nomascus leucogenys	ENSNLEG00000003791	1 retrocopy	retro_nleu_1718,
Otolemur garnettii	ENSOGAG00000002277	1 retrocopy	retro_ogar_305,
Pongo abelii	ENSPPYG00000018809	2 retrocopies	retro_pabe_1249, retro_pabe_3211,
Pan troglodytes	ENSPTRG00000020493	1 retrocopy	retro_ptro_1017,
Sarcophilus harrisii	ENSSHAG00000006588	1 retrocopy	retro_shar_507,