RetrogeneDB ID: retro_cfam_990

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 20:36900035..36900696(-)
• Located in intron of: ENSCAFG00000008763

Retrocopy information

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

Parental gene information

• Parental gene symbol: DCAKD
• Ensembl ID: ENSCAFG00000032388
• Aliases: None
• Description: dephospho-CoA kinase domain containing [Source:HGNC Symbol;Acc:26238]

Sequence

>retro_cfam_990
ATGTTCCTGGTGGGCCTCACAGGGGGTATTGCCTCGAGCAAGAGCTCAGTGATTCACGTGTTCCAGGAGCTGAGCTGTGC
AGTGATTGATGTTGATGTCATCGCCTGGCATGTCGTCCAGCCAGGATACCCCACCCACCGGTGCATCATGGAGGCCTTTG
GCACCAAGGTCTTACTGGAGAACGGTGACATCAATCGCAAGGTCCTGGGGGACCTGATCTTTAACTAGCCTGACTGGCGG
CATCTGCTCAACACCATCACCCACCTGAGATCCGCAAAGAAATGATGAAGGAGACCTTCAAGTATTTCCTCCGAGGATAC
CGCTATGTGATTCTGGATATTCCCCTGCTGTTTGAGACCAAGAAGTGCTCAAGTACATGAAGCACACCGTGGTGGTGTAC
TGTGACCAAGACACCCAGCTGGCGCGGCTGATGCGGCGGAACAGCCTGACCTGGAAGGATGTGGAGGTCCGGATCTAGGC
CCAGCTGCCCCTGAAGGACAAAGTCCACAAGGGACGCCACGTCCTGGACAACTCGGGGGAGTGGAGCACCACCAAACGCC
AGGTCCTGTTCCTGCATGCCACGCTGGAGCGCTCCCTGGACTACCTGCCACTGCGGCTCAGGGTCCTGATCGGTCTAGTG
GGCATTGCCAGCCTCCTCTAC

Alignment

ORF - retro_cfam_990 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.44 %
• Parental protein coverage: 95.67 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MFLVGLTGGIASGKSSVIQVFQQLGCAVIDVDVIARHVVQPGYPAHRRIVEAFGTEVLLENGDINRKVLG
          MFLVGLTGGIAS.KSSVI.VFQ.L.CAVIDVDVIA.HVVQPGYP.HR.I.EAFGT.VLLENGDINRKVLG
Retrocopy MFLVGLTGGIASSKSSVIHVFQELSCAVIDVDVIAWHVVQPGYPTHRCIMEAFGTKVLLENGDINRKVLG

Parental  DLIFNQPDRRHLLNTITH-PEIRKEMMKETFKYFLRGYRYVILDIPLLFETKK-LLKYMKHTVVVYCDRD
          DLIFN.PD.RHLLNTITH.PEIRKEMMKETFKYFLRGYRYVILDIPLLFETKK..LKYMKHTVVVYCD.D
Retrocopy DLIFN*PDWRHLLNTITH<PEIRKEMMKETFKYFLRGYRYVILDIPLLFETKK<VLKYMKHTVVVYCDQD

Parental  TQLARLMRRNSLTRKDAEARIEAQLPLKDKVLMARHVLDNSGEWSSTKRQVLLLYAELERSLDYLPLRLG
          TQLARLMRRNSLT.KD.E.RI.AQLPLKDKV...RHVLDNSGEWS.TKRQVL.L.A.LERSLDYLPLRL.
Retrocopy TQLARLMRRNSLTWKDVEVRI*AQLPLKDKVHKGRHVLDNSGEWSTTKRQVLFLHATLERSLDYLPLRLR

Parental  VLTGLVGIASLLY
          VL.GLVGIASLLY
Retrocopy VLIGLVGIASLLY

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	0.50 RPM	36.71 RPM
SRP017611_brain	0.32 RPM	20.88 RPM
SRP017611_kidney	0.20 RPM	22.78 RPM
SRP017611_liver	0.07 RPM	3.63 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_990 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_990 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_990 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000032388	1 retrocopy	retro_cfam_990 ,
Monodelphis domestica	ENSMODG00000011245	1 retrocopy	retro_mdom_1100,
Mus musculus	ENSMUSG00000020935	1 retrocopy	retro_mmus_1588,