RetrogeneDB ID: retro_cfam_293

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 1:18120976..18121351(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CIDEC
• Ensembl ID: ENSCAFG00000005266
• Aliases: None
• Description: cell death-inducing DFFA-like effector c [Source:HGNC Symbol;Acc:24229]

Sequence

>retro_cfam_293
TTAAGGGATGCTAATAACTACATCCCTGTCTTGATGCAAAAGACTAGGTATTAATTCTCCCTCTCCCATAAGTCTGCCAA
GAAGATCAAGGTGGCCTGCAGAACCTTTGGCTTGGTCAAGGTGAGTCTACTGGACTTCATTGGTTGTTTGACAGTGAAGG
CAACTCATGATGGCACATACTCCATTTCCTAGGATATGCACTGCTACGGGATAAGGTTTATCATGAAGGAAGTTCTTTAT
TGGCCCCTCTTCGGCATATAAACCATGTTTCTTGGCACCTTCTGTTACATCAAGCAACTCCTGGATGCCACAGAGGGAGG
GCAGCCCAAGGACAAGACCTCATCCCTCATCTCAACCAGTCTGAAGACACTACAA

Alignment

ORF - retro_cfam_293 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.91 %
• Parental protein coverage: 54.2 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LQKGQKWQPPQEQGSRYQLSLSHKPAKKIDVAQVTFDLYKMNPQDFIGCLNVKATLYGTYSLSYDLHCYG
          L.......P...Q..RY..SLSHK.AKKI.VA..TF.L.K....DFIGCL.VKAT..GTYS.S.D.HCYG
Retrocopy LRDANNYIPVLMQKTRY*FSLSHKSAKKIKVACRTFGLVKVSLLDFIGCLTVKATHDGTYSIS*DMHCYG

Parental  AKRIMKEVLRWALFSMKTTGHVLLGTSCYMQQLLDATEGGQPPEGKARSLIPTSLKMLQ
          ...IMKEVL.W.LF...T.....LGT.CY..QLLDATEGGQP...K..SLI.TSLK.LQ
Retrocopy IRFIMKEVLYWPLFGI*T---MFLGTFCYIKQLLDATEGGQPKD-KTSSLISTSLKTLQ

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	0.21 RPM
SRP017611_brain	0.00 RPM	0.64 RPM
SRP017611_kidney	0.00 RPM	3.30 RPM
SRP017611_liver	0.00 RPM	0.07 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_293 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_293 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_293 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000005266	1 retrocopy	retro_cfam_293 ,
Canis familiaris	ENSCAFG00000012240	1 retrocopy	retro_cfam_85,
Dasypus novemcinctus	ENSDNOG00000018422	2 retrocopies	retro_dnov_1559, retro_dnov_751,
Vicugna pacos	ENSVPAG00000002888	1 retrocopy	retro_vpac_132,