RetrogeneDB ID: retro_cfam_2172

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: X:63339242..63339805(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DCXR
• Ensembl ID: ENSCAFG00000005927
• Aliases: None
• Description: dicarbonyl/L-xylulose reductase [Source:HGNC Symbol;Acc:18985]

Sequence

>retro_cfam_2172
GTGTGTGTGGACCTGTGTGACTGGGAGGCCACAGAACACCCACTGTGCAGTGTGAGCCTAGTGCACCTGCTGGTGGACAA
CATTGCCATGGCACTGCTACAGCCCTTCTTGGAGGTCACCAAGAAGGCATGTAACATATTCTTTAATATGAACCTATGGA
CTGTTTCCAAGTGTTCCAGTTTATGGCCCATGACTTAATAGCTGGGAAAATCCTGGAGTCTATCATGAATGTCTCCATTC
AGACCTCACAGTGCACAATGACTAGTCACACAGCTACTGCTACCCCAAGGGTGCCATGGACATGCTGACCAAAAGGATGG
CTCTGGAGCTTAGGTCACATAAGATCTCCATGAACGCAGTGAACCCCACACTAGTGATGTCCCCATAGGACAGAGCAACT
GGAATGACCCTCCAGAAGGCCAAGAGCATGGTGGATTGAATCCCATTTGTAAAGCTATCTGAGGGTGGAGAATATGGTGG
ACACCATCTTTCTCCTGGTGAGTGACTAGAGCAGCATGACCACAGGTTCTACTATGCCAGTGGATAGGGGATTCCTTGGT
ACC

Alignment

ORF - retro_cfam_2172 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.62 %
• Parental protein coverage: 77.05 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  VCVDLGDWEATERALGSVGPVDLLVNNAAVALLQPFLEVTKEACDTSFHVNLRAI-IQVSQIVARGLIAR
          VCVDL.DWEATE..L.SV..V.LLV.N.A.ALLQPFLEVTK.AC...F..NL.....QV.Q..A..LIA.
Retrocopy VCVDLCDWEATEHPLCSVSLVHLLVDNIAMALLQPFLEVTKKACNIFFNMNLWTV<FQVFQFMAHDLIAG

Parental  GAPGSIVNISSQASQRAIANHSV-YCSTKGAMDMLTKVMALELGPHKIRVNTVNPTVVMT-PMGQANWSN
          ....SI.N.S.Q.SQ.....H...YC..KGAMDMLTK.MALEL..HKI..N.VNPT.VM..P.GQ.NW..
Retrocopy KILESIMNVSIQTSQCTMTSHTA<YCYPKGAMDMLTKRMALELRSHKISMNAVNPTLVMS<PIGQSNWND

Parental  P-QKAKTMLDRIPLGKFAE-VENVVDTILFLLSDRSSMTTGSAVPVDGGFLAT
          P.QKAK.M.D.IP..K..E.VEN.VDTI..L.SD.SSMTTGS..PVD.GFL.T
Retrocopy P>QKAKSMVD*IPFVKLSE>VENMVDTIFLLVSD*SSMTTGSTMPVDRGFLGT

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	17.14 RPM
SRP017611_brain	0.00 RPM	10.56 RPM
SRP017611_kidney	0.00 RPM	263.82 RPM
SRP017611_liver	0.00 RPM	64.75 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_2172 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_2172 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_2172 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000005927	1 retrocopy	retro_cfam_2172 ,
Canis familiaris	ENSCAFG00000007520	1 retrocopy	retro_cfam_1341,
Canis familiaris	ENSCAFG00000014368	4 retrocopies	retro_cfam_1199, retro_cfam_1212, retro_cfam_1273, retro_cfam_568,
Canis familiaris	ENSCAFG00000016277	1 retrocopy	retro_cfam_545,