RetrogeneDB ID: retro_cfam_1069

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 22:17388568..17388841(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: C1orf21
• Ensembl ID: ENSCAFG00000013460
• Aliases: None
• Description: chromosome 1 open reading frame 21 [Source:HGNC Symbol;Acc:15494]

Sequence

>retro_cfam_1069
GATGAGTGTAGGACCAAACTCGCGGAAGAGGTCAAATACATGAAAAATGGGGCAGAAGAGGAGCAGAAAATAGCAGCCAC
AGGAACCAAGAAAATGTGGAACAAAGTGCCAGTTCAAATGTGAGACTTAAAACTAATGAAGAGATTCCAGGCTTAGTTCA
TCAACCCAGAGCAAATAGGCACATCTCTGAGAGCCAACAGGAATTCTTCAGAATCCTGGATGAAAAAAATGGAAAAGGGT
CATGATTATTGTTTGGAAGAAGAGGATATCACA

Alignment

ORF - retro_cfam_1069 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.49 %
• Parental protein coverage: 74.38 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  DEYRIKPVEEVKYMKNGAE-EEQKIAA-RNQENLEKSASSNVRLKTNKEIPGLVHQPRANMHISESQQEF
          DE.R.K..EEVKYMKNGAE.E....A..RNQEN.E.SASSNVRLKTN.EIPGLVHQPRAN.HISESQQEF
Retrocopy DECRTKLAEEVKYMKNGAEEEQKIAAT<RNQENVEQSASSNVRLKTNEEIPGLVHQPRANRHISESQQEF

Parental  FRMLDE-KIEKGRDYCSEEEDIT
          FR.LDE.K.EKG.DYC.EEEDIT
Retrocopy FRILDE>KMEKGHDYCLEEEDIT

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	20.45 RPM
SRP017611_brain	0.00 RPM	17.47 RPM
SRP017611_kidney	0.00 RPM	7.59 RPM
SRP017611_liver	0.00 RPM	1.16 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1069 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1069 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1069 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000013468	2 retrocopies	retro_amel_508, retro_amel_590,
Bos taurus	ENSBTAG00000038079	3 retrocopies	retro_btau_1219, retro_btau_1661, retro_btau_18,
Canis familiaris	ENSCAFG00000013460	1 retrocopy	retro_cfam_1069 ,
Mustela putorius furo	ENSMPUG00000011816	1 retrocopy	retro_mputfur_1583,
Sorex araneus	ENSSARG00000013999	1 retrocopy	retro_sara_185,