RetrogeneDB ID: retro_cfam_530

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 12:62346349..62346609(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: APOC1
• Ensembl ID: ENSCAFG00000004615
• Aliases: APOC1, Apo-CIB, ApoC-IB
• Description: Canis lupus familiaris apolipoprotein C-I (APOC1), mRNA. [Source:RefSeq mRNA;Acc:NM_001197048]

Sequence

>retro_cfam_530
ATGAGGCTCATCCTGTCGCTCCCGGTTGTGGCGGTGGTTCTGTGGATGGTTTTGGAAGGCCCAGCCTTGGCCCAGGTGGC
CTCACAAATAATCAGAACTTTGGAGTGCATCCCAGATTAGCTGAAGGAGTTTGGTAACACCTGGAGGACAAGGCATGGGA
GGCCATTGAGAGCATCAAGCTGAGTGACATTCCTGCGAAGATCAGGAACTGGTTTATGGAGACTTACAATAAAGTGAAAG
AATGGCTTAAAACTAACTAC

Alignment

ORF - retro_cfam_530 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.73 %
• Parental protein coverage: 98.86 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MRLILSLPVLVVVLSMVLEGPAPAQAAGEISSTFERIPDKLKEFGNT-LEDKARAAIESIKKSDIPAKTR
          MRLILSLPV..VVL.MVLEGPA.AQ.A..I..T.E.IPD.LKEFGNT.LEDKA..AIESIK.SDIPAK.R
Retrocopy MRLILSLPVVAVVLWMVLEGPALAQVASQIIRTLECIPD*LKEFGNT<LEDKAWEAIESIKLSDIPAKIR

Parental  NWFSEAFKKVKEHLKTAF
          NWF.E...KVKE.LKT..
Retrocopy NWFMETYNKVKEWLKTNY

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	16.72 RPM
SRP017611_brain	0.00 RPM	2.46 RPM
SRP017611_kidney	0.00 RPM	1.72 RPM
SRP017611_liver	0.00 RPM	1585.50 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_530 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_530 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_530 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000012737	1 retrocopy	retro_amel_582,
Canis familiaris	ENSCAFG00000004615	1 retrocopy	retro_cfam_530 ,
Otolemur garnettii	ENSOGAG00000028159	1 retrocopy	retro_ogar_2801,
Rattus norvegicus	ENSRNOG00000018426	1 retrocopy	retro_rnor_204,
Tupaia belangeri	ENSTBEG00000007093	2 retrocopies	retro_tbel_1243, retro_tbel_2226,