RetrogeneDB ID: retro_cfam_1116

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 23:7185837..7186176(-)
• Located in intron of: ENSCAFG00000004806

Retrocopy information

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

Parental gene information

• Parental gene symbol: ARL2
• Ensembl ID: ENSCAFG00000028760
• Aliases: None
• Description: ADP-ribosylation factor-like 2 [Source:HGNC Symbol;Acc:693]

Sequence

>retro_cfam_1116
ATGGGGCTTCTGACCATTCTGAAGAAGATGAAACAGAAAGAGCGGGAGCTGCGACTGCTCACGCTCGGCCTAGACAATGC
TGGCAAAACAACCATCCTCAAGAAGTTCAACGGGGTAGACACTGACACCATCTCCCCGATGCTAGGCTTCAACATTAAGA
CCCTGGAACATCGAGGATTCAAGGTGAACATCTGGGATGTGGGAGGCTAGAAGTCCTTGCGGTCCTACTGGCGGAACTAC
TTTGAGAGCACCAATGGCCTCATCTGGGTGGTGGACAGCGCCAACCGCCAGCGCATGCAGGACTGCCAGTGGGAGCTCCA
GAGCTTGTTGGTGGAGGAG

Alignment

ORF - retro_cfam_1116 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.04 %
• Parental protein coverage: 73.86 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MGLLTILKKMKQKERELRLLMLGLDNAGKTTILKKFNGEDIDTISPTLGFNIKTLEHRGFKLNIWDVGGQ
          MGLLTILKKMKQKERELRLL.LGLDNAGKTTILKKFNG.D.DTISP.LGFNIKTLEHRGFK.NIWDVGG.
Retrocopy MGLLTILKKMKQKERELRLLTLGLDNAGKTTILKKFNGVDTDTISPMLGFNIKTLEHRGFKVNIWDVGG*

Parental  KSLRSYWRNYFESTDGLIWVVDSADRQRMQDCQRELQSLLVEE
          KSLRSYWRNYFEST.GLIWVVDSA.RQRMQDCQ.ELQSLLVEE
Retrocopy KSLRSYWRNYFESTNGLIWVVDSANRQRMQDCQWELQSLLVEE

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	2.02 RPM	43.64 RPM
SRP017611_brain	2.70 RPM	37.08 RPM
SRP017611_kidney	2.05 RPM	28.26 RPM
SRP017611_liver	0.65 RPM	8.27 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1116 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1116 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1116 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000028760	1 retrocopy	retro_cfam_1116 ,
Callithrix jacchus	ENSCJAG00000002545	1 retrocopy	retro_cjac_3266,