RetrogeneDB ID: retro_cfam_371

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 10:387398..387694(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCAFG00000017884
• Aliases: None
• Description: None

Sequence

>retro_cfam_371
GCTCAAATTGCAATTGCGGCCACCACTTCCACTCCAGAATGGCCCGGGACAGCGAGGAGACGCCAGCCGTCCTTCCCACA
AGGGCAGGGGCGCTGGAGATTATAGCAGCAGGAAGAAGAAGGCAGCGTCTGCCGCCAGCTTTAGGTAGGGGATCAGCATG
GAAGGCAAGAGCGAGAATAAAGTGGTGCCCTTTGATTTCAGCCCGAGACCCCTGGGGAAAGCTGCCCAGCCACTGCCATT
AAGGATCCAAACTTGGTGCACCGTGCAATGGTGGCGCAGTAGCTGGCAGGCAGAAC

Alignment

ORF - retro_cfam_371 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.58 %
• Parental protein coverage: 52.08 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  AQIPIVATTSTPG-IARNSKKRPA-SPSHNGSSAGSYGASKKKKVSAASFTQGISMEAMSENKMVTSDFS
          AQI.I.ATTSTP...AR.S...PA..PSH.G..AG.Y...KKK..SAASF..GISME..SENK.V..DFS
Retrocopy AQIAIAATTSTPE<MARDSEETPA<RPSHKGRGAGDYSSRKKKAASAASFR*GISMEGKSENKVVPFDFS

Parental  TGPMEKAAKPLP-FKDPNFVHSG-HGGAVAGKKN
          ..P..KAA.PLP..KDPN.VH....GGAVAG..N
Retrocopy PRPLGKAAQPLP<IKDPNLVHRA<NGGAVAGRQN

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	19.91 RPM
SRP017611_brain	0.00 RPM	15.01 RPM
SRP017611_kidney	0.00 RPM	17.10 RPM
SRP017611_liver	0.00 RPM	3.77 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_371 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_371 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_371 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000017884	1 retrocopy	retro_cfam_371 ,
Myotis lucifugus	ENSMLUG00000030708	3 retrocopies	retro_mluc_118, retro_mluc_1892, retro_mluc_1942,
Macaca mulatta	ENSMMUG00000020108	1 retrocopy	retro_mmul_1340,
Ochotona princeps	ENSOPRG00000011443	1 retrocopy	retro_opri_721,
Pteropus vampyrus	ENSPVAG00000017436	1 retrocopy	retro_pvam_899,