RetrogeneDB ID: retro_cfam_1686

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 4:20538055..20538427(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCAFG00000014614
• Aliases: None
• Description: None

Sequence

>retro_cfam_1686
GTGGCCTTCGTGGCTCTGGGAGCCTCCGCCCACGCTCTATGCCTGCAGAGCTGGCTTCTGGGAACTGGGCAGGCACAGAT
GAGAGACATCCACCGGCGAGCTTCATTGTTGTCCTTCTGGGAACTCATCCCCATGAGAGCAAAACCTCTGCAAAAGAAGA
AAAAGGTAGATCCTAAAAAAAGACCAAGCAGCAAAGGCCCATTTGAAAAAAAAAGGATCAGACAACTGGAGAAAGCCAGC
TAGGAACTAATTCCCACTGACAATTTTATTATACCTGTGAGGCTCTTAGAGAAAACAAGACGGCAGCCTCTCCTGGAGCT
TCCCTTTGAAGAGAGTGAGTGGAGAGCTCTGCTTCTGAGGAAGTGGTCCCTA

Alignment

ORF - retro_cfam_1686 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.13 %
• Parental protein coverage: 59.71 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAVAALGASARALRSRSGLLGPWQTQMRETHQRAALLSFWELIPMRAEPLRKKKKVDPKKDQAVKDRLKK
          .A..ALGASA.AL...S.LLG..Q.QMR..H.RA.LLSFWELIPMRA.PL.KKKKVDPKK....K.....
Retrocopy VAFVALGASAHALCLQSWLLGTGQAQMRDIHRRASLLSFWELIPMRAKPLQKKKKVDPKKRPSSKGPFXX

Parental  R-IRRLEKASQELIPIEDFITPVKLLDKTRQRPKVELPFEESERRALLLKKWSL
          ..IR.LEKAS.ELIP...FI.PV.LL.KTR..P..ELPFEESE.RALLL.KWSL
Retrocopy XXIRQLEKAS*ELIPTDNFIIPVRLLEKTRRQPLLELPFEESEWRALLLRKWSL

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	27.64 RPM
SRP017611_brain	0.00 RPM	17.55 RPM
SRP017611_kidney	0.00 RPM	75.08 RPM
SRP017611_liver	0.00 RPM	15.81 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1686 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1686 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1686 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000014614	2 retrocopies	retro_cfam_1686 , retro_cfam_662,