RetrogeneDB ID: retro_cfam_1627

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 38:9305070..9305356(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCAFG00000032335
• Aliases: None
• Description: None

Sequence

>retro_cfam_1627
CCTCAAGAGCTCCATAGAAAGCTGCACCACCACCATGAAAGATGAGGACATCAGAGGGCACAAACAGGAGGTCATTAAGA
TCATTGAACAACAGATAGAGGTTGTTAACAATGGGGTCCTTGAGATCTACAGGAAGATTAGTGATTTAATCCTTACATTT
TTTTGAGCCCCAAGCCCAGTATAGCCTCCCAGAGATGGACTTCCATAAGTCTTACTTGAAGAATCTCTTACCTCAAAGCA
ACAAGCCCATTCAAACTGCCTCTTGAACCCACACATCTACCTCATT

Alignment

ORF - retro_cfam_1627 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 55.56 %
• Parental protein coverage: 54.86 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  PQE-SSDSTHTTIEDEDTKARKQEVIKITEQLIEAVNNGDFEAYAKICDPGLT-SFEPEALGNLVEGMDF
          PQE.S..S..TT..DED....KQEVIKI.EQ.IE.VNNG..E.Y.KI.D..LT..FEP.A...L.E.MDF
Retrocopy PQE>SIESCTTTMKDEDIRGHKQEVIKIIEQQIEVVNNGVLEIYRKISDLILT>FFEPQAQYSLPE-MDF

Parental  HRFYFENLLAKNSKPIHTT-ILNPHVHVI
          H..Y..NLL....KPI.T...LNPH...I
Retrocopy HKSYLKNLLPQSNKPIQTA<LLNPHIYLI

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	29.90 RPM
SRP017611_brain	0.00 RPM	88.05 RPM
SRP017611_kidney	0.00 RPM	0.00 RPM
SRP017611_liver	0.00 RPM	0.00 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1627 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1627 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1627 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000032335	1 retrocopy	retro_cfam_1627 ,