RetrogeneDB ID: retro_cfam_746

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 17:4712784..4713123(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCAFG00000028564
• Aliases: None
• Description: None

Sequence

>retro_cfam_746
AAAGACCTGGGTGCACCTGTTTATGTCCCCTTTTTCCATGATCAAGCTGAGGTGAAGAAAGAACACGCAAGGCAGTTCAT
AAGATATCTGAAGGAGCGTAAGAGTAAAGTCTGCCTTCCAGTGGTTAAGAGGCTTGACCAAGGATACTGGGGAACGAACG
TGCAAGCTATAGTGATGGCTCTGGAGTTGGAAAACGGGTTACACAAGCTCCTGCAAGACCTGCAGAACTTGGCTTCTCAG
AAGAATGAAACTGATCTCTTAGAATTCCTGAAAAGGTTCATGGGTAAACAGAAGAGGAACATAAAATATCTGGAATACCA
GCATAGCTATCAGAAGGAA

Alignment

ORF - retro_cfam_746 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.04 %
• Parental protein coverage: 65.32 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EDPDAPVYVPFFQDQVEVKKGHARQFIRYLKERKSKVCLPVVKRLDKEYWGTNVQAIVMALELENGLHKL
          .D..APVYVPFF.DQ.EVKK.HARQFIRYLKERKSKVCLPVVKRLD..YWGTNVQAIVMALELENGLHKL
Retrocopy KDLGAPVYVPFFHDQAEVKKEHARQFIRYLKERKSKVCLPVVKRLDQGYWGTNVQAIVMALELENGLHKL

Parental  LQDLQNLASQKNETDLLEFLKRFVGKQKRNIKYLEYQHSYQKE
          LQDLQNLASQKNETDLLEFLKRF.GKQKRNIKYLEYQHSYQKE
Retrocopy LQDLQNLASQKNETDLLEFLKRFMGKQKRNIKYLEYQHSYQKE

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	0.00 RPM
SRP017611_brain	0.00 RPM	0.00 RPM
SRP017611_kidney	0.00 RPM	0.07 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_746 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_746 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_746 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000015497	1 retrocopy	retro_amel_333,
Canis familiaris	ENSCAFG00000028564	9 retrocopies	retro_cfam_1158, retro_cfam_1163, retro_cfam_1432, retro_cfam_1901, retro_cfam_365, retro_cfam_448, retro_cfam_567, retro_cfam_715, retro_cfam_746 ,
Ictidomys tridecemlineatus	ENSSTOG00000022867	1 retrocopy	retro_itri_1495,