RetrogeneDB ID: retro_cfam_1901

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 8:16697304..16697699(+)
• 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_1901
GCTTCCCTCCCTCAGTCTGTCAGTGATGGTTATTTACCTATGGTCTGTTACTTCGATGAAGACCCGGATGCACCTGTTTA
TGTCCCCTTTTTCCAAGACCAAGCTGAGGTGAAGAAAGAACACGCAGGCAGTTCATAAGATACCTGAAGGAGCCTAAGAG
TAAAGTCTGCCTTCCGGTGGTTAAGAGGCTTGACAAAGAGTACTGGGGAACGAACGTGCAAGCTATAGTGATGGCTCTGG
AGTTGGAAAACGGGTTACACAAGCTCCTGCAAGACCTGCAGACCTTGCCTTCTCAGAAGAATGAAACTGATCTCTTAGAA
TTCCTGAAAAGGTTCATGGGTAAACAGAAGAGGAACATAAAATATCTGGAATACCAGCATAGCTATCAGAAGGAA

Alignment

ORF - retro_cfam_1901 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.98 %
• Parental protein coverage: 76.3 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  ASYELNVSDGYLSMVCYFDEDPDAPVYVPFFQDQVEVKKGHA-RQFIRYLKERKSKVCLPVVKRLDKEYW
          AS....VSDGYL.MVCYFDEDPDAPVYVPFFQDQ.EVKK.HA.RQFIRYLKE.KSKVCLPVVKRLDKEYW
Retrocopy ASLPQSVSDGYLPMVCYFDEDPDAPVYVPFFQDQAEVKKEHA<RQFIRYLKEPKSKVCLPVVKRLDKEYW

Parental  GTNVQAIVMALELENGLHKLLQDLQNLASQKNETDLLEFLKRFVGKQKRNIKYLEYQHSYQKE
          GTNVQAIVMALELENGLHKLLQDLQ.L.SQKNETDLLEFLKRF.GKQKRNIKYLEYQHSYQKE
Retrocopy GTNVQAIVMALELENGLHKLLQDLQTLPSQKNETDLLEFLKRFMGKQKRNIKYLEYQHSYQKE

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_1901 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1901 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1901 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,