RetrogeneDB ID: retro_cfam_1491

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 32:5635694..5635943(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: LAMTOR4
• Ensembl ID: ENSCAFG00000014561
• Aliases: None
• Description: late endosomal/lysosomal adaptor, MAPK and MTOR activator 4 [Source:HGNC Symbol;Acc:33772]

Sequence

>retro_cfam_1491
GGCTACCTGGTGCTGAGTGAAGGTGCGGTGCTGGCGTAATCTGGGGATCTAGAGAATGAGGAGCAGGCAGCCAGTGCCAT
CTCTGAGCTGGTCAGCACAGCCTGTGGTTTCCGGCTGCACCACAGCACAAACATACCCTTCAAGCGCCTGTCCCTGGTCT
TTGGAGAACACACGCTGCTGGTGACCGTGTCAGGACAGAGGGTATTTGTGGTGAAGAGGCAGAACTGAGGGCGGGAGCCT
GTTGACGTC

Alignment

ORF - retro_cfam_1491 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.18 %
• Parental protein coverage: 84.69 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GYLVLSEGAVLASSGDLENDEQAASAISELVSTACGFRLHHSTNIPFKRLSVVFGEHTLLVTVSGQRVFV
          GYLVLSEGAVLA.SGDLEN.EQAASAISELVSTACGFRLHHSTNIPFKRLS.VFGEHTLLVTVSGQRVFV
Retrocopy GYLVLSEGAVLA*SGDLENEEQAASAISELVSTACGFRLHHSTNIPFKRLSLVFGEHTLLVTVSGQRVFV

Parental  VKRQNRGREPVDV
          VKRQN.GREPVDV
Retrocopy VKRQN*GREPVDV

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	0.13 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_1491 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1491 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1491 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000014561	1 retrocopy	retro_cfam_1491 ,
Cavia porcellus	ENSCPOG00000013370	1 retrocopy	retro_cpor_119,
Mus musculus	ENSMUSG00000050552	1 retrocopy	retro_mmus_3544,
Ochotona princeps	ENSOPRG00000003476	1 retrocopy	retro_opri_640,
Pteropus vampyrus	ENSPVAG00000011987	1 retrocopy	retro_pvam_1449,