RetrogeneDB ID: retro_cfam_1954

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 8:39018677..39019121(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCAFG00000016040
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: LSM4
• Ensembl ID: ENSCAFG00000014900
• Aliases: None
• Description: Canis lupus familiaris LSM4 homolog, U6 small nuclear RNA associated (S. cerevisiae) (LSM4), mRNA. [Source:RefSeq mRNA;Acc:NM_001110805]

Sequence

>retro_cfam_1954
TGGTCGGCGAGCCCGCTCCCCGCCGACACCATGCTTCCTTTGTCGCTGCTGAAGACGGCTCAGAATCATCCCATGTTGGT
GGAACTCAAAAATGGGGAGACATACAATGGGCACCTGGTGAGCTGTGATAACTGGATGAACATTAACCTTCGAGAGGTGA
TCTGCACATCCAGGGATGGGGACAAGTTTTGGCGGATGCCCGAGTGCTACATCCGTGGCAGCACCATCAAGTACCTGCGT
ATCCCTGATGAGATCATCGACATGGTCAAGGAGGAGGTGGTGGCCAAGGGCCGTGGCCGCGGTGGCCTGCAGCAGCAGAA
GCAGCAGAAGGGCCGAGGCATGGGGGGTGCTGGGCGAGGTGTGTTTGGTGGCCGGGGCCGAGGTGGGATCCCAGGCACAG
GCAGAGGTCAGCCGGAAAAGAAGCCAGGCAGACAGGCGGGCAAA

Alignment

ORF - retro_cfam_1954 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.27 %
• Parental protein coverage: 96.73 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  WSASPLPADTMLPLSLLKTAQNHPMLVELKNGETYNGHLVSCDNWMNINLREVICTSRDGDKFWRMPECY
          WSASPLPADTMLPLSLLKTAQNHPMLVELKNGETYNGHLVSCDNWMNINLREVICTSRDGDKFWRMPECY
Retrocopy WSASPLPADTMLPLSLLKTAQNHPMLVELKNGETYNGHLVSCDNWMNINLREVICTSRDGDKFWRMPECY

Parental  IRGSTIKYLRIPDEIIDMVKEEVVAKGRGRGGLQQQKQQKGRGMGGAGRGVFGGRGRGGIPGTGRGQPEK
          IRGSTIKYLRIPDEIIDMVKEEVVAKGRGRGGL.......GRGMGGAGRGVFGGRGRGGIPGTGRGQPEK
Retrocopy IRGSTIKYLRIPDEIIDMVKEEVVAKGRGRGGLXXXXXXXGRGMGGAGRGVFGGRGRGGIPGTGRGQPEK

Parental  KPGRQAGK
          KPGRQAGK
Retrocopy KPGRQAGK

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	10.63 RPM
SRP017611_brain	0.08 RPM	6.67 RPM
SRP017611_kidney	0.07 RPM	13.87 RPM
SRP017611_liver	0.00 RPM	4.28 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1954 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1954 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1954 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000014900	1 retrocopy	retro_cfam_1954 ,
Echinops telfairi	ENSETEG00000007762	2 retrocopies	retro_etel_1656, retro_etel_51,
Latimeria chalumnae	ENSLACG00000015861	1 retrocopy	retro_lcha_28,
Myotis lucifugus	ENSMLUG00000004010	1 retrocopy	retro_mluc_832,