RetrogeneDB ID: retro_cfam_1720

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 5:13427397..13427851(+)
• Located in intron of: ENSCAFG00000011880

Retrocopy information

• Ensembl ID: ENSCAFG00000030991
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: MRPL43
• Ensembl ID: ENSCAFG00000009742
• Aliases: None
• Description: mitochondrial ribosomal protein L43 [Source:HGNC Symbol;Acc:14517]

Sequence

>retro_cfam_1720
GCGCGCGGGACCCCGAGCCGCTTCCTGGCCAGTGTCCTCTACAACAGGCTGGGCCGGTACGTGCAGCAGTTGCAGCGTCT
CAGCTTTAACCTCAGCCGCGATGCGCCCTCGTCCCGCGGTGCCAGGGAGTTCGTGGAACGGGAGGTGGCCGACTCCGCGC
GACGGAACCGGGGGTCGTAATATACGTGAAGTCGAGGCCGCGCTGTGTGCCCAGAGTAGTGGCCGAATACCTTAATGGGG
CAGTGCCAAGGAGAGCATCCACTGCAAGTCAGTCGAAGAGACTGCGACGCTGGTGCAGAAGCTGGCGAACCAGTCGGGCC
TGGATGTGATCCGCGTCCGCAAGCCCTTCCACACTGACAGTCCTAGCGTCCAGGGCCAGTGGCACCCCTTCACCAACAAA
CCGACGTTGGGTGGGCTACGCCCGCGAGAAGTCCAGGATGCTGCGCTAGCCCAG

Alignment

ORF - retro_cfam_1720 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.26 %
• Parental protein coverage: 58.62 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  ARGTPSRFLASVLYNGLGRYVQQLQRLSFNLSRDAPSSRGAREFVEREVADFARRN-PGVVIYVNSRPCC
          ARGTPSRFLASVLYN.LGRYVQQLQRLSFNLSRDAPSSRGAREFVEREVAD.ARRN.PGVVIYV.SRP.C
Retrocopy ARGTPSRFLASVLYNRLGRYVQQLQRLSFNLSRDAPSSRGAREFVEREVADSARRN<PGVVIYVKSRPRC

Parental  VPRVVAEYLNGAV-REESIHCKSVEEIATLVQKLANQSGLDVIRIRKPFHTDSPSIQGQWHPFTNKPTML
          VPRVVAEYLNGAV...ESIHCKSVEE.ATLVQKLANQSGLDVIR.RKPFHTDSPS.QGQWHPFTNKPT.L
Retrocopy VPRVVAEYLNGAV<AKESIHCKSVEETATLVQKLANQSGLDVIRVRKPFHTDSPSVQGQWHPFTNKPT-L

Parental  GGLRPREVQDAALAQ
          GGLRPREVQDAALAQ
Retrocopy GGLRPREVQDAALAQ

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	14.57 RPM
SRP017611_brain	0.00 RPM	7.94 RPM
SRP017611_kidney	0.00 RPM	39.95 RPM
SRP017611_liver	0.00 RPM	7.98 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1720 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1720 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1720 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000009742	1 retrocopy	retro_cfam_1720 ,
Erinaceus europaeus	ENSEEUG00000004807	1 retrocopy	retro_eeur_444,
Echinops telfairi	ENSETEG00000012498	1 retrocopy	retro_etel_2213,
Microcebus murinus	ENSMICG00000000014	1 retrocopy	retro_mmur_370,
Macaca mulatta	ENSMMUG00000010679	1 retrocopy	retro_mmul_1882,
Nomascus leucogenys	ENSNLEG00000014812	1 retrocopy	retro_nleu_17,