RetrogeneDB ID: retro_cfam_177

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 2:10497499..10497907(-)
• Located in intron of: ENSCAFG00000004186

Retrocopy information

• Ensembl ID: ENSCAFG00000004198
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: RPL32
• Ensembl ID: ENSCAFG00000004871
• Aliases: EFCAB12, C20H3orf25
• Description: 60S ribosomal protein L32 [Source:UniProtKB/Swiss-Prot;Acc:E2RKA8]

Sequence

>retro_cfam_177
ATGGCTGCCCTCAGACCTCTGGTGAAGCCCAAGATCATTAAAAAGAGGACCAAGAAGTTCATCCAGCACCAGTCAGACCA
ATATGTCAAAATTAAGCGCAACTGGCGGAAACCCAGAGGCATTGACAATAGGGTACGCAGAAGATTCAAGGGCCAAATCT
TGATGCCCAACATTGGTTACGGGACCAACAAGAAAACAAAGCACATGCTGCCCAGTGGCTTCCGGAAGTTCCTAGTCCAC
AATGTCAAGGAGCTTGAAGTGCTGCTGATGTGCAACAAATCTTATTGTGCAGAGATTGCTCACAATGTATCCTCCAAGAA
CTGCAAAGCCATTGTGGAAAGAGCAGCCCAGCTGGCCATCAGAGTCACCAATCCCAATGCCAGGCTGCGTAGTGAAGAAA
ATGAATAA

Alignment

ORF - retro_cfam_177 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.3 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAALRPLVKPKIVKKRTKKFIRHQSDRYVKIKRNWRKPRGIDNRVRRRFKGQILMPNIGYGSNKKTKHML
          MAALRPLVKPKI.KKRTKKFI.HQSD.YVKIKRNWRKPRGIDNRVRRRFKGQILMPNIGYG.NKKTKHML
Retrocopy MAALRPLVKPKIIKKRTKKFIQHQSDQYVKIKRNWRKPRGIDNRVRRRFKGQILMPNIGYGTNKKTKHML

Parental  PSGFRKFLVHNVKELEVLLMCNKSYCAEIAHNVSSKNRKAIVERAAQLAIRVTNPNARLRSEENE
          PSGFRKFLVHNVKELEVLLMCNKSYCAEIAHNVSSKN.KAIVERAAQLAIRVTNPNARLRSEENE
Retrocopy PSGFRKFLVHNVKELEVLLMCNKSYCAEIAHNVSSKNCKAIVERAAQLAIRVTNPNARLRSEENE

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	0.29 RPM	200.54 RPM
SRP017611_brain	0.08 RPM	51.13 RPM
SRP017611_kidney	0.07 RPM	519.25 RPM
SRP017611_liver	0.00 RPM	122.62 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_177 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_177 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_177 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000004871	6 retrocopies	retro_cfam_100, retro_cfam_107, retro_cfam_1747, retro_cfam_177 , retro_cfam_204, retro_cfam_234,