RetrogeneDB ID: retro_cfam_100

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 15:20406477..20406885(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCAFG00000005722
• 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_100
ATGGCTGCCCTCAGACCTCTGGTGAAGCCCAAGATCGTTAACAAGAGGACCAAGAAGTTCATCCGGCACCAGTCAGACCG
GTATGTCAAAATTAAGCGCAACTGGCGGAAACCCAGAGGCATTGACAATAGGGTATGCAGAAGATTCAAGGGCCAAATCC
TGATGCCCAACATTGGTTACGGGAGCAACAAGAAAACAAAGCACATGCTGCCCAGTGGCTTCCGGAAGTTCCTAGTCCAC
AACGTCAAGGAGCTTGAAGTGCTGCTTATGTGCAACAAATCTTATTGTGCAGAGGTTGCTCACAATGTATCCTCCAAGAA
CCCTAAAGCCATTGTGGAAAGAGCAGCCCAGCTGGCCATCAGAGTCACCAATCCCAATGCCAGGCTGCGTAGCGAAGAAA
ATGAATAA

Alignment

ORF - retro_cfam_100 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.04 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAALRPLVKPKIVKKRTKKFIRHQSDRYVKIKRNWRKPRGIDNRVRRRFKGQILMPNIGYGSNKKTKHML
          MAALRPLVKPKIV.KRTKKFIRHQSDRYVKIKRNWRKPRGIDNRV.RRFKGQILMPNIGYGSNKKTKHML
Retrocopy MAALRPLVKPKIVNKRTKKFIRHQSDRYVKIKRNWRKPRGIDNRVCRRFKGQILMPNIGYGSNKKTKHML

Parental  PSGFRKFLVHNVKELEVLLMCNKSYCAEIAHNVSSKNRKAIVERAAQLAIRVTNPNARLRSEENE
          PSGFRKFLVHNVKELEVLLMCNKSYCAE.AHNVSSKN.KAIVERAAQLAIRVTNPNARLRSEENE
Retrocopy PSGFRKFLVHNVKELEVLLMCNKSYCAEVAHNVSSKNPKAIVERAAQLAIRVTNPNARLRSEENE

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	9.79 RPM	200.54 RPM
SRP017611_brain	1.43 RPM	51.13 RPM
SRP017611_kidney	13.60 RPM	519.25 RPM
SRP017611_liver	3.48 RPM	122.62 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_100 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_100 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_100 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,