RetrogeneDB ID: retro_cfam_826

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 18:39635680..39636010(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MRPL20
• Ensembl ID: ENSCAFG00000019259
• Aliases: None
• Description: None

Sequence

>retro_cfam_826
AAGCTGACGGTGAGAGCCGTGACCAGAGCGTTTGTGAAATGCACAAAAGCAAGGAGACTGAAGAAGAGGAATATGCGGAC
CCTCTGGATTAATCGAATCACAGCTGCCTCCCAGGAACATGGCCTGAAGTACCCGGCATTCATTGTCCATTTAATTAAGT
GCCAGGTGGAGCTCAACAGGAAAGTACTTGTGGATCTAGCCATCTATGAACCAAAGACTTTTAAGTCTTTGGCTGCTTTG
GCCAAAAGGAGGCGACTGGAAGGATTTGTTGCTGCCCTAGGGGATGGCAAAGAGCCTGAAGGCATATTTTCCAGAGTGGT
GCAGCATCAC

Alignment

ORF - retro_cfam_826 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.36 %
• Parental protein coverage: 73.83 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KLAVRAVTRAFVKCTKARRLKKRNMRTLWINRITAASQEHGLKYPAFIVNLIKCQVELNRKVLADLAIYE
          KL.VRAVTRAFVKCTKARRLKKRNMRTLWINRITAASQEHGLKYPAFIV.LIKCQVELNRKVL.DLAIYE
Retrocopy KLTVRAVTRAFVKCTKARRLKKRNMRTLWINRITAASQEHGLKYPAFIVHLIKCQVELNRKVLVDLAIYE

Parental  PKTFKSLAALAKRRRLEGFAAALGDGKEPEGIFSRVVQHH
          PKTFKSLAALAKRRRLEGF.AALGDGKEPEGIFSRVVQHH
Retrocopy PKTFKSLAALAKRRRLEGFVAALGDGKEPEGIFSRVVQHH

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	28.85 RPM
SRP017611_brain	0.08 RPM	25.17 RPM
SRP017611_kidney	0.00 RPM	62.34 RPM
SRP017611_liver	0.00 RPM	13.34 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_826 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_826 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_826 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000013932	2 retrocopies	retro_amel_143, retro_amel_545,
Canis familiaris	ENSCAFG00000019259	2 retrocopies	retro_cfam_2112, retro_cfam_826 ,
Dasypus novemcinctus	ENSDNOG00000010105	1 retrocopy	retro_dnov_1620,
Homo sapiens	ENSG00000242485	1 retrocopy	retro_hsap_2508,
Gorilla gorilla	ENSGGOG00000027251	1 retrocopy	retro_ggor_1565,
Myotis lucifugus	ENSMLUG00000011857	1 retrocopy	retro_mluc_1423,
Monodelphis domestica	ENSMODG00000006562	2 retrocopies	retro_mdom_1424, retro_mdom_719,
Mus musculus	ENSMUSG00000029066	1 retrocopy	retro_mmus_1624,
Otolemur garnettii	ENSOGAG00000005968	1 retrocopy	retro_ogar_2263,
Procavia capensis	ENSPCAG00000001425	1 retrocopy	retro_pcap_238,
Tupaia belangeri	ENSTBEG00000008735	2 retrocopies	retro_tbel_2193, retro_tbel_892,