RetrogeneDB ID: retro_cfam_761

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 17:36794315..36794747(+)
• Located in intron of: ENSCAFG00000007174

Retrocopy information

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

Parental gene information

• Parental gene symbol: MRPL11
• Ensembl ID: ENSCAFG00000012706
• Aliases: None
• Description: mitochondrial ribosomal protein L11 [Source:HGNC Symbol;Acc:14042]

Sequence

>retro_cfam_761
ATGTCGATGCTGAACCGAGCGACTCAGGCCCTCAGGAAGCCCGAGGCCAGAGGCATGATCCGGACCATCATGCGGGCAGG
CCAGGCCACATCTGGGCCTCCATTAGGTCCCATCCTGGGTCAGAGAGGTGTTTCCATCAACCAGTTCTGTGCAAGGAGTT
CAACAAGAAGACAAAAGACATCAAAGAAGGCATTCCTTTGCCCACAAGATTTTTGTGAAGCCTAATAGGACATTTGAAAT
CAAATTGGACAGCCCACTGTTTCCTACTTCCTGAAAGCAGCTGCTGGGATTGAGAAGGGGGCCTGGCAGACAGGGAAGGA
GGTGGCCAGCCTGGTGACCTTGAAGCATGTGTATGAAATCGCCCAAATTAAAGCTCAGGATGAGGCCTTCGCCCTGCAGG
ATGTGGTTCACTCTGTCCTCTGTGGTTCACTC

Alignment

ORF - retro_cfam_761 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.38 %
• Parental protein coverage: 75.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MSKLNRAARALRKPEAGGVIRTIVRAGQAMTGPPLGPILGQRGVSINQFC-KEFNEKTKDIK-EGIPLPT
          MS.LNRA..ALRKPEA.G.IRTI.RAGQA..GPPLGPILGQRGVSINQFC........K..K.EGIPLPT
Retrocopy MSMLNRATQALRKPEARGMIRTIMRAGQATSGPPLGPILGQRGVSINQFCARSSTRRQKTSK<EGIPLPT

Parental  -KIFVKPDRTFEIK-IGQPTVSYFLKAAAGIEKGARQTGKEVAGLVTLKHVYEIAQVKAQDEAFALQDVP
          .KIFVKP.RTFEIK.IGQPTVSYFLKAAAGIEKGA.QTGKEVA.LVTLKHVYEIAQ.KAQDEAFALQDV.
Retrocopy <KIFVKPNRTFEIK<IGQPTVSYFLKAAAGIEKGAWQTGKEVASLVTLKHVYEIAQIKAQDEAFALQDVV

Parental  LSSVVRSI
          .S....S.
Retrocopy HSVLCGSL

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	19.91 RPM
SRP017611_brain	0.08 RPM	18.66 RPM
SRP017611_kidney	0.00 RPM	41.54 RPM
SRP017611_liver	0.22 RPM	10.66 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_761 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_761 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_761 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000012706	1 retrocopy	retro_cfam_761 ,
Callithrix jacchus	ENSCJAG00000001470	1 retrocopy	retro_cjac_803,
Dasypus novemcinctus	ENSDNOG00000004111	2 retrocopies	retro_dnov_1607, retro_dnov_566,
Echinops telfairi	ENSETEG00000015216	2 retrocopies	retro_etel_1754, retro_etel_333,
Homo sapiens	ENSG00000174547	1 retrocopy	retro_hsap_3390,
Gorilla gorilla	ENSGGOG00000001300	1 retrocopy	retro_ggor_2296,
Myotis lucifugus	ENSMLUG00000004047	1 retrocopy	retro_mluc_2131,
Mus musculus	ENSMUSG00000024902	1 retrocopy	retro_mmus_2118,
Nomascus leucogenys	ENSNLEG00000006111	1 retrocopy	retro_nleu_1705,
Otolemur garnettii	ENSOGAG00000010448	2 retrocopies	retro_ogar_1143, retro_ogar_3159,
Pongo abelii	ENSPPYG00000003025	1 retrocopy	retro_pabe_2786,
Pan troglodytes	ENSPTRG00000003924	1 retrocopy	retro_ptro_2305,
Ictidomys tridecemlineatus	ENSSTOG00000025971	1 retrocopy	retro_itri_941,
Tarsius syrichta	ENSTSYG00000008712	1 retrocopy	retro_tsyr_1095,
Tursiops truncatus	ENSTTRG00000002678	1 retrocopy	retro_ttru_431,