RetrogeneDB ID: retro_cfam_1104

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 23:32556963..32557338(+)
• Located in intron of: ENSCAFG00000007061

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCAFG00000015719
• Aliases: None
• Description: None

Sequence

>retro_cfam_1104
CCTCCTGGGGGGAAGATCAACCGGCCCCGAACGGAGCTGAAGAAGAAGCTGTTCTAGCGCTGGCGGGTGTTGAACCGGGA
GAGGCGACTGAAGCATCGGGTAGTCGGGGCTGTGATAGACGAAGGGCTGATCACACGGCAACACTTGAAGAAGCAGGCGT
CCAGTGCCTGTGCCAACATTACTCTGTCTGGGAAGAAGCGCAGAAAGCTCCTCCAGCAGATCTGGCTGGCCCAGAAAGAG
AAAGCAGCCATGGAAGTGGAAGCCCCCACAAGGCCAGTCAGGACTAGTGGACCACAGCCCAAGCAGCAAAAGAAGACAAA
AGCACCCCAGGATATAGACATGGAGGACCTTGGAGATGAGAGGGGAATCTCTCAC

Alignment

ORF - retro_cfam_1104 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.4 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  PPGGKINRPRTELKKKLFKRRRVLNRERRLKHRVVGAVIDEGLITRHHLKKRASSARANITLSGKKRRKL
          PPGGKINRPRTELKKKLF.R.RVLNRERRLKHRVVGAVIDEGLITR.HLKK.ASSA.ANITLSGKKRRKL
Retrocopy PPGGKINRPRTELKKKLF*RWRVLNRERRLKHRVVGAVIDEGLITRQHLKKQASSACANITLSGKKRRKL

Parental  LQQIRLAQKEKAAMEVEAPTRPVRTSGPQPKRQKKTKAPQDIDMEDLGDERGISH
          LQQI.LAQKEKAAMEVEAPTRPVRTSGPQPK.QKKTKAPQDIDMEDLGDERGISH
Retrocopy LQQIWLAQKEKAAMEVEAPTRPVRTSGPQPKQQKKTKAPQDIDMEDLGDERGISH

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	18.94 RPM
SRP017611_brain	0.08 RPM	13.26 RPM
SRP017611_kidney	0.07 RPM	14.66 RPM
SRP017611_liver	0.00 RPM	5.80 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1104 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1104 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1104 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006512	1 retrocopy	retro_amel_1386,
Bos taurus	ENSBTAG00000010465	2 retrocopies	retro_btau_1195, retro_btau_1799,
Canis familiaris	ENSCAFG00000015719	2 retrocopies	retro_cfam_1104 , retro_cfam_757,
Felis catus	ENSFCAG00000025454	2 retrocopies	retro_fcat_1722, retro_fcat_773,
Macaca mulatta	ENSMMUG00000013949	4 retrocopies	retro_mmul_1186, retro_mmul_1541, retro_mmul_1785, retro_mmul_1981,
Mus musculus	ENSMUSG00000071653	2 retrocopies	retro_mmus_1809, retro_mmus_759,
Otolemur garnettii	ENSOGAG00000033103	1 retrocopy	retro_ogar_811,
Rattus norvegicus	ENSRNOG00000019701	4 retrocopies	retro_rnor_1066, retro_rnor_1955, retro_rnor_851, retro_rnor_883,
Sus scrofa	ENSSSCG00000023323	2 retrocopies	retro_sscr_1162, retro_sscr_1163,