RetrogeneDB ID: retro_cfam_1156

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 25:4607768..4608132(+)
• Located in intron of: ENSCAFG00000006231

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCAFG00000000061
• Aliases: RDH5, BLOC1S1
• Description: None

Sequence

>retro_cfam_1156
GTGCTGTGGCGCCTGCTGAGGGAGCACCAGGCCAAGCAGAGGGGACGCAAGAAGCTGCAGGAGAAGAGGAGGCGGGAGGC
CATCCCCGCAGCGACCTGCCTCACCGAAGCGCTGCTGCATCACCTCAGTGTGGGTGTGGCCCAGGCTCCATGAACCAGAG
AAGCTGGACCACGAGGCGAAGACCCTACACGTCTAGGCTGCCCAGTTTGCCAAGCAGACAGGCCAGTGGGTCGGGATGGT
GGAGAACTTCAATCAGGCACTCAAGGAAATCGGGGATGTGGAGAACTGGGCTCGGAGCATCGAGCTGGACATGCGCACCA
TTGCCACCGCCCTGGAATATGTGTACAAAGGGCAGCTGCAGGCC

Alignment

ORF - retro_cfam_1156 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.29 %
• Parental protein coverage: 97.6 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MLSRLLREHQAKQSERKELQEKRRREAIAAATCLTEALVDHLNVGVAQA-YMNQR-KLDHEVKTLQVQAA
          .L.RLLREHQAKQ..RK.LQEKRRREAI.AATCLTEAL..HL.VGVAQA..MNQR.KLDHE.KTL.V.AA
Retrocopy VLWRLLREHQAKQRGRKKLQEKRRREAIPAATCLTEALLHHLSVGVAQA<SMNQR<KLDHEAKTLHV*AA

Parental  QFAKQTGQWIGMVENFNQALKEIGDVENWARSIELDMRTIATALEYVYKGQLQS
          QFAKQTGQW.GMVENFNQALKEIGDVENWARSIELDMRTIATALEYVYKGQLQ.
Retrocopy QFAKQTGQWVGMVENFNQALKEIGDVENWARSIELDMRTIATALEYVYKGQLQA

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	18.35 RPM
SRP017611_brain	0.00 RPM	17.07 RPM
SRP017611_kidney	0.00 RPM	100.71 RPM
SRP017611_liver	0.07 RPM	25.23 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1156 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1156 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1156 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000000061	1 retrocopy	retro_cfam_1156 ,
Callithrix jacchus	ENSCJAG00000008026	1 retrocopy	retro_cjac_148,
Macropus eugenii	ENSMEUG00000001570	3 retrocopies	retro_meug_12, retro_meug_1307, retro_meug_242,
Mus musculus	ENSMUSG00000090247	1 retrocopy	retro_mmus_1761,
Otolemur garnettii	ENSOGAG00000010506	1 retrocopy	retro_ogar_786,