RetrogeneDB ID: retro_cfam_1818

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 6:40716279..40716674(-)
• Located in intron of: ENSCAFG00000019741

Retrocopy information

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

Parental gene information

• Parental gene symbol: C6orf203
• Ensembl ID: ENSCAFG00000003732
• Aliases: None
• Description: chromosome 6 open reading frame 203 [Source:HGNC Symbol;Acc:17971]

Sequence

>retro_cfam_1818
GCCGAAGAGGAAGAGGACTCTGATGAAGAGAGTGATCATGAGATGAGTGAGCAGGAAGAGGAGCTCGAGGATGACCCCAG
TGTGGTCAAAGACTATAAAGACCTGGAAAAAGTAGTGCAGTCTTTCCGGTATGATGTTATCTTAAAGACAGGCCTAGATG
TTGGAAGAAACAAAGTAGAAGATGCATTCTACAAAGGTGAACTCAGGCTGAATGGGGAAAAATTATGGAAGAAAAGCAGA
ACGGTAAAAGTGAGAGATACATTGGATCTTCTAATTGGAGAGTATAAAGAAGCTGAAACAGAGACGTCATGAGAGTTCTT
CTGAAAAAAGTGTTGGAGGAGAAAACGGAAAGTGAAAAGTACAGAGTGGTCCTACACCGGTGGAAAAAGTTAAAA

Alignment

ORF - retro_cfam_1818 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.49 %
• Parental protein coverage: 55.23 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  AEEEEDSDEESDREMSEREEELEDDPSVVKDYKDLEKVVQSFRYDVILKTGLDVGRNKVEDAFYKGELRL
          AEEEEDSDEESD.EMSE.EEELEDDPSVVKDYKDLEKVVQSFRYDVILKTGLDVGRNKVEDAFYKGELRL
Retrocopy AEEEEDSDEESDHEMSEQEEELEDDPSVVKDYKDLEKVVQSFRYDVILKTGLDVGRNKVEDAFYKGELRL

Parental  NGEKLWKKSRTVKVGDTLDLLIGEDKEAETET-VMRVLLKKVLEEKTESEKYRVVLRRWKKLK
          NGEKLWKKSRTVKV.DTLDLLIGE.KEAETET.VMRVLLKKVLEEKTESEKYRVVL.RWKKLK
Retrocopy NGEKLWKKSRTVKVRDTLDLLIGEYKEAETET<VMRVLLKKVLEEKTESEKYRVVLHRWKKLK

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	11.47 RPM
SRP017611_brain	0.00 RPM	11.04 RPM
SRP017611_kidney	0.00 RPM	41.60 RPM
SRP017611_liver	0.00 RPM	16.53 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1818 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1818 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1818 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
Canis familiaris	ENSCAFG00000003732	1 retrocopy	retro_cfam_1818 ,
Homo sapiens	ENSG00000130349	1 retrocopy	retro_hsap_3538,
Gorilla gorilla	ENSGGOG00000006113	1 retrocopy	retro_ggor_2389,
Macropus eugenii	ENSMEUG00000013534	1 retrocopy	retro_meug_2181,
Microcebus murinus	ENSMICG00000004137	1 retrocopy	retro_mmur_1269,
Macaca mulatta	ENSMMUG00000007391	1 retrocopy	retro_mmul_115,
Nomascus leucogenys	ENSNLEG00000013450	2 retrocopies	retro_nleu_1433, retro_nleu_499,
Otolemur garnettii	ENSOGAG00000008839	2 retrocopies	retro_ogar_1396, retro_ogar_390,
Pongo abelii	ENSPPYG00000016885	1 retrocopy	retro_pabe_2922,
Pan troglodytes	ENSPTRG00000018464	2 retrocopies	retro_ptro_1453, retro_ptro_2405,
Tursiops truncatus	ENSTTRG00000008837	2 retrocopies	retro_ttru_324, retro_ttru_432,