RetrogeneDB ID: retro_cfam_479

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 12:6356496..6356757(+)
• Located in intron of: ENSCAFG00000001458

Retrocopy information

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

Parental gene information

• Parental gene symbol: FAM96B
• Ensembl ID: ENSCAFG00000020394
• Aliases: None
• Description: family with sequence similarity 96, member B [Source:HGNC Symbol;Acc:24261]

Sequence

>retro_cfam_479
GGAGAACTGGAGACCAGCAACCTCCTCGTCTGTGAGCACTCTGGAGAATACCTGGGAATTATGAATAAAGAGGACAAGCA
GGTTCCAGTGAGCAGTGTGCCCGGGGTCTTTGATCTGATTTGCTCCATCTGTGTCCCAGAGCTGCCACAGATTCTAGAAA
AATTGAATGTAGTACAGCAAGTCTGGCTTCAGGTGAGTGACCCTGAGAAGGTGGCCATGGCCTTCATACCCACTCTCCCG
CACTATAGCATGCTGTCCATC

Alignment

ORF - retro_cfam_479 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 53.93 %
• Parental protein coverage: 55.28 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GLLENANPLIYERSGERPVTAGEEDEQVPDSIDAREIFDLIRSINDPEHPLTLEELNVVEQVRVQVSDPE
          G.LE..N.L..E.SGE.......ED.QVP.S......FDLI.SI..PE.P..LE.LNVV.QV..QVSDPE
Retrocopy GELETSNLLVCEHSGEYLGIMNKEDKQVPVS-SVPGVFDLICSICVPELPQILEKLNVVQQVWLQVSDPE

Parental  STVAVAFTPTIPHCSMATL
          ..VA.AF.PT.PH.SM...
Retrocopy K-VAMAFIPTLPHYSMLSI

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	0.08 RPM	42.33 RPM
SRP017611_brain	0.00 RPM	16.99 RPM
SRP017611_kidney	0.07 RPM	53.89 RPM
SRP017611_liver	0.00 RPM	16.97 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_479 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_479 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_479 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000017164	1 retrocopy	retro_amel_1340,
Bos taurus	ENSBTAG00000013931	1 retrocopy	retro_btau_609,
Canis familiaris	ENSCAFG00000017035	2 retrocopies	retro_cfam_1450, retro_cfam_439,
Canis familiaris	ENSCAFG00000020394	2 retrocopies	retro_cfam_479 , retro_cfam_802,
Felis catus	ENSFCAG00000029216	2 retrocopies	retro_fcat_1464, retro_fcat_697,
Mustela putorius furo	ENSMPUG00000005303	2 retrocopies	retro_mputfur_1547, retro_mputfur_302,
Mus musculus	ENSMUSG00000031879	1 retrocopy	retro_mmus_2927,
Sarcophilus harrisii	ENSSHAG00000004698	1 retrocopy	retro_shar_590,
Tarsius syrichta	ENSTSYG00000005006	2 retrocopies	retro_tsyr_1305, retro_tsyr_149,