RetrogeneDB ID: retro_cfam_1368

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 3:26566442..26566643(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SEPW1
• Ensembl ID: ENSCAFG00000004074
• Aliases: None
• Description: Canis lupus familiaris selenoprotein W, 1 (SEPW1), mRNA. [Source:RefSeq mRNA;Acc:NM_001115012]

Sequence

>retro_cfam_1368
CTTAAGCTCAAGAAGAAGTTAGAAGATGAGTCCCCTGGATGCTTGGACATCTGAGGCAAGAGGACTCCTCAGGCCACCAG
CCTCTCTGAAGTGATGGTAGCAGGGATGTTGGTTCACTCCAAGAACACAGGTGATGGCTACATGGACATGGAGAGCAAGC
TTCTGAAGCTGGTGGCTGAAATCAAGGCCACCTTGGCTCAG

Alignment

ORF - retro_cfam_1368 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.64 %
• Parental protein coverage: 91.78 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LQLKKKLEDEFPGCLDICGEGTPQATGFFEVTVAGKLVHSKKRGDGYVDTESKFLRLVAAIKTALAQ
          L.LKKKLEDE.PGCLDI.G..TPQAT...EV.VAG.LVHSK..GDGY.D.ESK.L.LVA.IK..LAQ
Retrocopy LKLKKKLEDESPGCLDI*GKRTPQATSLSEVMVAGMLVHSKNTGDGYMDMESKLLKLVAEIKATLAQ

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	153.55 RPM
SRP017611_brain	0.08 RPM	203.01 RPM
SRP017611_kidney	0.00 RPM	79.44 RPM
SRP017611_liver	0.07 RPM	26.10 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1368 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1368 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1368 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000015208	1 retrocopy	retro_amel_1135,
Bos taurus	ENSBTAG00000008203	2 retrocopies	retro_btau_1527, retro_btau_756,
Canis familiaris	ENSCAFG00000004074	1 retrocopy	retro_cfam_1368 ,
Choloepus hoffmanni	ENSCHOG00000013206	2 retrocopies	retro_chof_1486, retro_chof_61,
Felis catus	ENSFCAG00000015176	2 retrocopies	retro_fcat_108, retro_fcat_186,
Mustela putorius furo	ENSMPUG00000004433	1 retrocopy	retro_mputfur_326,
Rattus norvegicus	ENSRNOG00000013548	2 retrocopies	retro_rnor_1819, retro_rnor_688,
Ictidomys tridecemlineatus	ENSSTOG00000001294	1 retrocopy	retro_itri_578,