RetrogeneDB ID: retro_cfam_1729

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 5:29816564..29816939(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CMPK1
• Ensembl ID: ENSCAFG00000004030
• Aliases: None
• Description: cytidine monophosphate (UMP-CMP) kinase 1, cytosolic [Source:HGNC Symbol;Acc:18170]

Sequence

>retro_cfam_1729
ACCATGAATTTGTTAATGAGGGAAATGGATCAGACAATGGCCACCATTGCTCAGAAGAATAAGTTCTTGATTGATGGGTT
TCCACGAAATTAAGACAACATTTAAGGTTGGAACAAAGCCATGGATGGGAAGGCAGGTGTGTCTTTGGTTCTCTTTTTCG
ACTCTAAAAATGAGATCTGTGTTGAACGATGTCTTGAGAGGGGAAACAGTAGTTAGTCCAATGATGACAACAGAGAGAGC
TTGGAAAAGAGAATTCAGACCTATCTTTAGTCAACACATCCAGTTATTGACATATGTGAAGAAATGTGAGGCATCAAGAA
AATAGATGCCTCTAAGTCTGCTGATGAAGTTGTGAAGATTTTGGACAAAGAAGGC

Alignment

ORF - retro_cfam_1729 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.19 %
• Parental protein coverage: 56.58 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  TISLLKREMDQTMAANAQKNKFLIDGFPRNQDNLQGWNKTMDGKADVSFVLFFDCNNEICIERCLERGKS
          T..LL.REMDQTMA..AQKNKFLIDGFPRN.DN..GWNK.MDGKA.VS.VLFFD..NEIC.ERCLERG.S
Retrocopy TMNLLMREMDQTMATIAQKNKFLIDGFPRN*DNI*GWNKAMDGKAGVSLVLFFDSKNEICVERCLERGNS

Parental  SGRSDDNRESLEKRIQTYLQSTKPIIDLYEEMGKVKKIDASKSVDEVFDEVVKIFDKEG
          S...DDNRESLEKRIQTYL.ST.P.ID..EEM...KKIDASKS.DEV....VKI.DKEG
Retrocopy S*SNDDNRESLEKRIQTYL*STHPVIDICEEM*GIKKIDASKSADEV----VKILDKEG

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	39.39 RPM
SRP017611_brain	0.00 RPM	29.85 RPM
SRP017611_kidney	0.00 RPM	49.86 RPM
SRP017611_liver	0.00 RPM	23.64 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1729 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1729 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1729 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000004030	1 retrocopy	retro_cfam_1729 ,
Choloepus hoffmanni	ENSCHOG00000004014	2 retrocopies	retro_chof_609, retro_chof_840,
Cavia porcellus	ENSCPOG00000014747	4 retrocopies	retro_cpor_1070, retro_cpor_1295, retro_cpor_417, retro_cpor_799,
Macaca mulatta	ENSMMUG00000017375	2 retrocopies	retro_mmul_1572, retro_mmul_66,
Mustela putorius furo	ENSMPUG00000012394	1 retrocopy	retro_mputfur_1061,
Mus musculus	ENSMUSG00000028719	1 retrocopy	retro_mmus_2576,
Rattus norvegicus	ENSRNOG00000007775	1 retrocopy	retro_rnor_1940,
Sus scrofa	ENSSSCG00000003885	1 retrocopy	retro_sscr_454,