RetrogeneDB ID: retro_cfam_1841

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 7:20455070..20455385(+)
• Located in intron of: ENSCAFG00000013861

Retrocopy information

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

Parental gene information

• Parental gene symbol: ITPA
• Ensembl ID: ENSCAFG00000031613
• Aliases: None
• Description: inosine triphosphatase (nucleoside triphosphate pyrophosphatase) [Source:HGNC Symbol;Acc:6176]

Sequence

>retro_cfam_1841
CCCCTACCCTACATGAAGTGGTTTCTGGAGAAGTTAAAGCCTGTAGGTCTCTATCAGATCCTGGCTGGGTTCAAGGACAG
ACTTGTCTCTGTGCTCTGCACATTTGTACTCAGCACCAGGGGCCCTAGCAAGCCAGTGTCCCTATTTAGGGGCCAGATCA
TGGTGCCCAGAAGCTGCCAGGACTTTGGCTGGGACCCCTACTTTCAGCCTGATGGATACAAGCAGACGTATGCAAAGATG
CCCATAGCTGAGAAGAAGGCCATCTCCCATCACTTTCAGGCCCTTCTTGAGCTAGAAAAACACTTTTGCAGTCTG

Alignment

ORF - retro_cfam_1841 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.97 %
• Parental protein coverage: 56.77 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  PGPYIKWFLEKLKPEGLHQLLAGFEDKSAYALCTFAFSTGDPSEPVRLFRGQTSGRIVVPRGCRDFGWDP
          P.PY.KWFLEKLKP.GL.Q.LAGF.D.....LCTF..ST..PS.PV.LFR....G.I.VPR.C.DFGWDP
Retrocopy PLPYMKWFLEKLKPVGLYQILAGFKDRLVSVLCTFVLSTRGPSKPVSLFR----GQIMVPRSCQDFGWDP

Parental  CFQPDGYEQTYAEMPKAKKNAISHRFRALLELQKYFGSL
          .FQPDGY.QTYA.MP.A.K.AISH.F.ALLEL.K.F.SL
Retrocopy YFQPDGYKQTYAKMPIAEKKAISHHFQALLELEKHFCSL

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	14.70 RPM
SRP017611_brain	0.00 RPM	10.56 RPM
SRP017611_kidney	0.00 RPM	22.25 RPM
SRP017611_liver	0.00 RPM	8.48 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1841 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1841 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1841 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000011021	1 retrocopy	retro_amel_476,
Canis familiaris	ENSCAFG00000031613	1 retrocopy	retro_cfam_1841 ,
Felis catus	ENSFCAG00000013414	1 retrocopy	retro_fcat_1776,
Microcebus murinus	ENSMICG00000013833	1 retrocopy	retro_mmur_1207,
Mustela putorius furo	ENSMPUG00000008868	1 retrocopy	retro_mputfur_971,
Mus musculus	ENSMUSG00000074797	3 retrocopies	retro_mmus_2063, retro_mmus_3369, retro_mmus_3604,