RetrogeneDB ID: retro_cfam_1806

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 6:70311541..70311854(+)
• Located in intron of: ENSCAFG00000020387

Retrocopy information

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

Parental gene information

• Parental gene symbol: PLCB3
• Ensembl ID: ENSCAFG00000014542
• Aliases: None
• Description: phospholipase C, beta 3 (phosphatidylinositol-specific) [Source:HGNC Symbol;Acc:9056]

Sequence

>retro_cfam_1806
ACCCACTTGCTAGGGTTTGTGGAGTAGCAGAGGCTGTGAAGTCCAAAGGGGTCCAAGTCTGTCTGAGTGTCAATGTCACT
GTGACTGGCAAGTGGGTACGAGCCCACAACAAGGAAGGCAAAGTGCAGCTCCCGGGTGATCCTAATGGGGCCTTTGGGGA
GGTGAGAAATTTATTACAACATGATTCTTTGTTGCCACTCTTTGCAATTGCTTGGCTTAAGGGTTTCTCCATGGCAATGG
ATGAAGGTATGGTGAAGGCCTGAATGCAGAGCCTGAAGTGACAGGCCTCACCTGCCGTCTGGCCTCCAGCATC

Alignment

ORF - retro_cfam_1806 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.09 %
• Parental protein coverage: 54.82 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  THLPGFME-QAEALKAKGVQVIACLSVNDVFVTEAWGRAHNSGGKVRLLADPTGAFGKETDLLLDDSLVS
          THL.GF.E..AEA.K.KGVQV..CLSVN.V.VT..W.RAHN..GKV.L..DP.GAFG....LL..DSL..
Retrocopy THLLGFVE<VAEAVKSKGVQV--CLSVN-VTVTGKWVRAHNKEGKVQLPGDPNGAFGEVRNLLQHDSLLP

Parental  LFGNHRLKRFSMVIENGIVKS-LNVEPDGTGLTCSLAPNI
          LF....LK.FSM....G.VK..LN.EP..TGLTC.LA..I
Retrocopy LFAIAWLKGFSMAMDEGMVKA<LNAEPEVTGLTCRLASSI

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	96.26 RPM
SRP017611_brain	0.00 RPM	76.14 RPM
SRP017611_kidney	0.00 RPM	90.14 RPM
SRP017611_liver	0.00 RPM	78.02 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1806 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1806 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1806 has 8 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_408
Pan troglodytes	retro_ptro_313
Gorilla gorilla	retro_ggor_404
Pongo abelii	retro_pabe_310
Macaca mulatta	retro_mmul_504
Callithrix jacchus	retro_cjac_3013
Sus scrofa	retro_sscr_888
Equus caballus	retro_ecab_844

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000014542	2 retrocopies	retro_cfam_1806 , retro_cfam_896,