RetrogeneDB ID: retro_cfam_896

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 2:40515039..40515507(+)
• Located in intron of: None

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_896
GTGGGAGATGCCATCCCTTCGGTGATAGTTTTTGAAGGGGAACCTGGAAACAAGGTGAACCTGGCAGAGCTGTTCAAGGG
CAAAAAGGGGGTGCTGTTTGGAGTCCCTAGGTCCTTTAGCCCTGGCTGTTCCAAGACCCACCTGCCAGGATTCATGGAGC
AGGCTGAGGCTCTGAAGGCCAAGGGGGTCCAAGTGATAGCCTGTCTGAGCGTTAATGATGTCTTCGTGACTGAGGCCTGG
GGACGAGCTCACAACTCAGGAGGCAAGGTTAGGCTGTTGGCTGACCCCACTGGGGCCTTTGGGAAGGAGACAGATTTGTT
ACTGGATGATTCATTGGTATCTCTCTTTGGAAATCATCAGCTCAAGAGGTTCTCTATGGTGATAGAGAATGGCATAGTGA
AGTCCTTGAATGTGGAGCCAGATGGTACAGGCCTCACCTGCAGCCTGGCTCCCAACATCCTCTCGCGC

Alignment

ORF - retro_cfam_896 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.51 %
• Parental protein coverage: 79.19 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VGDAIPSVTVFEGEPGNEVNLAELFKGKKGVLFGVPGAFTPGCSKTHLPGFMEQAEALKAKGVQVIACLS
          VGDAIPSV.VFEGEPGN.VNLAELFKGKKGVLFGVP..F.PGCSKTHLPGFMEQAEALKAKGVQVIACLS
Retrocopy VGDAIPSVIVFEGEPGNKVNLAELFKGKKGVLFGVPRSFSPGCSKTHLPGFMEQAEALKAKGVQVIACLS

Parental  VNDVFVTEAWGRAHNSGGKVRLLADPTGAFGKETDLLLDDSLVSLFGNHRLKRFSMVIENGIVKSLNVEP
          VNDVFVTEAWGRAHNSGGKVRLLADPTGAFGKETDLLLDDSLVSLFGNH.LKRFSMVIENGIVKSLNVEP
Retrocopy VNDVFVTEAWGRAHNSGGKVRLLADPTGAFGKETDLLLDDSLVSLFGNHQLKRFSMVIENGIVKSLNVEP

Parental  DGTGLTCSLAPNILSQ
          DGTGLTCSLAPNILS.
Retrocopy DGTGLTCSLAPNILSR

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	0.17 RPM	96.26 RPM
SRP017611_brain	0.08 RPM	76.14 RPM
SRP017611_kidney	0.07 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_896 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_896 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_896 has 0 orthologous retrocopies within eutheria group .

---

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 ,