RetrogeneDB ID: retro_cfam_630

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 14:22373798..22374701(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PPP2CA
• Ensembl ID: ENSCAFG00000001010
• Aliases: None
• Description: Canis lupus familiaris protein phosphatase 2, catalytic subunit, alpha isozyme (PPP2CA), mRNA. [Source:RefSeq mRNA;Acc:NM_001003063]

Sequence

>retro_cfam_630
ATGGATGAGAAGGTATTCACCAAGGAGCTGGACCAGTGGATCGAATGGCTGAAGGGTACAAAGAGCTGTCAGAGTCCCAG
GTCAAGAGCCTTTGCCAGAAGGCTAAAGAAATCCTGACAAAAGAATGCAACATGCAAGAGGTTCCATATCCAGTCACCAT
CTGTGGAGATGTGCAGGGACAATTTCAGGATCTCATGAACTGTTTAGGTTTGGTGAGAAATCACCAGGTACAAACTACCT
GTTTATGAGAGATCATGCTGACAGAGGATATTACACAGTTGAAACAGTCACTCCTGTTGTAGCTCTTCAGGTCTGTTACC
ATGAATGCATCACCATTCTCCTAGGAAATCACGAGAGTAGACAGATCACACAAGTCTACGATGAGTGTTTAGTGAAATAT
GGAAATGCAAATATTTGGAAACATTTTATGTATCTTTTTGACTTTTCCTTTCACTGCTTGGTGGATAGGCAGATATTCTG
TCTACATGGTGGACTCTCATCATGCCTACATACAGTGGATCACATCAGAGTGCTTGATCACCTAGAAGTCCCTCATGAGG
GTCTAATGTGTGACTTGTGGTCAGATGCAGACAATCATTTGGGTTAGGGTGTATCTCCTCGAAGAGCTGGTTACACCTTT
GGGCAAGACATTTCCAAAACATTTAATCATGCCAATGGCCTCACGTTGGTGTCCAGAGCTCACCAGCTAGTGATGGAGGG
ATATAACTGGTGCTTAAGACTGGAGTGTCATAATAATTTTTAGTGCTCCAAACTATTGTTATCATTGTGGTATTCAAGCT
GTGATCATGGAACTTGATGATAATCTATAATACTTTCTTGCAGTTTGATCCAGCACCTAGCAGAGGAGAGCCAAATATTA
CTCATAGTACTCCAGAAAGCTTC

Alignment

ORF - retro_cfam_630 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.72 %
• Parental protein coverage: 99.68 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MDEKVFTKELDQWIEQLNECK-QLSESQVKSLCEKAKEILTKESNVQEVRCPVTVCGDVHGQFHDLM-EL
          MDEKVFTKELDQWIE.L...K..LSESQVKSLC.KAKEILTKE.N.QEV..PVT.CGDV.GQF.DLM.EL
Retrocopy MDEKVFTKELDQWIEWLKGTK<ELSESQVKSLCQKAKEILTKECNMQEVPYPVTICGDVQGQFQDLM<EL

Parental  FRIGGKSPDTNYLFMGDYVDRGYYSVETVTLLVALKVRYRERITILRGNHESRQITQVYGFYDECLRKYG
          FR.G.KSP.TNYLFM.D..DRGYY.VETVT..VAL.V.Y.E.ITIL.GNHESRQITQV...YDECL.KYG
Retrocopy FRFGEKSPGTNYLFMRDHADRGYYTVETVTPVVALQVCYHECITILLGNHESRQITQV---YDECLVKYG

Parental  NANVWKYFTDLFDYLPLTALVDGQIFCLHGGLSPSIDTLDHIRALDRLQEVPHEGPMCDLLWSDPDDRGG
          NAN.WK.F..LFD......LVD.QIFCLHGGLS....T.DHIR.LD.L.EVPHEG.MCDL.WSD.D...G
Retrocopy NANIWKHFMYLFDF-SFHCLVDRQIFCLHGGLSSCLHTVDHIRVLDHL-EVPHEGLMCDL-WSDADNHLG

Parental  WGISPRGAGYTFGQDISETFNHANGLTLVSRAHQLVMEGYNWCH-DRNVVTIFSAPNYCYRCGNQAAIME
          .G.SPR.AGYTFGQDIS.TFNHANGLTLVSRAHQLVMEGYNWC..D..V..IFSAPNYCY.CG.QA.IME
Retrocopy *GVSPRRAGYTFGQDISKTFNHANGLTLVSRAHQLVMEGYNWCL>DWSVIIIFSAPNYCYHCGIQAVIME

Parental  LDDTLKYSFL-QFDPAPRRGEPHVTRRTPDYF
          LDD.L.Y.FL.QFDPAP.RGEP..T..TP..F
Retrocopy LDDNL*Y-FL>QFDPAPSRGEPNITHSTPESF

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	106.34 RPM
SRP017611_brain	0.00 RPM	107.74 RPM
SRP017611_kidney	0.00 RPM	77.33 RPM
SRP017611_liver	0.00 RPM	27.12 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_630 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_630 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_630 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000001010	1 retrocopy	retro_cfam_630 ,
Gadus morhua	ENSGMOG00000015957	3 retrocopies	retro_gmor_25, retro_gmor_33, retro_gmor_34,