RetrogeneDB ID: retro_cfam_397

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 10:56015462..56016014(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PPAP2C
• Ensembl ID: ENSCAFG00000019734
• Aliases: None
• Description: phosphatidic acid phosphatase type 2C [Source:HGNC Symbol;Acc:9230]

Sequence

>retro_cfam_397
GCCATCCTGACTCTGGGAAACGCCCATAGAAGAATGGATCTACTGCAGAGGACACTATCTGGTACCCTATTGTCCAGACA
CCATCACCTGTGGACTCATGGCCAGGGTCACCATCACAGCCACCATCACCCCCGTCTCAGCCAGCGAGGCCTCCCTGGTG
TACAGAGACCACCTCTATTCCCACTCCAACTTCAACCGCTTCAGCCACTATGTGGCTGCCGTGGACAAGGTGATGGGGAA
GTTCCTGTTGGGGCTGCAGTGAGTCAGTCGCTGACAGACCTGGGCCAAGTACACGATGGCCAGTCTGTGGTCCAACTTCC
TGGAGGTGTGTGACCCCCACTGGAGCCCCGGCAACTGCGCGAACTCTGTGCAGTTGGAGAAGGTATGCAGGGGAAGCCTG
GCTAGCTGACTGCCTTTCCACTGGGACACTCCCCCTTTGGGATGTACAGCATGCTGCTCCGGGAGCTCTGTGTGCAGGCC
CAGCTCCGCTGGAAGTGGGCACGACTTCTGTGGCCCACAGAGCACTTCTTCCCGTTGGCCTTTGCACTCCAT

Alignment

ORF - retro_cfam_397 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.56 %
• Parental protein coverage: 64.93 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  AILTLVNA-PYKRGFYCADDSIRYP-YRPDTITHGLMAGVTITATVVLVSAGEAYLVYTDRLYSRSDFN-
          AILTL.NA.P.K.G...A.D.I.YP.Y.PDTIT.GLMA.VTITAT...VSA.EA.LVY.D.LYS.S.FN.
Retrocopy AILTLGNA<P*KNGS-TAEDTIWYP<YCPDTITCGLMARVTITATITPVSASEASLVYRDHLYSHSNFNR

Parental  --NYVAAVYKVLGTFLFG-AAVSQSLTDL-AKYMIGRLRPNFLAVCDPDWSRVNCSLYVQVEKVCR-GSP
          ...YVAAV.KV.G.FL.G.AAVSQSLTDL.AKY....L..NFL.VCDP.WS..NC...VQ.EKVCR.G.P
Retrocopy FSHYVAAVDKVMGKFLLG<AAVSQSLTDL>AKYTMASLWSNFLEVCDPHWSPGNCANSVQLEKVCR<GKP

Parental  ANVTESRLSFYSGHSSFGMYCMMFLALYVQARLCWKWARLLRPTVQFFLLAFALY
          ...T.....F..GHS.FGMY.M....L.VQA.L.WKWARLL.PT..FF.LAFAL.
Retrocopy G*LT----AFPLGHSPFGMYSMLLRELCVQAQLRWKWARLLWPTEHFFPLAFALH

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	6.72 RPM
SRP017611_brain	0.16 RPM	14.37 RPM
SRP017611_kidney	0.13 RPM	74.62 RPM
SRP017611_liver	0.00 RPM	16.90 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_397 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_397 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_397 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000019734	1 retrocopy	retro_cfam_397 ,
Felis catus	ENSFCAG00000024319	1 retrocopy	retro_fcat_483,
Ictidomys tridecemlineatus	ENSSTOG00000019777	2 retrocopies	retro_itri_1139, retro_itri_1721,