RetrogeneDB ID: retro_cfam_16

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 5:43094941..43095856(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCAFG00000018536
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: PPP4C
• Ensembl ID: ENSCAFG00000017089
• Aliases: None
• Description: Serine/threonine-protein phosphatase [Source:UniProtKB/TrEMBL;Acc:E2QU52]

Sequence

>retro_cfam_16
ATGGCGCCCCTAGACTTGGACAAGTATGTGGAGATAGCGCGGTTGTGCAAGTACCTACCGGAGAACGACCTGAAGCGGCT
ATGTGACTATGTTTGTGACCTCCTCTTAGAAGAGTCAAACGTCCAGCCAGTATCGACACCAGTAACAGTGTGTGGAGACA
TACACGGACAGTTTTATGACCTTTGCGAACTATTCAGAACTGGAGGTCAGGTTCCTGACACAAACTACATATTTATGGGT
GATTTTGTAGACAGAGGTTACTATAGTTTGGAGACCTTCACTTACCTTCTTGCACTAAAGGCTAAATGGCCTGATCGTAT
CACACTTTTGCGAGGAAATCATGAAAGTAGACAGATAACACAGGTGTATGGATTTTATGATGAGTGCCAAACCAAATATG
GAAATGCTAATGCCTGGAGATACTGTACCAAAGTTTTTGACATGCTCACAGTAGCAGCTTTAATAGATGAGCAGATTTTG
TGTGTTCATGGTGGTTTATCTCCTGATATCAAAACACTGGATCAAATTCGAACCATTGAACGGAATCAGGAAATTCCTCA
TAAAGGAGCCTTTTGTGATCTGGTTTGGTCAGATCCTGAAGACGTGGATACTTGGGCAATCAGTCCCGGAGGAGCAGGTT
GGCTTTTTGGCGCAAAGGTCACAAATGAGTTTGTTCATATCAACAACTTAAAACTCATCTGCAGAGCACACCAACAAGTG
CACGAAGGCTATAAATTTATGTTTGATGAGAAGCTGGTAACAGTATGGTCTGCTCCTAATTACTGCTATCGTTGTGGAAA
TATCGCTTCGATCATGGTCTTCAAAGATGTAAATACAAGAGAACCAAAGTTAGTCCGGGCAGTTCCAGATTCAGAACGTG
TTATTCCTCCCAGAACAACGACGCCGTATTTTCTC

Alignment

ORF - retro_cfam_16 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.93 %
• Parental protein coverage: 98.37 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  DLDRQIEQLRRCELIKESEVKALCAKAREILVEESNVQRVDSPVTVCGDIHGQFYDLKELFRVGGDVPET
          DLD...E..R.C....E...K.LC......L.EESNVQ.V..PVTVCGDIHGQFYDL.ELFR.GG.VP.T
Retrocopy DLDKYVEIARLCKYLPENDLKRLCDYVCDLLLEESNVQPVSTPVTVCGDIHGQFYDLCELFRTGGQVPDT

Parental  NYLFMGDFVDRGFYSVETFLLLLALKVRYPDRITLIRGNHESRQITQVYGFYDECLRKYGSVTVWRYCTE
          NY.FMGDFVDRG.YS.ETF..LLALK...PDRITL.RGNHESRQITQVYGFYDEC..KYG....WRYCT.
Retrocopy NYIFMGDFVDRGYYSLETFTYLLALKAKWPDRITLLRGNHESRQITQVYGFYDECQTKYGNANAWRYCTK

Parental  IFDYLSLSAIIDGKIFCVHGGLSPSIQTLDQIRTIDRKQEVPHDGPMCDLLWSDPEDTTGWGVSPRGAGY
          .FD.L...A.ID..I.CVHGGLSP.I.TLDQIRTI.R.QE.PH.G..CDL.WSDPED...W..SP.GAG.
Retrocopy VFDMLTVAALIDEQILCVHGGLSPDIKTLDQIRTIERNQEIPHKGAFCDLVWSDPEDVDTWAISPGGAGW

Parental  LFGSDVVAQFNAANDIDMICRAHQLVMEGYKWHFNETVLTVWSAPNYCYRCGNVAAILELDEHLQKDFII
          LFG..V...F...N....ICRAHQ.V.EGYK..F.E...TVWSAPNYCYRCGN.A.I.............
Retrocopy LFGAKVTNEFVHINNLKLICRAHQQVHEGYKFMFDEKLVTVWSAPNYCYRCGNIASIMVFKDVNTREPKL

Parental  FEAAPQETRGIPSKKPVADYFL
          ..A.P...R.IP.......YFL
Retrocopy VRAVPDSERVIP-PRTTTPYFL

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	14.70 RPM	43.80 RPM
SRP017611_brain	13.73 RPM	18.18 RPM
SRP017611_kidney	10.43 RPM	64.98 RPM
SRP017611_liver	4.50 RPM	20.30 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_16 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_16 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_16 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000015223	1 retrocopy	retro_amel_286,
Canis familiaris	ENSCAFG00000017089	1 retrocopy	retro_cfam_16 ,
Ciona savignyi	ENSCSAVG00000004266	1 retrocopy	retro_csav_27,
Equus caballus	ENSECAG00000022179	1 retrocopy	retro_ecab_911,
Felis catus	ENSFCAG00000014171	1 retrocopy	retro_fcat_1043,
Macropus eugenii	ENSMEUG00000000397	5 retrocopies	retro_meug_1014, retro_meug_1188, retro_meug_1336, retro_meug_560, retro_meug_859,
Ornithorhynchus anatinus	ENSOANG00000008136	1 retrocopy	retro_oana_25,
Pan troglodytes	ENSPTRG00000007984	1 retrocopy	retro_ptro_28,
Tursiops truncatus	ENSTTRG00000005532	1 retrocopy	retro_ttru_1015,