RetrogeneDB ID: retro_oana_25

Retrocopy location

• Organism: Platypus (Ornithorhynchus anatinus)
• Coordinates: Contig108920:7..778(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PPP4C
• Ensembl ID: ENSOANG00000008136
• Aliases: None
• Description: protein phosphatase 4, catalytic subunit [Source:HGNC Symbol;Acc:9319]

Sequence

>retro_oana_25
GTTTGCGGGGATATACATGGGCAATTCTATGATTTTAAACAATTGCTGGAGGTGGGGAAGGATGTTCCCGAGACAAACTA
TTTGTTTATGGGAGACTTCGTTGATAGAGGCTATTATTCAGTGGAGACGTTTCTTTTACTGTTATGCTTCAAAGTTCGCT
ACCCAGATCGCATTACATTAATTCGTGGGAATCATGAATCCCGCCAAATAACACAAGTTTACGGATTTTACGACGAATGC
ATAAGGAAATATGGAAGTGTTAATGTTTGGCGGTACTGTACCGAGATTTTTGATTATTTTGCGATCGGTGCTATAATAGA
CGACCATTATTTTTGTGTTCATGGTGGACTCTCGCCTTCAATTTCTTCTATTGATGAAATAAGATGTTTAGACAGGAAGC
AAGAAGTTCCGCATGAGGGGCCTATGTGTGACTTGATGTGGTCGGATCCTGAAATTATTGAGGGCTGGGGGGCCAGCCCC
CGTGGTGCCGGTTTTCTTTTTGGGAGCGACGTAGTCAGGCAGTTTTGCTTTCTTAATAGGATTCAGGTAATTGCTAGAGC
ACATCAGCTTGTAATGGAGGGGTACAAGTGGTGGTTCAACAAAATGTTAATAACTGTTTGGTCTGCTCCCAACTACTGTT
ATAGGTGTGGTAACGTCGCTAGTATAATGGAATTGGACGAGAACCTAAATTGTAATTTCAAAACATTTGAAGCAGCGCCA
CCCAACAAAAGAGGGATTCTCGCGAAAAAGCCCCCTCCTGACTATTTCTTA

Alignment

ORF - retro_oana_25 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.09 %
• Parental protein coverage: 83.71 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VCGDIHGQFYDLKELFRVTGSAPKREGVSVWINEPRGLDGEERADFSNAAKVRYPDRITLIRGNHESRQI
          VCGDIHGQFYD.K.L..V....P............RG....E........KVRYPDRITLIRGNHESRQI
Retrocopy VCGDIHGQFYDFKQLLEVGKDVPETNYLFMGDFVDRGYYSVETFLLLLCFKVRYPDRITLIRGNHESRQI

Parental  TQVYGFYDECLRKYGSVTVWRYCTEIFDYLSLSAIIDGKIFCVHGGLSPSIQTLDQIRTIDRKQEVPHDG
          TQVYGFYDEC.RKYGSV.VWRYCTEIFDY....AIID...FCVHGGLSPSI...D.IR..DRKQEVPH.G
Retrocopy TQVYGFYDECIRKYGSVNVWRYCTEIFDYFAIGAIIDDHYFCVHGGLSPSISSIDEIRCLDRKQEVPHEG

Parental  PMCDLLWSDPEDTTGWGVSPRGAGYLFGSDVVAQFNAANDIDMICRAHQLVMEGYKWHFNETVLTVWSAP
          PMCDL.WSDPE...GWG.SPRGAG.LFGSDVV.QF...N.I..I.RAHQLVMEGYKW.FN....TVWSAP
Retrocopy PMCDLMWSDPEIIEGWGASPRGAGFLFGSDVVRQFCFLNRIQVIARAHQLVMEGYKWWFNKMLITVWSAP

Parental  NYCYRCGNVAAILELDEHLQKDFIIFEAAPQETRGIPSKKPVADYFL
          NYCYRCGNVA.I.ELDE.L...F..FEAAP...RGI..KKP..DYFL
Retrocopy NYCYRCGNVASIMELDENLNCNFKTFEAAPPNKRGILAKKPPPDYFL

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
SRP007412_brain	0.00 RPM	19.69 RPM
SRP007412_cerebellum	0.00 RPM	45.78 RPM
SRP007412_heart	0.00 RPM	14.88 RPM
SRP007412_kidney	0.00 RPM	16.58 RPM
SRP007412_liver	0.00 RPM	14.74 RPM
SRP007412_testis	0.00 RPM	23.84 RPM

ChIP-Seq

Ornithorhynchus anatinus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_oana_25 retrocopy.

TSS

Ornithorhynchus anatinus was not studied using FANTOM5 data.

Lab

retro_oana_25 was not experimentally validated.

Homology

Retrocopy orthology:

Ornithorhynchus anatinus does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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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,