RetrogeneDB ID: retro_meug_560

Retrocopy location

• Organism: Wallaby (Macropus eugenii)
• Coordinates: Scaffold137041:142..898(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PPP4C
• Ensembl ID: ENSMEUG00000000397
• Aliases: None
• Description: protein phosphatase 4, catalytic subunit [Source:HGNC Symbol;Acc:9319]

Sequence

>retro_meug_560
AAAGAATCCAACGTCCAAGAGATCCATTGTCCTGTCACCTTCTGCGGGGATGTCCATGGCCAATTCTACAACCTGATGGG
ACTCGTTCGAATTGGTGAGGTCTCCAGACACAAACTATCTTTTTATGGGTGACTATGTGGACAGAGGCTACTACTCAGTG
GAGACTGTGACTCTTCTTGTATCACTAAAGGTGTGCTATCCAGAGTGGATCACAATACTGAGGGGGAACCATGAGAGCTG
ACAGATCACACAAGTGTATACCTTTTATGATGAATGCCTGAGGAAGTCCGGCAATGCCAATGTGTGGAAAGACTTTACCC
ACCTGTTTGATTATCTCCCACTCATAGCATTAGTGGATGGACAGATATTTTGCCTCCATGGTGGCCTTTCTCCATCCATC
AATACACTGAATCATATCCGAGCCCTAGATCGTCTGCAAGAAGTTCCAGATGAAGGCCCAATCTGTGACCTGTTATGGCT
GATCCTGATGATCATGGTGGATGGGGCATTTCTCCACGAGGAGCTGGCTACACATTTGGACAGGACATTTCAGAAACATT
TAACCACACCAATGGCCTCACACTGGTTTCCTGGGCTCACCAACTTGTGATGAAGGGCTACAACGGGTATCACCACCGTA
ATGTGGTTACCATTTTCAGTGCATCCAATTACTGCTACCGTTGTGGGAAGCAGGCTGCTATCATGGAATTCGATGACACT
TTGAAATATTCCTTTCTTCAGTTTGACCCTGAACCC

Alignment

ORF - retro_meug_560 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.78 %
• Parental protein coverage: 92.34 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  EESNVQRVDSPVTVCGDIHGQFYDLKELFRVGGDV-PETNYLFMGDFVDRGFYSVETFLLLLALKVRYPD
          .ESNVQ....PVT.CGD.HGQFY.L..L.R..G.V.P.TNYLFMGD.VDRG.YSVET..LL..LKV.YP.
Retrocopy KESNVQEIHCPVTFCGDVHGQFYNLMGLVRI-GEV>PDTNYLFMGDYVDRGYYSVETVTLLVSLKVCYPE

Parental  RITLIRGNHESRQITQVYGFYDECLRKYGSVTVWRYCTEIFDYLSLSAIIDGKIFCVHGGLSPSIQTLDQ
          .IT..RGNHES.QITQVY.FYDECLRK.G...VW...T..FDYL.L.A..DG.IFC.HGGLSPSI.TL..
Retrocopy WITILRGNHES*QITQVYTFYDECLRKSGNANVWKDFTHLFDYLPLIALVDGQIFCLHGGLSPSINTLNH

Parental  IRTIDRKQEVPHDGPMCDLLW-SDPEDTTGWGVSPRGAGYLFGSDVVAQFNAANDIDMICRAHQLVMEGY
          IR..DR.QEVP..GP.CDLLW..DP.D..GWG.SPRGAGY.FG.D....FN..N.......AHQLVM.GY
Retrocopy IRALDRLQEVPDEGPICDLLW<ADPDDHGGWGISPRGAGYTFGQDISETFNHTNGLTLVSWAHQLVMKGY

Parental  KWHFNETVLTVWSAPNYCYRCGNVAAILELDEHLQKDFIIFEAAP
          .......V.T..SA.NYCYRCG..AAI.E.D..L...F..F...P
Retrocopy NGYHHRNVVTIFSASNYCYRCGKQAAIMEFDDTLKYSFLQFDPEP

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Macropus eugenii was not studied using RNA-Seq expression data.

ChIP-Seq

Macropus eugenii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_meug_560 retrocopy.

TSS

Macropus eugenii was not studied using FANTOM5 data.

Lab

retro_meug_560 was not experimentally validated.

Homology

Retrocopy orthology:

Macropus eugenii 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,