RetrogeneDB ID: retro_meug_1014

Retrocopy location

• Organism: Wallaby (Macropus eugenii)
• Coordinates: Scaffold25960:20409..21183(-)
• 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_1014
GAAATCCTAATGAAAGAGTCCAACGTTCAGGAGATCTCTTGTCCCATTATTGTCTGCGGTGATATTCATGGTCAATTTCA
GGATCTTTTGCAAATCTTTACGATTGGTGGGGAAATACCAGACAAAAACTACTTGTTTTTGGGTGACTATGTTGACAGAG
GCTTGTACTCAGTGGAGACTGTGACTTTACTTGTATCTTTAAAAGTGCAATATCCAGAGTGCATTACACTATTGAGAGGA
AACCACGAGAGTCGGGAAGTTACTCAAGCTTATGGTTTTTATGATGAATGCCAAAAGAAGTATGGAAATGCCAATGTCTG
GAAATATTTTACAGACTTATTCGATTATCTCCCCCTTACAGCTTTAGTTGACAGCCAGATATTTTGCGTCCATGGGGGTC
TGTCTCCCTCCATAGATACCCTGGATCATATAAGAGCTTTGGATCGCTTTAAAGATATACCCACGAGTGGACCAATGTGT
GATCTGTTATGGTCTGATCCAGATGATATGGAGGGTTGGGGGCCCTCTCCAAGAGGGGCTGGCTATACATTTGGACCAGA
CATTTCTGAAATATTTAACCACACCAATGAGCTTTCGCTGATTACCCGGGGTCACCAACTTGCAGAGGAGGGTTATTTCT
GGAATCATAATGAAAGGGTGGTGACCATTTTCAGTGCACCCAATTATTGTAACCGTTTTGGGAACCAGGCTGCTGTCATG
GAACTGGATGATCCTGTAAAATATTCCTTCATACAGTTTGACCAAGCACTTCAA

Alignment

ORF - retro_meug_1014 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.63 %
• Parental protein coverage: 94.16 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EILVEESNVQRVDSPVTVCGDIHGQFYDLKELFRVGGDVPETNYLFMGDFVDRGFYSVETFLLLLALKVR
          EIL..ESNVQ....P..VCGDIHGQF.DL...F..GG..P..NYLF.GD.VDRG.YSVET..LL..LKV.
Retrocopy EILMKESNVQEISCPIIVCGDIHGQFQDLLQIFTIGGEIPDKNYLFLGDYVDRGLYSVETVTLLVSLKVQ

Parental  YPDRITLIRGNHESRQITQVYGFYDECLRKYGSVTVWRYCTEIFDYLSLSAIIDGKIFCVHGGLSPSIQT
          YP..ITL.RGNHESR..TQ.YGFYDEC..KYG...VW.Y.T..FDYL.L.A..D..IFCVHGGLSPSI.T
Retrocopy YPECITLLRGNHESREVTQAYGFYDECQKKYGNANVWKYFTDLFDYLPLTALVDSQIFCVHGGLSPSIDT

Parental  LDQIRTIDRKQEVPHDGPMCDLLWSDPEDTTGWGVSPRGAGYLFGSDVVAQFNAANDIDMICRAHQLVME
          LD.IR..DR....P..GPMCDLLWSDP.D..GWG.SPRGAGY.FG.D....FN..N....I.R.HQL..E
Retrocopy LDHIRALDRFKDIPTSGPMCDLLWSDPDDMEGWGPSPRGAGYTFGPDISEIFNHTNELSLITRGHQLAEE

Parental  GYKWHFNETVLTVWSAPNYCYRCGNVAAILELDEHLQKDFIIFEAAPQ
          GY.W..NE.V.T..SAPNYC.R.GN.AA..ELD......FI.F..A.Q
Retrocopy GYFWNHNERVVTIFSAPNYCNRFGNQAAVMELDDPVKYSFIQFDQALQ

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_1014 retrocopy.

TSS

Macropus eugenii was not studied using FANTOM5 data.

Lab

retro_meug_1014 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,