RetrogeneDB ID: retro_meug_1527

Retrocopy location

• Organism: Wallaby (Macropus eugenii)
• Coordinates: Scaffold43727:5177..5906(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PRCC
• Ensembl ID: ENSMEUG00000016202
• Aliases: None
• Description: papillary renal cell carcinoma (translocation-associated) [Source:HGNC Symbol;Acc:9343]

Sequence

>retro_meug_1527
CAGGGATCTGGTTTATCTGCTTTGCTTCCACAACCCAAAAACCTGACCACAAAAGACTAACCTATTACTCCTGCCCCACA
CTTTCTCCCGAAAACCTACTGATGGCTCTGCCAACACCACGCTGTCCAAACCATCCCACAAGACCAAATCTGCTGCTTCT
ACTTCCTCTTTTGCCCCTTTTGTGGGTGCCACCACTACTACCCCAGGGCCTTCAGTCATCAGAGCAGCTGCCCACAAGAA
TGCTGCCCTACAGGTGACAAAGCAGAGCACACAAGAGGAGAACGACAATGATGAGGAAGTAGCCCCTAAGAACTTCTCTC
TTATAGTCAAAGGTGAGCCCTACCCTTACCCTGTCCCTGCTGCTTCTGAACAGCCACCCCCAGCACAGAACCAGATTGCA
CCTTCCAGGAGGATACAGCCAGTGCTCCCCTTGAATTCAAGATGGTGGCTGGCTCAAGTGGGGCCCCCTGGGTGCCTAAG
CCTAGAGAGGACCACAGCAGTCAGCCCTAGTCCCTGTTCCCTACATTTGGTGACACTAAGGCCACTGGCATTTACTATCA
GGATTATTAGAGTAATGGCTACTAGCCTTATCCAGCCTTAGATCCCCCTCCCCAGGAGATTGCCCATGATGCCTCTTTCA
CTGATGATAACCCATTCAAGAGCCTTTACAGCAAGTGGAACCAGGAAAGGGAGGAGATTAACTTTGTGGAGATCAGAGGG
GATGACCAG

Alignment

ORF - retro_meug_1527 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.98 %
• Parental protein coverage: 50.2 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  EGTGLSALLPQ-PKNLTTKETNRLLLPYAFSRKPTDGSADSKLSKPSPKTKSASSTSSSAPVVGATTTTP
          .G.GLSALLPQ.PK....K.TN.LLLP..FSRKPTDGSA...LSKPS.KTKSA.STSS.AP.VGATTTTP
Retrocopy QGSGLSALLPQ>PKT*PQK-TNLLLLPHTFSRKPTDGSANTTLSKPSHKTKSAASTSSFAPFVGATTTTP

Parental  SPSAIKAAA-KSAALQVTKQITQEEDDSDEEVAPENFFSLPDKAEPPGAEPYPYSVPAASEEPP-PGTEP
          .PS.I.AAA.K.AALQVTKQ.TQEE.D.DEEVAP.N.FSL..K.EP....PYP..VPAASE.PP.P.TEP
Retrocopy GPSVIRAAAHKNAALQVTKQSTQEENDNDEEVAPKN-FSLIVKGEP---YPYP--VPAASEQPP<PSTEP

Parental  DPTFQDDAANAPLEFKMVAGSSGAPWVPKPGEDYSSQPYNQFPTYGDANATGVYYQDYYSSGY--YPESD
          D.TFQ.D.A.APLEFKMVAGSSGAPWVPKP.ED.SSQP...FPT.GD..ATG.YYQDY.S.GY..YP..D
Retrocopy DCTFQEDTASAPLEFKMVAGSSGAPWVPKPREDHSSQP*SLFPTFGDTKATGIYYQDY*SNGY*PYPALD

Parental  PALAPPQEITPDASFIDDEAFKRLQGKRNRGREEINFVEIKGDDQ
          P...PPQEI..DASF.DD..FK.L..K.N..REEINFVEI.GDDQ
Retrocopy P---PPQEIAHDASFTDDNPFKSLYSKWNQEREEINFVEIRGDDQ

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_1527 retrocopy.

TSS

Macropus eugenii was not studied using FANTOM5 data.

Lab

retro_meug_1527 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 3 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Macropus eugenii	ENSMEUG00000016202	2 retrocopies	retro_meug_1448, retro_meug_1527 ,
Monodelphis domestica	ENSMODG00000016779	1 retrocopy	retro_mdom_1829,
Otolemur garnettii	ENSOGAG00000024539	1 retrocopy	retro_ogar_335,