RetrogeneDB ID: retro_meug_1448

Retrocopy location

• Organism: Wallaby (Macropus eugenii)
• Coordinates: Scaffold40885:12197..12957(+)
• 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_1448
GGATCTGATGAAGGGACAAGTTTATCAGCTTTGCTTCCCCAACCCAGAAACCTGACCACAGAAGAGACTGACCGATGGCT
CCTGCCCTACGCTTTCTCTGGAAAACCCACTGCTGGCTCTGCTGACAGCAAACTCTCCAGACCAAGCCCCAAGACCCAAT
CTGCTTCTTCTACTTCCTCCTCTGCCCTTCTTGTGGGTGCCATCACCACTACTCCATCACCCTCAGCCATCCAAGCAGCT
GCCAAGACTGCTGCCCTACAGGTGACAAAGCAGATCACACCAGAGGAGGATGACAGGGATGAGGAAGTAGCCCCTGAGAA
CTTCTTCTCCCTTCCAGACAAGGCTGAGCTTCCTGGAGCTGAGCCATACCCTTACCCTGTCCCTGCTGCTTCTGAAGAGC
CACCCCCAGGCACAGAGCCAGATCCCACCTTTCAGGACGATGAGGCAAATGCTCCCCTTGAATTCAAGATGGTGGCTGGC
TCAAGTGGGGCTCCCTGGGTGCCTAAGCCTGGGGAGGACTACAGCAGTCAGCCCTACAACCAGTTCCCTACATATGGTGA
CGCTAATGCCCCTGGCCTTTACTATCAGGATTATTACAGTAGTGGCTACTACTCTGATCGGATCCAGCCTTAGCTCCCCC
CCAGGAGATTACCCCAGACGCCTCTTTCATTGATGATGGAGCATTTAAGCGGCTTCAGGCAAGAGGAACCCGGGAAGGGA
GGAGATTAATTTTCTGGAGATCAAAGGGGATGACCAGCTC

Alignment

ORF - retro_meug_1448 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.67 %
• Parental protein coverage: 51. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  GSGEGTGLSALLPQPKNLTTKETNRLLLPYAFSRKPTDGSADSKLSKPSPKTKSASSTSSSAPVVGATTT
          GS.EGT.LSALLPQP.NLTT.ET.R.LLPYAFS.KPT.GSADSKLS.PSPKT.SASSTSSSA..VGA.TT
Retrocopy GSDEGTSLSALLPQPRNLTTEETDRWLLPYAFSGKPTAGSADSKLSRPSPKTQSASSTSSSALLVGAITT

Parental  TPSPSAIKAAAKSAALQVTKQITQEEDDSDEEVAPENFFSLPDKAEPPGAEPYPYSVPAASEEPPPGTEP
          TPSPSAI.AAAK.AALQVTKQIT.EEDD.DEEVAPENFFSLPDKAE.PGAEPYPY.VPAASEEPPPGTEP
Retrocopy TPSPSAIQAAAKTAALQVTKQITPEEDDRDEEVAPENFFSLPDKAELPGAEPYPYPVPAASEEPPPGTEP

Parental  DPTFQDDAANAPLEFKMVAGSSGAPWVPKPGEDYSSQPYNQFPTYGDANATGVYYQDYYSSGYYPE-SDP
          DPTFQDD.ANAPLEFKMVAGSSGAPWVPKPGEDYSSQPYNQFPTYGDANA.G.YYQDYYSSGYY...SDP
Retrocopy DPTFQDDEANAPLEFKMVAGSSGAPWVPKPGEDYSSQPYNQFPTYGDANAPGLYYQDYYSSGYYSD<SDP

Parental  ALAPPQEITPDASFIDDEAFKRLQ-GKRNRGREEINFVEIKGDDQL
          ALAPPQEITPDASFIDD.AFKRLQ.GKRN.GREEINF.EIKGDDQL
Retrocopy ALAPPQEITPDASFIDDGAFKRLQ<GKRNPGREEINFLEIKGDDQL

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_1448 retrocopy.

TSS

Macropus eugenii was not studied using FANTOM5 data.

Lab

retro_meug_1448 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,