RetrogeneDB ID: retro_ogar_335

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873520.1:31503186..31503926(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PRCC
• Ensembl ID: ENSOGAG00000024539
• Aliases: None
• Description: papillary renal cell carcinoma (translocation-associated) [Source:HGNC Symbol;Acc:9343]

Sequence

>retro_ogar_335
CCCCCAAGGCATGAGACGCCCCTGTGGCTGTTGCTGCCCCCACCCACCGGAGACTCCAGGCTTCAACCTCCTCCCCCGTT
GCCTCTCAGCCTGGGTGGCTTCCTTCTACCTGCAGGCGTGAGCCCGGCTGAGGCAGCGGGAGGTGGGGAGGGGTTGGGGT
TCGGCCCCCACCCCCCCACCCCCAGCCCCTGGCTTCGCAAGCCAAAGAAGAGGTAAGAGCCTGTGAGGATCGCGGCACTG
GAGCTGCATAAGGGAGATTCAGATTCCGAGGAGGATGAACCCACAAAGAAGAAAACTGTCCTTCAGGGATCCAGTGAGGG
GACTGGTCTGTTTGCCTGGCTTTCCCAACCTCAAAAACTGACTGTGAAAGAGACTAACAGGTTGCTCCTGCCCCAGCCTT
CTCCCGCAAACCCTCCGGTGGCTCCCCTGATACTAAGCCCTCTAGACTGGCTTCTAAGACCAAGACTTCCCCTCTTGCCC
CTGTTGTGGGCACTACAACCAGAACTCTGTCACCTTCTGCTATCAAGGTTGCTGCCAAGAGTGCAGCTCTGCAGGTGACC
AAGCAAATCACACAAGGGGAGGGTGACAGTGATGAGGAAGTAGCCCCGGAGAACTTTTTCTCCCTCCCTCAAAAGGCTGA
GCCACCTGGAGTCGAGCCATACCCTTACCCCGTCCCCACTGTCCCTGAGGAGCTGCCTCCAGGCATGGAACCAGAGCCCG
CTTTCCAGCACGAAGCAGCC

Alignment

ORF - retro_ogar_335 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.49 %
• Parental protein coverage: 50.51 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  PPTGDPRLQPPPPLPFGLGGFPPPPGVSPAEAAGVGEGLGLGLPSPRGPGLSLPPPIGGAGPPMGLPKPK
          PP.....L....P.P.G.....PPP...P....G.....G.......G.G..L............L.KPK
Retrocopy PPRHETPLWLLLPPPTGDSRLQPPPPL-PLSLGGFLLPAGVSPAEAAGGGEGLGFXXXXXXXXXWLRKPK

Parental  KRKEPVRIAAPELHKGDSDSEEDEPTKKKTVLQGSSEGTGLSALLPQPKNLTVKETNRLLLPH-AFSRKP
          KR.EPVRIAA.ELHKGDSDSEEDEPTKKKTVLQGSSEGTGL.A.L.QP..LTVKETNRLLLP..AFSRKP
Retrocopy KR*EPVRIAALELHKGDSDSEEDEPTKKKTVLQGSSEGTGLFAWLSQPQKLTVKETNRLLLPQ<AFSRKP

Parental  SDGSSDTKPSRLASKTKTSPLAPVVGTTTTTPSPSAIKAAAKSAALQVTKQITQEEDDSDEEVAPENFFS
          S.GS.DTKPSRLASKTKTSPLAPVVGTTT.T.SPSAIK.AAKSAALQVTKQITQ.E.DSDEEVAPENFFS
Retrocopy SGGSPDTKPSRLASKTKTSPLAPVVGTTTRTLSPSAIKVAAKSAALQVTKQITQGEGDSDEEVAPENFFS

Parental  LPEKAEPPGVEPYPYPVPTVPEELPPGTEPEPAFQDDAA
          LP.KAEPPGVEPYPYPVPTVPEELPPG.EPEPAFQ..AA
Retrocopy LPQKAEPPGVEPYPYPVPTVPEELPPGMEPEPAFQHEAA

Legend:

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

Expression

RNA-Seq

Otolemur garnettii was not studied using RNA-Seq expression data.

ChIP-Seq

Otolemur garnettii was not studied using ChIP-Seq data.

EST

Otolemur garnettii was not studied using EST data.

TSS

Otolemur garnettii was not studied using FANTOM5 data.

Lab

retro_ogar_335 was not experimentally validated.

Homology

Retrocopy orthology:

Otolemur garnettii 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 ,