RetrogeneDB ID: retro_ogar_3293

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873768.1:1391738..1392188(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: POP4
• Ensembl ID: ENSOGAG00000011168
• Aliases: None
• Description: processing of precursor 4, ribonuclease P/MRP subunit (S. cerevisiae) [Source:HGNC Symbol;Acc:30081]

Sequence

>retro_ogar_3293
GTGATCTACCATGCCTTTTCTCAGAAAGAGGCAAAAGACTCGGGTGTCCAGCAGGTGTGAGCCCAGAGGGCCAAGGCCTT
CATGAAGGCCTTCCTGAAGTGCAGCATGCCCCACATGAGCCAGCAAGCCTGTAAGGACCAGTTGGAGCGCTAGGCAGTCA
TTCTGGAGTACTTCACTTGCCCCAAGCAAAGGGAGAGGAGAAAGAAATCCAAAAGCCTTTCTGTCTGGCAGAGGAGGGAG
CTGAAACTCTTTGATATCAAACCAGAGCAGCAGAGATACAGCTTGTTTCTCCCTCTGCATGAGCTCTGGAAACAGTACAT
CAGGGACCTGTGCAATGGCCTTAAACCTGACACGCAGCCACAGATGATTCAAGCCAAGCTGTTAAAAGCAGATCTTCACG
GTGCTGTGATTTCAGTCACAAAATCCAAATGCCCTTCTTACACGGGTGTA

Alignment

ORF - retro_ogar_3293 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88. %
• Parental protein coverage: 68.18 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VIYHAFSQKEAKDLGVQQMGAQRAEAFMKAFLKRSTPHMSQQAREDQLDRKAVILEYFTRPKRRERRKKS
          VIYHAFSQKEAKD.GVQQ..AQRA.AFMKAFLK.S.PHMSQQA..DQL.R.AVILEYFT.PK.RERRKKS
Retrocopy VIYHAFSQKEAKDSGVQQV*AQRAKAFMKAFLKCSMPHMSQQACKDQLER*AVILEYFTCPKQRERRKKS

Parental  KGLSARQRRELHLFDIKPEQQRYSLFLPLHELWKQYIRDLCSGLKPDTQPQMIQAKLLKADLHGAVISVT
          K.LS..QRREL.LFDIKPEQQRYSLFLPLHELWKQYIRDLC.GLKPDTQPQMIQAKLLKADLHGAVISVT
Retrocopy KSLSVWQRRELKLFDIKPEQQRYSLFLPLHELWKQYIRDLCNGLKPDTQPQMIQAKLLKADLHGAVISVT

Parental  KSKCPSYVGV
          KSKCPSY.GV
Retrocopy KSKCPSYTGV

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_3293 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 5 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Mustela putorius furo	ENSMPUG00000008041	1 retrocopy	retro_mputfur_1088,
Oryctolagus cuniculus	ENSOCUG00000015974	1 retrocopy	retro_ocun_1367,
Otolemur garnettii	ENSOGAG00000011168	2 retrocopies	retro_ogar_3293 , retro_ogar_541,
Sorex araneus	ENSSARG00000004748	1 retrocopy	retro_sara_410,
Tupaia belangeri	ENSTBEG00000002194	6 retrocopies	retro_tbel_1225, retro_tbel_1516, retro_tbel_2043, retro_tbel_3671, retro_tbel_3821, retro_tbel_89,