RetrogeneDB ID: retro_ogar_541

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873523.1:23857784..23858273(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOGAG00000032583
• Aliases: None
• Status: KNOWN_PSEUDOGENE

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_541
GTGGTCTACCACGCCTTTTCTCAGAAAGAGGCAGAAGACTTGCGTGTCCAGATGGGAGCCAGGCGGGCCGAGGCCTTCAT
GAAGGCCTTCCCGAAGCGCAGCACGGCCCACATGGGCCAGCAAGCCCCTGAGGACCAGCGGGAGCTCAAGGCCGTCATTC
TGGAGTACTTCACTCGCCCCAAGCGAAGGGAGAGGAGAAAGAAATCCAAAGCCCTTTCTGCCCGACAGAGGAGGGACCTG
CAGCTCTTTGATATCAAACCAGAGCAGCAGAGATACAGCCTGTTTCTCCCTCTGCATGGGCTCTGGAAACAGTACATCAG
GGACCTGTGCAATGGCCTTAAACCTGACACGCAGCCACAGATGATTCAAGCCAAGCTTTTAAAGGCAGATCTTCATGGCG
CTGTGATTTCAGTCACAAAATCCAAATGCCCTTCTTATGTGTGTGTTACCGGAATCTTTCTGCAGGAAACAAAGCACATC
CTCAAAATT

Alignment

ORF - retro_ogar_541 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.2 %
• Parental protein coverage: 74.55 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VIYHAFSQKEAKDLGVQQMGAQRAEAFMKAFLKRSTPHMSQQAREDQLDRKAVILEYFTRPKRRERRKKS
          V.YHAFSQKEA.DL.VQ.MGA.RAEAFMKAF.KRST.HM.QQA.EDQ...KAVILEYFTRPKRRERRKKS
Retrocopy VVYHAFSQKEAEDLRVQ-MGARRAEAFMKAFPKRSTAHMGQQAPEDQRELKAVILEYFTRPKRRERRKKS

Parental  KGLSARQRRELHLFDIKPEQQRYSLFLPLHELWKQYIRDLCSGLKPDTQPQMIQAKLLKADLHGAVISVT
          K.LSARQRR.L.LFDIKPEQQRYSLFLPLH.LWKQYIRDLC.GLKPDTQPQMIQAKLLKADLHGAVISVT
Retrocopy KALSARQRRDLQLFDIKPEQQRYSLFLPLHGLWKQYIRDLCNGLKPDTQPQMIQAKLLKADLHGAVISVT

Parental  KSKCPSYVGVTGILLQETKHVFKI
          KSKCPSYV.VTGI.LQETKH..KI
Retrocopy KSKCPSYVCVTGIFLQETKHILKI

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_541 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,