RetrogeneDB ID: retro_ogar_3324

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873778.1:1320802..1321558(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOGAG00000013650
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: UTP11L
• Ensembl ID: ENSOGAG00000016492
• Aliases: None
• Description: UTP11-like, U3 small nucleolar ribonucleoprotein, (yeast) [Source:HGNC Symbol;Acc:24329]

Sequence

>retro_ogar_3324
ATGGCTGTGGCTTTTCGGAAGGTGGCTAAGTCTCGACAGTGACATCGAGAGCAAAGTCAGCCTGACTTTCAAAAACATCT
GGGCCTGCTGGAGAAAAAGAAAGATTACAAACTTCGTGCAGATGACTACCATAAAAAACAAGAATACCTCAGAGCTCTCC
GGAAGAAGGCACTTGAAAAAAATCCAGATGAATTCTACTATAAAATGACTCGGGTTAAACTCCAGGATGGAGTTCATGTT
ATTAAGGAAACTAAGGAAGAAGTAACTCCAGAACAGCTAAAGCTGATGAGAACTCAGGATGTCAAATATATAGAAATGAA
AAGAGTTGCAAAAGCTAAGAAAATTGAAAGACTAAAATCAGAACTCCATCTGCTGGATTTCCAGGGGAAGCAACAGAATA
AGCATGTGTTCTTTTTTGATGCCAAAAAGGAAGTTGAACAGTTTGATATTGCAACTCACCTGCATACGGCTCTGGAACTA
GTCGACAGAGTCTTTAATAGACCCAGGATAGAGACGTTGCGGAAGGAAAAAGTGAAAGGAGTCACTCATCCATCTCGACT
TAAGCGGATAGCTAAAGAAAGGGAAAAGCAATATAACTGCCTGACACAGGGGATTGAGCGAGAGAAGAAATTGTTCGTTA
ATGCACAGAAAATTCAAACATGCAAAGATCTTCTGGATAAAACTCAGAAGGTGAAGGTGAAGAAAGAAACAGTGAACTCC
CCAGCTATTTACAAATTTCAGAGCCCTCAAAAACGT

Alignment

ORF - retro_ogar_3324 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.28 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAAAFRKAAKSRQREHRERSQPGFRKHLGLLEKKKDYKLRADDYHKKQEYLRALRKKALEKNPDEFYYKM
          MA.AFRK.AKSRQ..HRE.SQP.F.KHLGLLEKKKDYKLRADDYHKKQEYLRALRKKALEKNPDEFYYKM
Retrocopy MAVAFRKVAKSRQ*-HREQSQPDFQKHLGLLEKKKDYKLRADDYHKKQEYLRALRKKALEKNPDEFYYKM

Parental  TRVKLQDGVHVIKETKEEVTPEQLKLMRTQDVKYIEMKRVAEAKKIERLKSELHLLDFQGKQQNKHVFFF
          TRVKLQDGVHVIKETKEEVTPEQLKLMRTQDVKYIEMKRVA.AKKIERLKSELHLLDFQGKQQNKHVFFF
Retrocopy TRVKLQDGVHVIKETKEEVTPEQLKLMRTQDVKYIEMKRVAKAKKIERLKSELHLLDFQGKQQNKHVFFF

Parental  DTKKEVEQFDIATHLRTAPELVDRVFNRPRIETLQKEKVKGVTHPSRLKRIAKEREKQYNCLTQRIEREK
          D.KKEVEQFDIATHL.TA.ELVDRVFNRPRIETL.KEKVKGVTHPSRLKRIAKEREKQYNCLTQ.IEREK
Retrocopy DAKKEVEQFDIATHLHTALELVDRVFNRPRIETLRKEKVKGVTHPSRLKRIAKEREKQYNCLTQGIEREK

Parental  KLFVIAQKIQTRKDLLDKTQKVKVKKETVNSPAIYKFQSRRKR
          KLFV.AQKIQT.KDLLDKTQKVKVKKETVNSPAIYKFQS..KR
Retrocopy KLFVNAQKIQTCKDLLDKTQKVKVKKETVNSPAIYKFQSPQKR

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_3324 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 7 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000001043	1 retrocopy	retro_cpor_1084,
Microcebus murinus	ENSMICG00000001496	1 retrocopy	retro_mmur_894,
Myotis lucifugus	ENSMLUG00000001003	1 retrocopy	retro_mluc_2386,
Mus musculus	ENSMUSG00000028907	1 retrocopy	retro_mmus_1968,
Oryctolagus cuniculus	ENSOCUG00000007154	2 retrocopies	retro_ocun_1285, retro_ocun_669,
Otolemur garnettii	ENSOGAG00000016492	2 retrocopies	retro_ogar_3229, retro_ogar_3324 ,
Rattus norvegicus	ENSRNOG00000007174	1 retrocopy	retro_rnor_1838,