RetrogeneDB ID: retro_ogar_2285

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873609.1:6974298..6974956(+)
• Located in intron of: ENSOGAG00000007887

Retrocopy information

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

Parental gene information

• Parental gene symbol: UCHL3
• Ensembl ID: ENSOGAG00000017114
• Aliases: None
• Description: ubiquitin carboxyl-terminal esterase L3 (ubiquitin thiolesterase) [Source:HGNC Symbol;Acc:12515]

Sequence

>retro_ogar_2285
CAAGGTCAATGCTGGCTGCCTCCAGAGGCCAATCCTGAAGTCACCAACAGGTTTTTCAAACAACTAGGTTTACCCGCTAA
CTGGCAATTTGCTGATGTATGTGGAATGGTCCTGAACTCCTCGGCACAGCACCAAGACCAGTCTGTCCTGTGCTGCTTCT
CTTCCCTATTACAGAAAAGTATGAAGTATTCAGAAGAGAGGAGGAGGAAAATTAAAATCTCAGGGACAGGATGTTACGTC
ATTAGTGCATTTCATGAAGGAAACAATCAACAAGACCTGTGGAACAAATGGAGTGATCCACGATGTTGTGAACAATAAAG
ACAGATGCACTTTGAATCTGAACCAACCTTGAAAAAATTCCTGCCAGAGTCTGCATCAATGAGCCCTCAAGAACAAAGCA
GATACCTGGAGAGCTCTGGGCTACTCGAGTTACTCAAGAAATCAGAGCCCAGGAAGGCCAGGCTGAGGCACCAAGTATAG
ATGAAAAAGTGGATCCTCATTTTACTGCATTAATAGATGGGCATCTCAATGAATTAGATGGGTGGAAACTATTTCCAGTT
AACCGTGAGAAAACTAGGGATGAGACTTTATTAGAGGATGCACAGGAGTTTGCAAGAAGTTTATGGAGTGTGACCCAGAT
GAATTAAGATTTAACGCC

Alignment

ORF - retro_ogar_2285 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.62 %
• Parental protein coverage: 96.97 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  EGQRWLPLEANPEVTNQQFLKQLGLHPNWQFVDVYGM-DPELLSMVPRPVCAVLLLFPITEKYEVFRTEE
          .GQ.WLP.EANPEVTN..F.KQLGL..NWQF.DV.GM..PELL...PRPVC.VLLLFPITEKYEVFR.EE
Retrocopy QGQCWLPPEANPEVTNR-FFKQLGLPANWQFADVCGM<GPELLGTAPRPVCPVLLLFPITEKYEVFRREE

Parental  EE-KIKSQGQDVTSSVYFMKQTISNACGTIGLIHAIANNKDK-MHFESGSTLKKFLEESVSMSPEERARY
          EE.K.KSQGQDVTS.V.FMK.TI...CGT.G.IH...NNKD..MHFES..TLKKFL.ES.SMSP.E..RY
Retrocopy EE<KLKSQGQDVTSLVHFMKETINKTCGTNGVIHDVVNNKDR<MHFESEPTLKKFLPESASMSPQEQSRY

Parental  LENYD-AIRVTHETSAHEGQTEAPSIDEKVDLHFIALVHVDGHLYELDGRKPFPINHGETSDETLLEDAI
          LE....A.RVT.E..A.EGQ.EAPSIDEKVD.HF.AL...DGHL.ELDG.K.FP.N...T.DETLLEDA.
Retrocopy LESSG<ATRVTQEIRAQEGQAEAPSIDEKVDPHFTAL--IDGHLNELDGWKLFPVNREKTRDETLLEDAQ

Parental  E-VCKKFMERDPDELRFNA
          E.VCKKFME.DPDELRFNA
Retrocopy E<VCKKFMECDPDELRFNA

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_2285 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 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000012261	1 retrocopy	retro_cpor_1217,
Equus caballus	ENSECAG00000024190	1 retrocopy	retro_ecab_400,
Myotis lucifugus	ENSMLUG00000003442	1 retrocopy	retro_mluc_362,
Mus musculus	ENSMUSG00000022111	1 retrocopy	retro_mmus_177,
Oryctolagus cuniculus	ENSOCUG00000006789	1 retrocopy	retro_ocun_382,
Otolemur garnettii	ENSOGAG00000017114	1 retrocopy	retro_ogar_2285 ,
Rattus norvegicus	ENSRNOG00000009530	1 retrocopy	retro_rnor_2227,