RetrogeneDB ID: retro_ogar_1868

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873570.1:1297486..1298266(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: UBA3
• Ensembl ID: ENSOGAG00000007771
• Aliases: None
• Description: ubiquitin-like modifier activating enzyme 3 [Source:HGNC Symbol;Acc:12470]

Sequence

>retro_ogar_1868
TTAGATACATGTAAAGTTCTAGTCATTGGAGCTGGCAGCTTAGGATGTGAGCTCCTGAAAACCTGGCATTGTCTGGTTTT
CAACAGATTAATGTTATAGACATGGACACTATAGATGTTTCCAATCTAAATAGGCGATTTTTATTTAGGCCTAAAGATGT
TGGAAGACCTAAGGCTGAATTTGCTGTAGAATTTATAGATGACAGAGTTCCTAATTGCAATGTAGGTCCACATTTCAACA
AGATTCAGGATTTTAACTATACTTTCTACTGATAATTTCATATTTTTGTATGTGGACTGAACTCTACCATAGCCAGAAGA
TGGATAAATGGTATGCTGATATCTCTTCTAAATTATGAAGATGGTGTGTTAGATCCAAGCTCCATTGTTCCTTTGATCGA
TGGTGGGACAGAAGGTTCTAAAGGAAATGCAAGGGTAATTCTGCCTGGAATGACTGCTTGTATTGAGTGCACACTGGAAC
TTTATCCACCACAGATCAATTTTCCCATGTGCACCATTGCATCTATGCCCAGGCTACCTGAACACTGTATTGAGTATGTA
AGGGTGTTGCAGTGGCCTAAGGAGCAGCCTTTTGGAGAAGGGGTTCCATTAGATAGAGATGATCCTGAACATATTCAATG
GATTTTCCAAAAATCCCTAGAGAAAGCATCACAATATAGTATTACGGGGTGTTACATATAGACTCACTCAAGGAGTAGTA
ATCATTCTTGCAGTAGCTTCCACAAATGCAGTCATTGCAGCTGTGTGTGCCACTGAGGTT

Alignment

ORF - retro_ogar_1868 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.29 %
• Parental protein coverage: 56.59 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LDTCKVLVIGAGGLGCELLK-NLALSGFRQIHVIDMDTIDVSNLNRQFLFRPKDVGRPKAEVAAEFLNDR
          LDTCKVLVIGAG.LGCELLK.NLALSGF.QI.VIDMDTIDVSNLNR.FLFRPKDVGRPKAE.A.EF..DR
Retrocopy LDTCKVLVIGAGSLGCELLK<NLALSGFQQINVIDMDTIDVSNLNRRFLFRPKDVGRPKAEFAVEFIDDR

Parental  VPNCNVVPHFNKIQDFNDTFYRQFHIIVCGLDSIIARRWINGMLISLLNYEDGVLDPSSIVPLIDGGTEG
          VPNCNV.PHFNKIQDFN.TFY..FHI.VCGL.S.IARRWINGMLISLLNYEDGVLDPSSIVPLIDGGTEG
Retrocopy VPNCNVGPHFNKIQDFNYTFY**FHIFVCGLNSTIARRWINGMLISLLNYEDGVLDPSSIVPLIDGGTEG

Parental  FKGNARVILPGMTACIECTLELYPPQINFPMCTIASMPRLPEHCIEYVRVLQWPKEQPFGEGVPLDGDDP
          .KGNARVILPGMTACIECTLELYPPQINFPMCTIASMPRLPEHCIEYVRVLQWPKEQPFGEGVPLD.DDP
Retrocopy SKGNARVILPGMTACIECTLELYPPQINFPMCTIASMPRLPEHCIEYVRVLQWPKEQPFGEGVPLDRDDP

Parental  EHIQWIFQKSLERASQYSI-RGVTYRLTQGVVKRIIPAVASTNAVIAAVCATEV
          EHIQWIFQKSLE.ASQYSI.RGVTYRLTQGVV..II.AVASTNAVIAAVCATEV
Retrocopy EHIQWIFQKSLEKASQYSI>RGVTYRLTQGVV--IILAVASTNAVIAAVCATEV

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_1868 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 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000010117	1 retrocopy	retro_amel_204,
Choloepus hoffmanni	ENSCHOG00000013626	2 retrocopies	retro_chof_1740, retro_chof_553,
Callithrix jacchus	ENSCJAG00000013395	2 retrocopies	retro_cjac_2827, retro_cjac_2986,
Erinaceus europaeus	ENSEEUG00000005430	2 retrocopies	retro_eeur_374, retro_eeur_663,
Otolemur garnettii	ENSOGAG00000007771	2 retrocopies	retro_ogar_1868 , retro_ogar_2776,
Rattus norvegicus	ENSRNOG00000006221	1 retrocopy	retro_rnor_852,
Sus scrofa	ENSSSCG00000011506	1 retrocopy	retro_sscr_192,