RetrogeneDB ID: retro_ogar_2040

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873583.1:5701808..5702441(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: UBE2R2
• Ensembl ID: ENSOGAG00000029045
• Aliases: None
• Description: ubiquitin-conjugating enzyme E2R 2 [Source:HGNC Symbol;Acc:19907]

Sequence

>retro_ogar_2040
ATGGAGGGCTTCTGGATCACCCTGGTGGATGAGTCTAACCTCTACAACTGGGAGGGGTCATCTATGGAGCCCCTAACACC
CTCTATGAAGGCAGCTACATCAAGATGCTTATTAAATTTCTCATTGACTATCCATGTTCACCACTTACTTTCATATTCTT
GACCAAAATGTGGCACTCCAAAATTAATGAGAAAGGAGGTGTTTGCTTTTCTATTTTCCACTCACCTATCGATGACCCAT
AGAGTGGAGGACTGCCCTCTGACAGGTGGAAATCCTACTCTGAATGTGAGGACTATTCCATTAAGTGTCATCTCACTGCT
TGATGAGCCCAACACCTTCTCCCTAGATGATGTGGATGCTTCTGTTATGTTCAGGAGATAGAGAGATGGTAAAGGAAAAG
ACAGAGAATATGCCAAAATCTTTAGGAAACAGGTTTCAGCCACTAAGGCGGAGCCAGAAAGGATGGAGTGAAGGTCCCCA
TGACTGACTCAGGCAGAATACTGCATCCAAACTGATGTGTCTTCCAAGGACATCAGCTCAGATTTGCTGTATGACTTGTA
TGACAACAACATCGATGATGGAGATGGAAGAGCGGACTATTAAGATGATGATGATTCTGGGAATGAGGTGTCA

Alignment

ORF - retro_ogar_2040 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.98 %
• Parental protein coverage: 95.09 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  VEGFRITLVDESDLYNWEVA-IFGPPNTLYEGGYFKAHIKFPIDYPYSPPTFRFLTKMWHPNIYENGDVC
          .EGF.ITLVDES.LYNWE...I.G.PNTLYEG.Y.K..IKF.IDYP.SP.TF.FLTKMWH..I.E.G.VC
Retrocopy MEGFWITLVDESNLYNWEGS<IYGAPNTLYEGSYIKMLIKFLIDYPCSPLTFIFLTKMWHSKINEKGGVC

Parental  ISILHPPVDDPQSGELPSERW-NPTQNVRTILLSVISLLNEPNTFSPANVDASVMFRKWRDSKGKDKEYA
          .SI.H.P.DDP.SG.LPS.RW.NPT.NVRTI.LSVISLL.EPNTFS...VDASVMFR..RD.KGKD.EYA
Retrocopy FSIFHSPIDDP*SGGLPSDRW>NPTLNVRTIPLSVISLLDEPNTFSLDDVDASVMFRR*RDGKGKDREYA

Parental  EIIRKQVSATKAEAEKDGVKVP-TTLAEYCIKTKVPSNDNSSDLLYDLYDDDIDDEDEEEEDADCYDDDD
          .I.RKQVSATKAE.E......P..T.AEYCI.T.V.S.D.SSDLLYDLYD..IDD.D.....AD..DDDD
Retrocopy KIFRKQVSATKAEPERME*RSP*LTQAEYCIQTDVSSKDISSDLLYDLYDNNIDDGDGR---ADY*DDDD

Parental  SGNEES
          SGNE.S
Retrocopy SGNEVS

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_2040 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
Canis familiaris	ENSCAFG00000031810	1 retrocopy	retro_cfam_1138,
Dipodomys ordii	ENSDORG00000007589	1 retrocopy	retro_dord_306,
Myotis lucifugus	ENSMLUG00000006793	1 retrocopy	retro_mluc_2175,
Oryctolagus cuniculus	ENSOCUG00000023588	3 retrocopies	retro_ocun_131, retro_ocun_1719, retro_ocun_1793,
Otolemur garnettii	ENSOGAG00000008795	1 retrocopy	retro_ogar_2554,
Otolemur garnettii	ENSOGAG00000029045	3 retrocopies	retro_ogar_1211, retro_ogar_2040 , retro_ogar_2946,
Rattus norvegicus	ENSRNOG00000010727	1 retrocopy	retro_rnor_1508,