RetrogeneDB ID: retro_ogar_942

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873531.1:9352188..9353228(+)
• Located in intron of: ENSOGAG00000002055

Retrocopy information

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

Parental gene information

• Parental gene symbol: NUP50
• Ensembl ID: ENSOGAG00000002320
• Aliases: None
• Description: nucleoporin 50kDa [Source:HGNC Symbol;Acc:8065]

Sequence

>retro_ogar_942
GACTCTCTTGCTGCACATGGCCCTACCAACTGGGATGATAAAAGGATTTCAAAGCCCTAAACTAATGGTAGCAGTCTGCG
GGTTCTTCCCGTGGCCTTGCTCCTAGTAAAGCTTGTATCAGGAATGCCGGTAACAAAGGGTTGGCTGCCTTGGACACTGT
TTGGGACTGAATAGTGAAGCAGTGAACCCAAAACCCACTCTGTGATCTGACACCAATTTTTAAAGACTATGAGAAATATT
TAGTGAATATTGGACATCACTGGGACAGTGTCAGTAGTAACTCTCAAAGTGAAAGTAGCAAGATGTTGGCTGAAAAGCAG
TTTCCTTCCCAATTTGGTTCAATGAAATTACAGTGAGAGTCAGCATTTTTGTTACATGATAGCACAACTGAAGATACATC
TGAAAGGAAGATTGTGGTTGTGTTTGAAAAGAAAATGGACCCATCACTGGGACCAACAAGTGCTTTAGTTTTGGCAAGAA
AATCAATATCTCTGCTTTAGGCTCATTAAGCTCTGCCCCCCCGGCTGGATTTTCATTTTCCTCTGGAAACACCAGTTTAT
TTGACAAAACATATTACCACAAGTAAACTGGTTTTTTCACCATTTTCCACTAAAACATCAGAAAGTGAAGCAGAATGTGG
CCCTAATGAATGCACAGGTGGAGCTGAGGAAGAGACGGATGGGCTCCCTAAAGTAGCAGTTACTGAAGTAAAAGAAGATG
CTTTCTTACTCCCCAAAGTGTAAACTATTTAACAAGAAAGGCAAGGAATTTAAAGAGAAAGGTGTGGCAACTCTGCATTT
AAAAACCAAGAAGACAGAGCTTTTGGTGTGAGCAGGCACCAATTTAGGCAACATATTGCAGAAGGTTCTGATTCCATCCA
TATGCCATGTACCTAAACAGGGAAAAATACTTACTGTCTGTGTCACAAATCCTCCAGCTGATGAGAGGAATGCCACTGTC
CCGGTGATCATGTTCATTCAGGTATAACGAGTGAGGATGCAGTTGAATTGCACAAAATCTTACTGGAGAAAATTAATGCC

Alignment

ORF - retro_ogar_942 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.71 %
• Parental protein coverage: 75.96 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 7

Retrocopy - Parental Gene Alignment:

Parental  ESVTANGPTMLVDKKISNPRTNGDSQQP-SSSGLASSKAYVRNAYNNQLAALNCSVRDWIAKHVNVNPLC
          .S..A.GPT...DK.IS.P.TNG.S....SS.GLA.SKA..RNA.N..LAAL...V.D.I.K....NPLC
Retrocopy DSLAAHGPTNWDDKRISKP*TNGSSLRV<SSRGLAPSKACIRNAGNKGLAALD-TVWD*IVKQ*TQNPLC

Parental  DLTPIFKDYEKYLASIEQQHGSSASGTAQSEANKTVVDVQSPSPLGSAKLQKESEFLFHGNKTEDTPEKK
          DLTPIFKDYEKYL..I...H..S.S...QSE..K.....Q.PS..GS.KLQ.ES.FL.H...TEDT.E.K
Retrocopy DLTPIFKDYEKYLVNIGH-HWDSVSSNSQSESSKMLAEKQFPSQFGSMKLQ*ESAFLLHDSTTEDTSERK

Parental  TEATSEKKTD-PSLGATSASFNFGKKIDSSVLGSLSSGPLAGFSFSSGNAPLFGKD-TSQSKLGSSPLPT
          .....EKK.D.P..G.T...F.FGKKI..S.LGSLSS.P.AGFSFSSGN..LF.K.....SKL..SP..T
Retrocopy IVVVFEKKMD<PITG-TNKCFSFGKKINISALGSLSSAPPAGFSFSSGNTSLFDKT>ITTSKLVFSPFST

Parental  KTLVSQAEGGGNECKEGGDEEENDEPPKVVVTEVKEEDAF-YSKKCKLFYKKDNEFKEKGVGTLHLKPTA
          KT..S.AE.G.NEC..GG.EEE.D..PKV.VTEVKE.DAF.YS.KCKLF.KK..EFKEKGV.TLHLK...
Retrocopy KTSESEAECGPNECT-GGAEEETDGLPKVAVTEVKE-DAF>YSPKCKLFNKKGKEFKEKGVATLHLK---

Parental  NQKTQLLVRADTNLGNILLNVLIPP-NMPCTRT-GKNNVLIVCVPNPPIDEKNASVPVTMLIRV-KTSED
          ..KT.LLV.A.TNLGNIL..VLIP...MPCT.T.GK...L.VCV.NPP.DE.NA.VPV.M.I.V..TSED
Retrocopy TKKTELLV*AGTNLGNILQKVLIPS<HMPCT*T>GK--ILTVCVTNPPADERNATVPVIMFIQV<ITSED

Parental  ADELHKILLEKKDA
          A.ELHKILLEK..A
Retrocopy AVELHKILLEKINA

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_942 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.

---

Parental genes homology:

Parental genes homology involve 7 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000016242	1 retrocopy	retro_cjac_4080,
Homo sapiens	ENSG00000093000	3 retrocopies	retro_hsap_1429, retro_hsap_3301, retro_hsap_3434,
Microcebus murinus	ENSMICG00000006840	1 retrocopy	retro_mmur_534,
Mus musculus	ENSMUSG00000016619	1 retrocopy	retro_mmus_1905,
Nomascus leucogenys	ENSNLEG00000013154	2 retrocopies	retro_nleu_1359, retro_nleu_1844,
Otolemur garnettii	ENSOGAG00000002320	1 retrocopy	retro_ogar_942 ,
Pongo abelii	ENSPPYG00000011928	1 retrocopy	retro_pabe_2723,