RetrogeneDB ID: retro_ogar_991

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873532.1:27852553..27853924(-)
• Located in intron of: ENSOGAG00000015089

Retrocopy information

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

Parental gene information

• Parental gene symbol: EIF3D
• Ensembl ID: ENSOGAG00000002978
• Aliases: None
• Description: eukaryotic translation initiation factor 3, subunit D [Source:HGNC Symbol;Acc:3278]

Sequence

>retro_ogar_991
ATGGCAAAAGTCATGACACTTGTGATCCAGGACAATCCCTCAGGCTGGGGTCCCTGTGCCGTTCCTGAGCAGTTTCGGGA
TATGCCCTACCAGCCATTCAGCAAAGGAGATCCGTTAGGAAAGTTGGAGACTGGACAGGAACCATATCCCAAGATAAAAG
GTACACAAATAAGTACTCCTCTCAATTTGGTGGTGGAAGTCAATATGCTTATTTCCATGAGGAGGATGAAACTAGCTTTC
AACTGGTGGATTCTGCACAAACACAGAAGACTGCCTACCAGCATAATCGGATGAGATTTGCACAGCGGACCCTTCACAGA
GACATAGATCAGCGGAACATGTTGCAGTTCAACTTGCAAGCCCTGCCTAAGAGCACTAAGCAGAAGAAGAGAGAACACAT
ATGACTACAGAAAAAATTCCAGAAGCAATTCAGGGTTAGGCAAAAATGGGATCAAAAATCACAGAAACCTCAAGACTCTT
CAGTTGAAGTTCATAGTGACTGGGAAGTGAAAGAAGAAATGGATTTTCCTCAGTTGATGAAGATGTGTTATCTGTAAGTG
TCAGAGTCACAGGACATCGAGTGTTGTGGAGCCCTAGAATACTACAATAAAGCTTTTGACCTCATCACCAGGAGGAGCTG
GAAGCCGCTGTGGAGCATCAAATGCATCTTCCACACTGGCACCACTACACATGACCCTGTCATCCGGAAGCTGGCAAAAA
CTCAAGGGAATGTGTTTGCCCCCAATGCCATCCTGGCCACTCTAATCAGCTGTACCCGCTCAGTGTACTCCTGGGATATT
GTCATCCAGAGAGTTGGGTCCAAGCTCTTATTTGATAAGAGGGCAACTCAGACTTTGACCTCCTTAATAGTGAGTGAGAC
AGCCAATGAGCCCCCTCAAGATGCAGGTAATTCCTTCAATTCACCCCACAATCTGGCCATGGAAGCAACCTACATTGACC
ACAGTTTCTCCCAGCAGTGCCTGAGAATGGGAAGAAAAGATACAATTTTCCCAGCCCAAACCCATTTGTGGAAGATGACA
TGGATAAGAATGAGATTGCATCTGTTGCATACCGGTATTGCGGGTGGAAGCTTGGGGATGATATTGACCTTATTGTTCGT
TGTAAGCATGATGGTGTCATGACTAGAGCCAATGGGGAGGTGTCCTTCATCAACATCAAGACACTTAATGAGTGAGATTC
CAGGCACTGAAACAGTGTTGACTGGCATCAGAAGCTGGACTCTCAGCGAGGAGCCATCATTGCCACTGAACTAAAGAACA
GCTATAAGCTGTCTAGATGACCTGCTGTGCTTTGCAGGCTGGATCTAAGTACCTCAAGCTCGGTTATGTGTCTCAATACC
ACGTGAAAGAC

Alignment

ORF - retro_ogar_991 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.21 %
• Parental protein coverage: 83.76 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  MAKFMTPVIQDNPSGWGPCAVPEQFRDMPYQPFSKGDRLGK-VADWTGATYQDKRYTNKYSSQFGGGSQY
          MAK.MT.VIQDNPSGWGPCAVPEQFRDMPYQPFSKGD.LGK.V.DWTG...QDKRYTNKYSSQFGGGSQY
Retrocopy MAKVMTLVIQDNPSGWGPCAVPEQFRDMPYQPFSKGDPLGK<VGDWTGTISQDKRYTNKYSSQFGGGSQY

Parental  AYFHEEDETSFQLVDTARTQKTAYQRNRMRFAQRTLRRDKDRRNMLQFNLQALPKSAKQKERERIRLQKK
          AYFHEEDETSFQLVD.A.TQKTAYQ.NRMRFAQRTL.RD.D.RNMLQFNLQALPKS.KQK.RE.I.LQKK
Retrocopy AYFHEEDETSFQLVDSAQTQKTAYQHNRMRFAQRTLHRDIDQRNMLQFNLQALPKSTKQKKREHI*LQKK

Parental  FQKQFGVRQKWDQKSQKPRDSSVEVRSDWEVKEEMDFPQLMKMRYLEVSEPQDIECCGALEYYDKAFDRI
          FQKQF.VRQKWDQKSQKP.DSSVEV.SDWEVKEEMDFPQLMKM.YL.VSE.QDIECCGALEYY.KAFD.I
Retrocopy FQKQFRVRQKWDQKSQKPQDSSVEVHSDWEVKEEMDFPQLMKMCYL*VSESQDIECCGALEYYNKAFDLI

Parental  TTRSEKPLRSIKRIFHTVTTTDDPVIRKLAKTQGNVFATDAILATLMSCTRSVYSWDIVVQRVGSKLFFD
          T.RS.KPL.SIK.IFHT.TTT.DPVIRKLAKTQGNVFA..AILATL.SCTRSVYSWDIV.QRVGSKL.FD
Retrocopy TRRSWKPLWSIKCIFHTGTTTHDPVIRKLAKTQGNVFAPNAILATLISCTRSVYSWDIVIQRVGSKLLFD

Parental  KR-DNSDFDLLT-VSETANEPPQDEGNSFNSPRNLAMEATYINHNFSQQCLRM-GKERYNFPNPNPFVED
          KR..NSDFDLL..VSETANEPPQD.GNSFNSP.NLAMEATYI.H.FSQQCLRM.GK.RYNFP.PNPFVED
Retrocopy KR<GNSDFDLLN>VSETANEPPQDAGNSFNSPHNLAMEATYIDHSFSQQCLRM<GKKRYNFPSPNPFVED

Parental  DMDKNEIASVAYRYRRWKLGDDIDLIVRCEHDGVMTGANGEVSFINIKTLNEWDSRHCNGVDWRQKLDSQ
          DMDKNEIASVAYRY..WKLGDDIDLIVRC.HDGVMT.ANGEVSFINIKTLNE.DSRH.N.VDW.QKLDSQ
Retrocopy DMDKNEIASVAYRYCGWKLGDDIDLIVRCKHDGVMTRANGEVSFINIKTLNE*DSRH*NSVDWHQKLDSQ

Parental  RGAVIATELKNNSYKLAR-WTCCALLAGSEYLKLGYVSRYHVKD
          RGA.IATELK.NSYKL.R..TCCAL.AGS.YLKLGYVS.YHVKD
Retrocopy RGAIIATELK-NSYKLSR<MTCCALQAGSKYLKLGYVSQYHVKD

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_991 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 2 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Macropus eugenii	ENSMEUG00000004561	2 retrocopies	retro_meug_1104, retro_meug_1150,
Otolemur garnettii	ENSOGAG00000002978	2 retrocopies	retro_ogar_779, retro_ogar_991 ,