RetrogeneDB ID: retro_ogar_779

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873527.1:11192471..11193450(-)
• Located in intron of: ENSOGAG00000016708

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_779
GATAAAGCCTTTGACCACATGACCACGAGGAGCGAGAAGCCGCTGTGGAGCATCAAGCGCATCTTCCACACTGTCACCAC
CACAGATAACCCTGTCATCCTGAAGCTGGCAAAAACTCAGGGGAATGTGTTTGCCACCGATGCCATCCTGGCCACACTAT
GAGCTGTACCCGCTCAGTGTATTCCTAGGATATTGTTGTCCAGAGAGTTGGGTCCAGGCTCTTCTTTGATAAGAGGGACA
ACTCAGACTTTGACCTCCTGACAGTGAGTGAGACAGCCAGTGAGCCCCCTCAAGATGAAGGTAATTCCTTCAATTCACCC
CGCAGTCTGGCCATGGAAGCAACCTACATCAACCACAATTTCTCCCAGCACAGTGCCTGAGAATGGGGAAGGAAAGATAC
AATTTCCCCAACCCAAACCCATTTGTGGAAGACGACATGGATAAGAATGAGATTGCATCTGTTGCATACCGGTATTGCAG
GTGGAAGCTGGGGGATGATATTGACCTTATTGTTCACTGTGAGCATGATGGTGTCATGACTGGAGCCAATGGGGAAGGGT
CCTTCATCAACATGAAGACACTCAATGAGTGGGATTCCAGGCACTGTAACGGTGTTGACTGGCATCAGAAGCTAGACTCT
AAGCGAGGAGCCGTCATTGCCACTGAGCTAAAGAACGACAGCTACAAGCTGGCCCGATGGACCTGCTGTGCTTTGCTGGC
TGGATCTGAGTACCTCAAGCTCGGTTATGTGTCTTGATACCATGTGAAAGACTCTTCATGCCACGTCATCCTGGGCACCT
AGCAGTTCAAGCCCCATGAGTTTGCCAGCCAGATCAACCTACGTGTGGAGAATGCCTGGGGCATTCTGCGCTGTGTCATC
AACATCTGCATGAAGCTGGAGGAAGGCAAATACCTCATCCTCAAGGACCCCAACAAGCAGGTCATCCGTATCTACAGCCT
GCCTGATGGTACCTTTAGC

Alignment

ORF - retro_ogar_779 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.06 %
• Parental protein coverage: 59.49 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  DKAFDRITTRSEKPLRSIKRIFHTVTTTDDPVIRKLAKTQGNVFATDAILATL-MSCTRSVYSWDIVVQR
          DKAFD..TTRSEKPL.SIKRIFHTVTTTD.PVI.KLAKTQGNVFATDAILATL.MSCTRSVYS.DIVVQR
Retrocopy DKAFDHMTTRSEKPLWSIKRIFHTVTTTDNPVILKLAKTQGNVFATDAILATL<MSCTRSVYS*DIVVQR

Parental  VGSKLFFDKRDNSDFDLLTVSETANEPPQDEGNSFNSPRNLAMEATYINHNFSQQCL-RMGKERYNFP-N
          VGS.LFFDKRDNSDFDLLTVSETA.EPPQDEGNSFNSPR.LAMEATYINHNFSQ......G.....FP.N
Retrocopy VGSRLFFDKRDNSDFDLLTVSETASEPPQDEGNSFNSPRSLAMEATYINHNFSQHSA>ENGEGKIQFP>N

Parental  PNPFVEDDMDKNEIASVAYRYRRWKLGDDIDLIVRCEHDGVMTGANGEVSFINIKTLNEWDSRHCNGVDW
          PNPFVEDDMDKNEIASVAYRY.RWKLGDDIDLIV.CEHDGVMTGANGE.SFIN.KTLNEWDSRHCNGVDW
Retrocopy PNPFVEDDMDKNEIASVAYRYCRWKLGDDIDLIVHCEHDGVMTGANGEGSFINMKTLNEWDSRHCNGVDW

Parental  RQKLDSQRGAVIATELKNNSYKLARWTCCALLAGSEYLKLGYVSRYHVKDSSRHVILGTQQFKPNEFASQ
          .QKLDS.RGAVIATELKN.SYKLARWTCCALLAGSEYLKLGYVS.YHVKDSS.HVILGT.QFKP.EFASQ
Retrocopy HQKLDSKRGAVIATELKNDSYKLARWTCCALLAGSEYLKLGYVS*YHVKDSSCHVILGT*QFKPHEFASQ

Parental  INLSVENAWGILRCVIDICMKLEEGKYLILKDPNKQVIRVYSLPDGTFS
          INL.VENAWGILRCVI.ICMKLEEGKYLILKDPNKQVIR.YSLPDGTFS
Retrocopy INLRVENAWGILRCVINICMKLEEGKYLILKDPNKQVIRIYSLPDGTFS

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_779 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,