RetrogeneDB ID: retro_ogar_2780

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873663.1:2607587..2608346(-)
• Located in intron of: ENSOGAG00000009115

Retrocopy information

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

Parental gene information

• Parental gene symbol: DDX47
• Ensembl ID: ENSOGAG00000003748
• Aliases: None
• Description: DEAD (Asp-Glu-Ala-Asp) box polypeptide 47 [Source:HGNC Symbol;Acc:18682]

Sequence

>retro_ogar_2780
GCTGCCCCTGAGGAGCATGAAGCTCCCTAGCCGGCAGCGGAGGAGGAGGAAATTAAAACATTTAAAGACTTGGGTGTAAC
AGATGTATTGTGTGAAGCCTGTGACCCGTTGGGATGGGCAAAGCCCACCAAGATCCAGATTGAAGCTATTCCGTTAGCTT
TACAAAGTCGTGATATCATTGGGCTGGCAGAAACTGGCTCTGAAAAAACAGGGGCTTTTGCTTTGCCCATTCTGAATGCG
CTGCTGGAGACAGCCCAGTGTTTATTTGCCCTAGTTCTCACTCCCATTTGGGAGCTGGCTTTTCAGATCTCAGAGCAGTT
TGAAGCCCTGGGATCCTCTATTGGAGTGCAGTGTGCTGTGATTGTGGGTGGAATTGATTCAACGTCTCAATCTCTGGCCC
TGGCAAAAAAACCACATGTAGTAATAGCAACCCCGGGGCAACTAATTGACCATCTGGAAAATACAAAAGGCTTCAACTTA
AGAGCTCTCAAATACTTGGTCATGGATGAAGCTGACCGAATATTGAACATGGATTTCGAGACAGAGGTTGACAAGATCCT
CAAAGTGATTCCCCGAGATCGGAAAACATTTCTCTTCTCTGCTACCATGACCAAGAAGGTGCAAAAGCTTCAACGAGCAG
CTCTGAAGAATCCTGTGAAATGTGCTGTTTCCTCTAAATACCAGACAGTTGAGAAATTACAGTAATACTATCTTTTTATT
CCTTCTAAATTCAAGGATACTTACTTGGTCTATATTCTA

Alignment

ORF - retro_ogar_2780 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.26 %
• Parental protein coverage: 56.1 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  AAPGEHEAPQPAAEEEEIKTFKDLGVTDVLCEACDQLGWAKPTKIQIEAIPLALQGRDIIGLAETGSGKT
          AAP.EHEAP.PAAEEEEIKTFKDLGVTDVLCEACD.LGWAKPTKIQIEAIPLALQ.RDIIGLAETGS.KT
Retrocopy AAPEEHEAP*PAAEEEEIKTFKDLGVTDVLCEACDPLGWAKPTKIQIEAIPLALQSRDIIGLAETGSEKT

Parental  GAFALPILNALLETPQRLFALVLTPTRELAFQISEQFEALGSSIGVQCAVIVGGIDSMSQSLALAKKPHV
          GAFALPILNALLET.Q.LFALVLTP..ELAFQISEQFEALGSSIGVQCAVIVGGIDS.SQSLALAKKPHV
Retrocopy GAFALPILNALLETAQCLFALVLTPIWELAFQISEQFEALGSSIGVQCAVIVGGIDSTSQSLALAKKPHV

Parental  VIATPGRLIDHLENTKGFNLRALKYLVMDEADRILNMDFETEVDKILKVIPRDRKTFLFSATMTKKVQKL
          VIATPG.LIDHLENTKGFNLRALKYLVMDEADRILNMDFETEVDKILKVIPRDRKTFLFSATMTKKVQKL
Retrocopy VIATPGQLIDHLENTKGFNLRALKYLVMDEADRILNMDFETEVDKILKVIPRDRKTFLFSATMTKKVQKL

Parental  QRAALKNPVKCAVSSKYQTVEKLQQYYLFIPSKFKDTYLVYIL
          QRAALKNPVKCAVSSKYQTVEKLQ.YYLFIPSKFKDTYLVYIL
Retrocopy QRAALKNPVKCAVSSKYQTVEKLQ*YYLFIPSKFKDTYLVYIL

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_2780 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 3 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Otolemur garnettii	ENSOGAG00000003748	2 retrocopies	retro_ogar_2780 , retro_ogar_802,
Ictidomys tridecemlineatus	ENSSTOG00000027266	1 retrocopy	retro_itri_375,
Tupaia belangeri	ENSTBEG00000013697	1 retrocopy	retro_tbel_2420,