RetrogeneDB ID: retro_ogar_555

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873523.1:38182071..38183288(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DDX50
• Ensembl ID: ENSOGAG00000001844
• Aliases: None
• Description: DEAD (Asp-Glu-Ala-Asp) box polypeptide 50 [Source:HGNC Symbol;Acc:17906]

Sequence

>retro_ogar_555
AGGAAGTCAAGGCCCCATTATGACTCAGATGCCAAATCAGAAACAAGAGAAAATGGCACTGTGAATGACTTGGATGCTGC
CAAGCCCAAAAAAGCTAAAATGAAAGAGAAGCTAAATGGAGACGCTGAAGAAGGATTTAATAGACTTTCAGATGAATTCT
CTAAATCTCATAAGTCAAGAAGAAAAGATCTACCAAATGGAGATATTGATGAATATGAAAAAAATCAAAATGAGTATCAC
ACTTAGATAGTTCTACTTATAAATCAAGTGACAATAAACTGGAGGAGACTCTAACATGTGAAGATCAAGAAGGAGCCTTC
TCAAATTTTCCTATCTCTGAAGAAACTATAAAGCTTCTGAAAGGTCAAGGGGTAACATATTTCTGTCCTATTCAAGTTAA
GACCTTTGGTCTTGCCTATGAAGGAAAAGATTTAATAGCTCAAGGATGAACCGCCAAAGGAAAGATATTCTCTTTTGCCA
TCCCCTTGATTGAAAGTCTCCAAAGAAATCAAGAAATAATTTTAAAAAGCTGCTCACCAAAGGTACTTGTTTTGGCTCCA
GCAAGGGAACTGGCAACCCAAGTAGCCAAAGACTTCAAATATATAACTAGGCAGCTCAGGGTGGCATGTTTTTATGGTGG
AACACCATATCAAAGCCAAATTAATCATATTTGAAATGGTATTGACATCCTGGTTGGGACCCCTGGTCATATCAAAGACC
ATGTGCAGAACAACTGATTGGATCTTTCTAAACTGCACCATGTCATGTTTGATGAAATGGATCAGATGTTAGATTTAGGT
TTTGCTGAGCAAGTTGAAGATATTATTTATGAATCCTACAAAACTGATTCTGAAGACAATCCTCAGACTTTACTTTATTC
TTTAACTTGCCCACAATGGGTATATAAAGTTGCAAAAAAAAAAAAAAAATACCCGAAATCCAGATATGAACAAGTTGACC
TTGTTGGAAAAATGACTCAAAAGGCTACAACTACTATGGGACATTTGGCCATCCAGTGTCATTGGTCTCAGAGATCAGGA
GTTACTGGACATGTCCTTCGAGTCTACAGTGGGTCTCAAAGGAGGGCTATCATTTTTTGTGAGACCAAGAAAAAAGTAAC
TGAAATGGCCATGAATCCACACATAAAACAGGATGCCCAGTGTTTACATGCAGACATTGCACAATCACAAAGAGAAATTA
CACTGAAAGGCTTTCAG

Alignment

ORF - retro_ogar_555 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.29 %
• Parental protein coverage: 54.68 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  RKSRHHYDSDEKSETRENGVVNDLDAPKPKKAKMKEKLNGDAEEGFNRLSDEFSKSHKSRRKDLPNGDID
          RKSR.HYDSD.KSETRENG.VNDLDA.KPKKAKMKEKLNGDAEEGFNRLSDEFSKSHKSRRKDLPNGDID
Retrocopy RKSRPHYDSDAKSETRENGTVNDLDAAKPKKAKMKEKLNGDAEEGFNRLSDEFSKSHKSRRKDLPNGDID

Parental  EYEK-KSKRISSLDSSTHKSNDNKLEETLTREQKEGAFSNFPISEETIKLLKGRGVTYLFPIQVKTFGPV
          EYEK.KSK..S.LDSST.KS.DNKLEETLT.E..EGAFSNFPISEETIKLLKG.GVTY..PIQVKTFG..
Retrocopy EYEK<KSK*VSHLDSSTYKSSDNKLEETLTCEDQEGAFSNFPISEETIKLLKGQGVTYFCPIQVKTFGLA

Parental  YEGKDLIAQARTGTGKTFSFAIPLIERLQRSQETIKKSRSPKVLVLAPTRELANQVAKDFKDITRKLSVA
          YEGKDLIAQ..T..GK.FSFAIPLIE.LQR.QE.I.KS.SPKVLVLAP.RELA.QVAKDFK.ITR.L.VA
Retrocopy YEGKDLIAQG*TAKGKIFSFAIPLIESLQRNQEIILKSCSPKVLVLAPARELATQVAKDFKYITRQLRVA

Parental  CFYGGTSYQSQINHIRNGIDILVGTPGRIKDHLQSGRLDLSKLRHVVLDEVDQMLDLGFAEQVEDIIHES
          CFYGGT.YQSQINHI.NGIDILVGTPG.IKDH.Q...LDLSKL.HV..DE.DQMLDLGFAEQVEDII.ES
Retrocopy CFYGGTPYQSQINHI*NGIDILVGTPGHIKDHVQNN*LDLSKLHHVMFDEMDQMLDLGFAEQVEDIIYES

Parental  YKTDSEDNPQTLLFSATCPQWVYKV---AKKYMKSRYEQVDLVGKMTQKAATTVEHLAIQCHWSQRPAVI
          YKTDSEDNPQTLL.S.TCPQWVYKV......Y.KSRYEQVDLVGKMTQKA.TT..HLAIQCHWSQR..V.
Retrocopy YKTDSEDNPQTLLYSLTCPQWVYKVXXXXXXYPKSRYEQVDLVGKMTQKATTTMGHLAIQCHWSQRSGVT

Parental  GDVLQVYSGSEGRAIIFCETKKNVTEMAMNPHIKQNAQCLHGDIAQSQREITLKGFR
          G.VL.VYSGS..RAIIFCETKK.VTEMAMNPHIKQ.AQCLH.DIAQSQREITLKGF.
Retrocopy GHVLRVYSGSQRRAIIFCETKKKVTEMAMNPHIKQDAQCLHADIAQSQREITLKGFQ

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_555 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 10 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000018844	1 retrocopy	retro_cjac_1298,
Homo sapiens	ENSG00000107625	2 retrocopies	retro_hsap_2089, retro_hsap_2866,
Macaca mulatta	ENSMMUG00000001006	1 retrocopy	retro_mmul_982,
Mus musculus	ENSMUSG00000020076	1 retrocopy	retro_mmus_3362,
Nomascus leucogenys	ENSNLEG00000011631	2 retrocopies	retro_nleu_1300, retro_nleu_609,
Otolemur garnettii	ENSOGAG00000001539	1 retrocopy	retro_ogar_3395,
Otolemur garnettii	ENSOGAG00000001844	2 retrocopies	retro_ogar_1492, retro_ogar_555 ,
Otolemur garnettii	ENSOGAG00000013660	1 retrocopy	retro_ogar_227,
Pongo abelii	ENSPPYG00000002390	3 retrocopies	retro_pabe_2007, retro_pabe_2369, retro_pabe_2418,
Pan troglodytes	ENSPTRG00000002562	2 retrocopies	retro_ptro_1536, retro_ptro_1938,