RetrogeneDB ID: retro_ogar_3314

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873775.1:997641..998390(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MRPS9
• Ensembl ID: ENSOGAG00000007255
• Aliases: None
• Description: mitochondrial ribosomal protein S9 [Source:HGNC Symbol;Acc:14501]

Sequence

>retro_ogar_3314
ATGGTGGCTCTGTGTGTGTCCCATAGCAGAGCAGTTTCCTACTGGCACTTTCTTGGGGGTAAGGTTAGCCTTTCCTGGAT
CCACAGACTCTGGAAAATCATGGTAGCAGAGTTTCAGACATGTATTGTATCCCAGATATTAAGGCACAGAAATGTCACCA
TTGTAATAACAAAGAAAAAGGTTACAGCTGTAAGACATGAAACTTACACAGAGGATTTTATTAAAAAGCAGATTGAAGAG
TTCAACATAGGAAAGAGACATTTAGCCAACATTATGGGAGAAGATCAGAAAAATTTACCGAAGAGGATATTGATAGAGCT
ATTGCTTACCTTTTTGCAAGTGATTTGTGTGAGAAATGAGCCAGGCCAGTGAAGAAGCATCCTGAACAGATTTTCCAAAA
CAAAAAGCAATCCAGTGGGGAGAAGATGGCTGCCTGTTTCATTTTCTCTTCTGTACTGGCAAACAATCCTATTATTCATT
AATGCATGATGTATATGGAAAGTTACTCAAAATGGAAAAACATCAAAATCAATCACAAGCCAAAGATCTCGTGCCAGAAA
AAAACTGAAACCAGAAATCTGTTTGGCAGCAGATGGCTGATTAAGGAGGAATTAGAAGAAATGATAGTGGAAAAACTGTC
AGATCAAGATTATATGCACTTCATTCAGCTGCTAGAAAAGTTATTGACATTGCAGTGTGGTGCTGCTGAGTAAGAATTTG
TACAGAGGTTTTGCAGAAGTGTAACTATT

Alignment

ORF - retro_ogar_3314 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.0 %
• Parental protein coverage: 63.13 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MAAPCVSYGGAVSYRLFLGGKVSLARNHALWKIAVAEFQTCTRSQILRQRNTTVVTTKKKVAALRHETYT
          M.A.CVS...AVSY..FLGGKVSL...H.LWKI.VAEFQTC..SQILR.RN.T.V.TKKKV.A.RHETYT
Retrocopy MVALCVSHSRAVSYWHFLGGKVSLSWIHRLWKIMVAEFQTCIVSQILRHRNVTIVITKKKVTAVRHETYT

Parental  EDFIKKQIEEFNIGKRHLANMMGED-PEKFTQEDIDRAIAYLFPSGLFEKGARPVMKHPEQI-FPKQRAI
          EDFIKKQIEEFNIGKRHLAN.MGED..EKFT.EDIDRAIAYLF.S.L.EK.ARPV.KHPEQI.FPKQ.AI
Retrocopy EDFIKKQIEEFNIGKRHLANIMGED<SEKFTEEDIDRAIAYLFASDLCEK*ARPVKKHPEQI<FPKQKAI

Parental  QWGEDGRPFHFLFYTGKQSYYSLMHDVYGMLLKMEKHQNQLQAKDLLP-KKTETRDLIGSRWLIKEELEE
          QWGEDG..FHFLF.TGKQSYYSLMHDVYG.LLKMEKHQNQ.QAKDL.P.KKTETR.L.GSRWLIKEELEE
Retrocopy QWGEDGCLFHFLFCTGKQSYYSLMHDVYGKLLKMEKHQNQSQAKDLVP>KKTETRNLFGSRWLIKEELEE

Parental  MLVEKLSDQDYMHFIQLLEKLLTLQCGAAEEEFVQRFRRSVTI
          M.VEKLSDQDYMHFIQLLEKLLTLQCGAAE.EFVQRF.RSVTI
Retrocopy MIVEKLSDQDYMHFIQLLEKLLTLQCGAAE*EFVQRFCRSVTI

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_3314 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 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000002122	1 retrocopy	retro_cfam_519,
Callithrix jacchus	ENSCJAG00000008156	1 retrocopy	retro_cjac_40,
Otolemur garnettii	ENSOGAG00000007255	1 retrocopy	retro_ogar_3314 ,
Pteropus vampyrus	ENSPVAG00000000927	1 retrocopy	retro_pvam_963,