RetrogeneDB ID: retro_ogar_372

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873520.1:12687700..12688160(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RM23_OTOGA
• Ensembl ID: ENSOGAG00000029988
• Aliases: None
• Description: 39S ribosomal protein L23, mitochondrial [Source:UniProtKB/Swiss-Prot;Acc:B5FWC0]

Sequence

>retro_ogar_372
ATGGCGTGGAACGTGCTGTACCATCTGTACCAGCTGGGTGGCCCACAGCTGCGGATATTCTGAATCAACTTCTTGATCCA
GCTGGTGCGACCTGCCATGGCCCAGGTCTGAGGACACTGTGCAGTTCTGGATTCCCCTGGAGATGACCAGGGTGAACTTC
AGGAATTATCTCCAACGAATTTACAATGTGCCTGTGGCTGTTGTGTGGATGCGTGTACAGCATGGCTCTCACAGGAAAAG
GGAGCACAGAAATGTTGGAATAAAGAAGCCAGATTACAAAGTTGCCTATGTGCAGCTGGCCCATGAACAGACCTTCACAT
TCCCAGACCTGTTTCCTGAGAAAGACCCGTGGCTTGACGGCAGCTTTGTCGATGAAGCCTAGAGCACGTTCATGGTGGAT
GAGCAGCAGAGACAAGGCAGCGACCCCCAGTGTGGTGGCATCCTCAACTGGTTCAGCCTG

Alignment

ORF - retro_ogar_372 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.17 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MARNVLYPLYQLGGPQLRVFRTNFFIQLVRPGTAQ-PEDTVQFRIPMEMTRVDLRNYLERIYNVPVAAVR
          MA.NVLY.LYQLGGPQLR.F..NF.IQLVRP..AQ..EDTVQF.IP.EMTRV..RNYL.RIYNVPVA.V.
Retrocopy MAWNVLYHLYQLGGPQLRIF*INFLIQLVRPAMAQ>SEDTVQFWIPLEMTRVNFRNYLQRIYNVPVAVVW

Parental  TRVQHGSHRKRDHRNVRIKKPDYKVAYVQLAHGQTFTFPDLFPEKDPRLEGSSVDEAQSTFMADEQQRQG
          .RVQHGSHRKR.HRNV.IKKPDYKVAYVQLAH.QTFTFPDLFPEKDP.L.GS.VDEA.STFM.DEQQRQG
Retrocopy MRVQHGSHRKREHRNVGIKKPDYKVAYVQLAHEQTFTFPDLFPEKDPWLDGSFVDEA*STFMVDEQQRQG

Parental  SDPQRGGVPNWFSL
          SDPQ.GG..NWFSL
Retrocopy SDPQCGGILNWFSL

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_372 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 6 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000000103	1 retrocopy	retro_btau_329,
Macaca mulatta	ENSMMUG00000031268	1 retrocopy	retro_mmul_1226,
Mus musculus	ENSMUSG00000037772	1 retrocopy	retro_mmus_2046,
Nomascus leucogenys	ENSNLEG00000026950	1 retrocopy	retro_nleu_1043,
Otolemur garnettii	ENSOGAG00000029988	1 retrocopy	retro_ogar_372 ,
Sarcophilus harrisii	ENSSHAG00000002716	1 retrocopy	retro_shar_411,