RetrogeneDB ID: retro_ogar_1121

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873536.1:28368893..28369521(+)
• Located in intron of: ENSOGAG00000004102

Retrocopy information

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

Parental gene information

• Parental gene symbol: MRPS35
• Ensembl ID: ENSOGAG00000010630
• Aliases: None
• Description: mitochondrial ribosomal protein S35 [Source:HGNC Symbol;Acc:16635]

Sequence

>retro_ogar_1121
GCAGAGCCATTTAAACCCTCTATAGTACCTCTTCCTATCAGAATGGGCTATCCATAAAATATGGCATACCCATGGCAAAG
GAGGGAAATCTAGAACTTTTAAAGATCCCCCATTTTCTGCATTTGACTCCTGTAGTGATTAAAAAGTATTGTGAGCTCTT
AAAGATTTTTGCATTGAATGGGCAGCTGCACTGGACAGTGGTGAGAAATGTGAAAAGCATTTTCCAATTGAAATTCACAC
TGCTGATTATGTTTCATCATGCCCATATGTTTGAAACCCCAAAGCACAAGTAGTAACCTTAAGGGTTAAACTTTCCCATT
TAAACTTAGATGACCATGCAAGAAAGAAACTTATTAAACTTGTTGGAGAGTGATACTGCAAGACCACAGATGTGCTTACC
ATCAAAACAGACAGGTACCCTTTAGAGACACAGAATTATGATTATGCAGTGTATCTACAAACAATTTTATATCCTGAGTC
TTGGAAAAGTGAAGAATTGGAAAAAAATAAGACTGAAGCAGACATGGAAGAGTATATTTGGGAAAACAGTTCCTTAGAAA
AAAATATCCTGGAAACACTTCTCCAGATTAAAGCTGCTGATAAGAATACAGAAATAGAGGAGAGGCAG

Alignment

ORF - retro_ogar_1121 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.08 %
• Parental protein coverage: 65.02 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  AAPFKPSTVPLPVRMGYP-VKKGVPMAKEGNLELLKIPNFLHLTPVAIKKHCE-ALKDFCTEWPAALDSD
          A.PFKPS.VPLP.RMGYP..K.G.PMAKEGNLELLKIP.FLHLTPV.IKK.CE.ALKDFC.EW.AALDS.
Retrocopy AEPFKPSIVPLPIRMGYP<IKYGIPMAKEGNLELLKIPHFLHLTPVVIKKYCE<ALKDFCIEWAAALDSG

Parental  EKCEKHFPIEIDTADYVSSGPSVRNPKARVVTLRVKLSSLNLDDHARKKLIKLVGERYCRTTDVLTIKTD
          EKCEKHFPIEI.TADYVSS.P.V.NPKA.VVTLRVKLS.LNLDDHARKKLIKLVGE.YC.TTDVLTIKTD
Retrocopy EKCEKHFPIEIHTADYVSSCPYV*NPKAQVVTLRVKLSHLNLDDHARKKLIKLVGE*YCKTTDVLTIKTD

Parental  RCPLKRQNYDYAMYLLTVLYHESWKTEEWEKNKTEADMEEYIWKNSSSEKNILETLLQIKAADKNTEVKK
          R.PL..QNYDYA.YL.T.LY.ESWK.EE.EKNKTEADMEEYIW.NSS.EKNILETLLQIKAADKNTE...
Retrocopy RYPLETQNYDYAVYLQTILYPESWKSEELEKNKTEADMEEYIWENSSLEKNILETLLQIKAADKNTEIEE

Parental  EE
          ..
Retrocopy RQ

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_1121 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 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Echinops telfairi	ENSETEG00000005034	1 retrocopy	retro_etel_2145,
Loxodonta africana	ENSLAFG00000010490	1 retrocopy	retro_lafr_449,
Oryctolagus cuniculus	ENSOCUG00000016214	1 retrocopy	retro_ocun_866,
Otolemur garnettii	ENSOGAG00000010630	2 retrocopies	retro_ogar_1121 , retro_ogar_2807,