RetrogeneDB ID: retro_ogar_1029

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873534.1:12227652..12228530(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MRPL45
• Ensembl ID: ENSOGAG00000015816
• Aliases: None
• Description: mitochondrial ribosomal protein L45 [Source:HGNC Symbol;Acc:16651]

Sequence

>retro_ogar_1029
GGACATTGGGATGGTGGTCTCAGCAGCCTGTTCTGGTGACTCAATCCAGAACTGTAGTTCCAGCAAGAACTAAAAACCAT
TTCACACCTCCTACTTATAAATCTAAACACAAAATGGAAAGAATTTATAGAACAAGCCCGGGAAGCAGGATTGGTCATTC
CTCCAGAATGTTTGGAGCATCCCATATATCTGGCCTGGACAGCTGGTATCTTTGATGCCTATGTGTTCCTCCAGACTCCA
GAAGGTAATGCTCACATGTCTTCTCTTTCAAAGGAAGGACTGGAACAGAGAACTGAGCGATTGTGGAAGAAAGTGGCATC
ACAATTGTCATTCTGGAAAATAAAATATGATGCTAATTTTAAAATTAAGGACTTCTCTGAAAAAGTGAAGGATATCTTCT
TGGAAGTTCACCTTTGTCTGCACAACTCAGATCAGACCAGCTTTATGCCTTTGTAACCGAATGGTGTTTCCTGTACATGG
TCTGGGACATCAAATATAACGCTATCTGCGGGCGCTTTGTGGAATCTTTAGAGCAACCTCAGATGGTCCAGGTTCGCTAT
TTAAGTCTGGTGAATCAGGGCAGCTTGTATGGCCAGGTCACCATCTGCATCACACCTGCTAGTCTCTGGCCATCTATGAC
CAGTTTGGATGGTTGATGTATGAACAGGAAAATGTACCCAAAGATGTCCTGGAGTGTGTTGTGTTTGAAATGCACCTGAA
AAACCCCTATGGAGCTGGAGAAGGCACGGCAAGATTGTTCCCTCATAGGCACTCCTTGAGCAGCCTACCCTCAAGATGGT
GATGATCCCTGGCGCCCAGCTGAAACCTTGCAAAACCATGAAGAAACACAATGAGAGGCCTATAAGCCTCAGCTGGTC

Alignment

ORF - retro_ogar_1029 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.15 %
• Parental protein coverage: 94.82 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  GWWSRQREKISWALENSL-VSGERKRQNNVYKENPDGMSKMLGRDAKKTTLLVKKSTPLICIMLLCTSGI
          G.W........W.L...L....E.K........N.....K.....A....L..........I.L..T.GI
Retrocopy GHWDGGLSSLFW*LNPEL*FQQELKTISHLLLINLNTKWKEFIEQAREAGLVIPPECLEHPIYLAWTAGI

Parental  FDAYV---PPEGDARISSLSKEGLKQRTERLKKKAASQLSLRKIKEYDADFKIKDFPEKAKDIFVEAHLC
          FDAYV....PEG.A..SSLSKEGL.QRTERL.KK.ASQLS..KIK.YDA.FKIKDF.EK.KDIF.E.HLC
Retrocopy FDAYVFLQTPEGNAHMSSLSKEGLEQRTERLWKKVASQLSFWKIK-YDANFKIKDFSEKVKDIFLEVHLC

Parental  LNNNSSR-DFIRELPTDHSFRWDMVWDIRYKTVRWRFVESLEQPQVVQIRCSSLVNQSNLYGQVTVRM-H
          L..NS...D......T...F...MVWDI.Y.....RFVESLEQPQ.VQ.R..SLVNQ..LYGQVT....H
Retrocopy LH-NSDQ<DQLYAFVTEWCFLY-MVWDIKYNAICGRFVESLEQPQMVQVRYLSLVNQGSLYGQVTICI<H

Parental  TRQTLAIYDRFGRLMYGQEDVPKDVLEYVVFEKHLTNPYG-SWRMHGKIVPSWAPPKQPILKTVMIPGPQ
          T...LAIYD.FG.LMY.QE.VPKDVLE.VVFE.HL.NPYG.SWR.HGKIVPS.A...QP.LK.VMIPG.Q
Retrocopy TC*SLAIYDQFGWLMYEQENVPKDVLECVVFEMHLKNPYG<SWRRHGKIVPS*ALLEQPTLKMVMIPGAQ

Parental  LKP-WEDHEEAQGGALKPQLV
          LKP....HEE.Q..A.KPQLV
Retrocopy LKP<LQNHEETQ*EAYKPQLV

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_1029 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.

---

Parental genes homology:

Parental genes homology involve 8 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Felis catus	ENSFCAG00000005808	2 retrocopies	retro_fcat_1677, retro_fcat_283,
Monodelphis domestica	ENSMODG00000012560	1 retrocopy	retro_mdom_403,
Nomascus leucogenys	ENSNLEG00000000530	1 retrocopy	retro_nleu_1967,
Otolemur garnettii	ENSOGAG00000015816	1 retrocopy	retro_ogar_1029 ,
Pan troglodytes	ENSPTRG00000009065	1 retrocopy	retro_ptro_107,
Ictidomys tridecemlineatus	ENSSTOG00000000304	2 retrocopies	retro_itri_102, retro_itri_1575,
Tupaia belangeri	ENSTBEG00000000585	1 retrocopy	retro_tbel_4621,
Vicugna pacos	ENSVPAG00000004977	1 retrocopy	retro_vpac_512,