RetrogeneDB ID: retro_ogar_1280

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873541.1:16957935..16958765(+)
• Located in intron of: ENSOGAG00000026662

Retrocopy information

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

Parental gene information

• Parental gene symbol: MRPL46
• Ensembl ID: ENSOGAG00000004736
• Aliases: None
• Description: mitochondrial ribosomal protein L46 [Source:HGNC Symbol;Acc:1192]

Sequence

>retro_ogar_1280
ACTCTGCTAGGGGTGGCAGTGGGCTGGCAGAGACTCGAGAGGCTCTAGATGGGTAGCCTGGGTTCTCACAGCCTGGTCTT
TGCAACTGCACCCTCAAACAAAGGATCCCCATAGTACCTGTCGGACACATTGTGACTGCAGCATTCACTGCTAGTCTCCT
AGCCATTGACCCCATTGCAGGAAGAAATAGTGGCTTTGCTACTACAGATCAAGATAGAGAAAAGTCTGTATTTAGACCAT
GAACTTTGCTAGATGAAAGTCCATGACTGGCAAGTTGGAAAGCTGACTTCTATAATGAAGGAGATCAACAGGATATATTG
CTGATGCAAGATTTGAAAGATAGATGAGAAAAGACATTCCTACAGTTCAAACCTGGAGCTCACATAACAGAAACTGATAA
AAAGAATGACTGAACTTCACTGCACTGCAAGCTTGATAGGAACCTCATTCCATTAGTCAGGGAGAAGCCTGGGGACCAGA
AAGTTTGGATGCTGCCCCAGGCAGAGTGGCAGCCTGGGGAGCCCCTTCAAGGAACAGCTGAGCAAATCCTGGGCACACTC
TCAAAAAACAACATGGAAGCCAAGTTCCTAAGAAACGCACCCCATGGGCACTTCCAGGTCAATTTCCCCAAGCAATCTGG
ACAGAGAGTAACCTCTGGGCCAAAGTATTCTTCTTCAAAGCACTGCTGTTAACTGGTGACTTTTCTTAGGCCAGGAAGAA
GGGCCATCATGTGTGAGTCAGTAAGGAGGAGCTGGTTGACTATTTGAAACCAAAAATACCTGGCCTAGGTTAGGAGCTTT
CTTTTGACCTCTGATGGACTGAGCTGCCTG

Alignment

ORF - retro_ogar_1280 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.73 %
• Parental protein coverage: 97.54 %
• Number of stop codons detected: 11
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  TLLGVARGWRQFERLWAGNLGSRSLALAAAPSNKGSPWRLLGAMCLQRPPLVSKPLTPL-QEEMEALLK-
          TLLGVA.GW...ERL..G.LGS.SL..A.APSNKGSP..L.....LQ...LVS.PLTPL..E....LL..
Retrocopy TLLGVAVGWQRLERL*MGSLGSHSLVFATAPSNKGSP*YLSDTL*LQHSLLVS*PLTPLQEEIVALLLQ<

Parental  QIEIEKSLYSDHELRGLEESQRLARKKADFYDEEDEEDILLAQDLEDMWEQTFLQFKPGARITEADNKND
          ....EKS......L..L.ES..LA..KADFY.E.D..DILL.QDL.D..E.TFLQFKPGA.ITE.D.KND
Retrocopy DQDREKSVFRP*TL--LDESP*LASWKADFYNEGDQQDILLMQDLKDR*EKTFLQFKPGAHITETDKKND

Parental  RTSLHRKLDRNLILLVREKLGDQDIWMLPQAEWQPGETLRGTAERTLATLSENNIEAKFLGNAPCGHYKF
          .TSLH.KLDRNLI.LVREK.GDQ..WMLPQAEWQPGE.L.GTAE..L.TLS.NN.EAKFL.NAP.GH...
Retrocopy *TSLHCKLDRNLIPLVREKPGDQKVWMLPQAEWQPGEPLQGTAEQILGTLSKNNMEAKFLRNAPHGHFQV

Parental  -KFPQALRTESNLGAKVFFFKALLLTGDFTQAGKKGHHVWVSKEELGDYLKP-KYLAQVRRFLL-SDGLS
          ..FPQA..TESNL.AKVFFFKALLLTGDF..A.KKGHHV.VSKEEL.DYLKP.KYLA.VR.FLL.SDGLS
Retrocopy <QFPQAIWTESNLWAKVFFFKALLLTGDFS*ARKKGHHV*VSKEELVDYLKP>KYLA*VRSFLLTSDGLS

Parental  CL
          CL
Retrocopy CL

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_1280 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 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000013019	1 retrocopy	retro_cjac_3018,
Felis catus	ENSFCAG00000014966	1 retrocopy	retro_fcat_480,
Microcebus murinus	ENSMICG00000015826	1 retrocopy	retro_mmur_741,
Otolemur garnettii	ENSOGAG00000004736	1 retrocopy	retro_ogar_1280 ,
Rattus norvegicus	ENSRNOG00000018547	1 retrocopy	retro_rnor_433,