RetrogeneDB ID: retro_ogar_1852

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873570.1:3469792..3470554(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MDM4
• Ensembl ID: ENSOGAG00000011679
• Aliases: None
• Description: Mdm4 p53 binding protein homolog (mouse) [Source:HGNC Symbol;Acc:6974]

Sequence

>retro_ogar_1852
GATGACCTGTGGGTTTTGAATGAGTCAGTATCTGAGCAGTCAGGTTCTATAATAAAAGTAGAAGCTACTGCTACTAATAA
AAGAAGGGAAAAAAGTAAGGAATGTGAGTAACAAGAAGCTGGTTGAAGTGGGAAAAAATGACTTTGAGGGCTCCCCATCC
TTAAGTGATGACACAGATGTGGGAGTCCTTTTGAGGATAAGTGGTAGTGTTACCGAGGCCGAGAAATTCAACCTTCCAAA
TAACAGGGGTTTCTGCTGAAGGCTCTTGAGGAAAGATTGGTATTCAGGTTGTTCTCACTCCACCCATTTTCTCTCCCTGC
CTGTTATCACTGCTGTACTTGAAGAAAAAGGAAAATGAAGAACTTGATGTCCCAGACCACCGAAGAATCATTTAGCTTCG
GCTGTTACAGCCCGAGAGCTATATATAAAGGAAGAAAAACCCAAACTTCTTGATCCCCGCAGCTCGGCAGAATTCTTGCA
CTTGGTTCACAGTTCTGAAAGCCTAGAGACCATCTAAAGCCCAGGAGAACAATCAGCTAGCCTTTCAGAACAGAGCAGAG
ATACAGAAAGCGTGGAGGACTGACAAGATCTCTTGAAGCCTTTCAGCATCTGTGAGAAAAAAACCGTGAGATGAGAATAT
TATTCATGGAAGGTACAGGCTACCTTGTCACTTGTTCTCACTGTGGCAGAAGATTAAAGCAGCCTGGGGCTTTATGCCTT
CTTTGCAAGAAGATTCAGCCGGTTATTAAGGTTTTTATGGCA

Alignment

ORF - retro_ogar_1852 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.23 %
• Parental protein coverage: 51.72 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 7

Retrocopy - Parental Gene Alignment:

Parental  DDLWFLNESVSEQLGVGVKVGASGTEQTSEE-IGKVSDKKLIEVGRSEDLEDSKSLSDDTDVEV-NSEDE
          DDLW.LNESVSEQ.G...KV.A..T....E.....VS.KKL.EVG...D.E.S.SLSDDTDV.V...ED.
Retrocopy DDLWVLNESVSEQSGSIIKVEATATNKRREK>VRNVSNKKLVEVGKN-DFEGSPSLSDDTDVGV<PFEDK

Parental  WQC-TECKKFNSPSKR-YCFRCWALRKDWYSDCSKLTHSLSTSDITAIPE-KKENEGIDVPDCRRTI-SA
          W.C.TE..KFN.P..R..C.R...LRKDWYS.CS..TH.LS...ITA..E.KKENE..DVPD.RR.I..A
Retrocopy W*C>TEAEKFNLPNNRGFC*RL--LRKDWYSGCSHSTHFLSLPVITAVLE>KKENEELDVPDHRRII<LA

Parental  PVVRPKDVYIKEENAKLFDPCSSVEFLDLAHNSESQETILSTGEQSDNLSEQRMDTENMEDCHNLLKPCS
          ..V.....YIKEE..KL.DP.SS.EFL.L.H.SES.ETI.S.GEQS..LSEQ..DTE..ED...LLKP.S
Retrocopy SAVTARELYIKEEKPKLLDPRSSAEFLHLVHSSESLETI*SPGEQSASLSEQSRDTESVED*QDLLKPFS

Parental  LCE-KRPRDGNIIHGK-TGHLVTCFHCARRLKKSGASCPICKKEIQLVIKVFIA
          .CE.K.P.D.NIIHG..TG.LVTC.HC.RRLK..GA.C..CKK.IQ.VIKVF.A
Retrocopy ICE>KKP*DENIIHGR>TGYLVTCSHCGRRLKQPGALCLLCKK-IQPVIKVFMA

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_1852 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 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000001126	1 retrocopy	retro_amel_1730,
Mus musculus	ENSMUSG00000054387	1 retrocopy	retro_mmus_3520,
Otolemur garnettii	ENSOGAG00000011679	1 retrocopy	retro_ogar_1852 ,
Otolemur garnettii	ENSOGAG00000034779	2 retrocopies	retro_ogar_1210, retro_ogar_49,
Ictidomys tridecemlineatus	ENSSTOG00000004184	1 retrocopy	retro_itri_428,