RetrogeneDB ID: retro_ogar_2890

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873676.1:3712388..3713187(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: IDH3B
• Ensembl ID: ENSOGAG00000004684
• Aliases: None
• Description: isocitrate dehydrogenase 3 (NAD+) beta [Source:HGNC Symbol;Acc:5385]

Sequence

>retro_ogar_2890
TATACCCCGACAGAGTGTAAGGGGGAACTGGGTTCCTACGAAATGAAGTAGAGGCATAAGTTGGATTTATTTGCCAACCT
AGTCCATGAGAAGTCACTTCCTGAGTATATGACTCAGCACAACAACCTATACCTGGTAATCATTCAAGAACAGACAGAGA
GGGAGTATAGCTCTCTGGAAAACAGGAGTGTAAGGTGTGTGATTGAGTGTTTGCAGATTGTCACATAATCCAAGTCTCAG
CGGATTGCAAAGTTTGCCTTTGACTATGCCACCAAGAAGGGGTGGGGCAAGGTCACTGCTGTCCTCAAGGCCAACATCAT
GAAATTGGTGATGGGTTGTTTCTGCAGTTCTGTGAGGAGGTTGCTAAACTGAACCCCAATTCAAATTTGAGACAATGATC
ATAGACAACTGCTGCATGCAGCTGGTGCAGAATCCTTACCAGTTTCATGCATAATTTCATGTGCCCACAGTGTATAGGAA
CATTATTGACAATCTGGCTGCTGGGCTGATTGGGAGAGCTGGTTTGGTCCTGATGAGTGCAACAGTGCAGAATATACAGT
CTTTGAGAAGGGTGCCCTGCACTCATTTGCCCAGGCAATAGGCAGGAATATAGCCAACCCCACAGTCATGCTACTGTTAG
CTTCCAATATGCTACATAATCTCAACCTTGAGTAACATTACAGCATGATTGCAGATGTAATGAAGGTGATCAAAGGTGCA
AACTTGAGAAATGAGCAGCTACAGCACCACAAATAACTTCATTAAATCTGTCATAGGCCACTTGCACCCCTGTGGGAGC

Alignment

ORF - retro_ogar_2890 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.45 %
• Parental protein coverage: 70.13 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  HTPMEYKGELASYDMRLRRKLDLFANVVHVKSLPGYMTRHNNLDLVIIREQTEGEYSSLEHESARGVIEC
          .TP.E.KGEL.SY.M..R.KLDLFAN.VH.KSLP.YMT.HNNL.LVII.EQTE.EYSSLE..S.R.VIEC
Retrocopy YTPTECKGELGSYEMK*RHKLDLFANLVHEKSLPEYMTQHNNLYLVIIQEQTEREYSSLENRSVRCVIEC

Parental  LKIVTRAKSQRIAKFAFDYATKKGRGKVTAVHKANIMKL-GDGLFLQCCEEVAELYP-KIKFETMIIDNC
          L.IVT..KSQRIAKFAFDYATKKG.GKVTAV.KANIMKL.GDGLFLQ.CEEVA.L.P...KFETMIIDNC
Retrocopy LQIVT*SKSQRIAKFAFDYATKKGWGKVTAVLKANIMKL<GDGLFLQFCEEVAKLNP<QFKFETMIIDNC

Parental  CMQLVQNPYQFDV-LVMPNLYGNIIDNLAAGLVGGAGVV-PGESYSAEYAVFETGARHPFAQAVGRNIAN
          CMQLVQNPYQF......P..Y.NIIDNLAAGL.G.AG.V.P.E..SAEY.VFE.GA.H.FAQA.GRNIAN
Retrocopy CMQLVQNPYQFHA*FHVPTVYRNIIDNLAAGLIGRAGLV<PDECNSAEYTVFEKGALHSFAQAIGRNIAN

Parental  PTAMLLSASNMLRHLNLEYHSSMIADAVKKVIKV-GKVRTRDMGGYSTTTDFIKSVIGHLHPHGS
          PT.MLL.ASNML..LNLE.H.SMIAD....V.KV..KV.T..M..YSTT..FIKSVIGHLHP.GS
Retrocopy PTVMLLLASNMLHNLNLE*HYSMIAD----VMKV>SKVQT*EMSSYSTTNNFIKSVIGHLHPCGS

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_2890 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
Monodelphis domestica	ENSMODG00000005208	1 retrocopy	retro_mdom_106,
Otolemur garnettii	ENSOGAG00000004684	1 retrocopy	retro_ogar_2890 ,
Otolemur garnettii	ENSOGAG00000006735	1 retrocopy	retro_ogar_25,
Sarcophilus harrisii	ENSSHAG00000017173	1 retrocopy	retro_shar_94,
Tupaia belangeri	ENSTBEG00000011579	2 retrocopies	retro_tbel_3404, retro_tbel_4122,