RetrogeneDB ID: retro_ogar_2181

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873599.1:3189902..3191267(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HDAC1
• Ensembl ID: ENSOGAG00000005709
• Aliases: None
• Description: histone deacetylase 1 [Source:HGNC Symbol;Acc:4852]

Sequence

>retro_ogar_2181
GGCAGCAAGAAGAAAGTCTGCTACGACTACGATGGTGATATTGGAAATTATTATTATGGGCAGGGTCATCCCATGAAACT
GCACAGAATCCGCATGACCCATAACTTGCTGTTAAATTATGGCTTATACAGAAAAATGGAAATATATAGGCCCCATAAAG
CTACTGCCGAAGAAATGACAAAATACCACAGTGATGAGTATATACAATTTCTACGGTCAATAAGACCAGATAACACGTCT
GAGTATAGTAAGCAGATGCAGAGATTTAATGTTGGAGAGGATTGGCCAGCGTTTGATGGACTCTTTGAGTTTTGTCAGCT
CTCAACCTGTGGCTCAGTTGCTGGGGCCATGAAGTTAAACAGACAACAAACTGATATGGCTGTTAATTGGGCTGGAGGAT
TACATCATGCTAAAAAATCAGAAGCATCAGGGTTCTGTTATGTTAATGATATTGTGCTTGCCATTCTTGAATTACTAAAG
TATCATCAGAGAGTCATATATGTTGATATAGATATCCATCATGGTGATGGTGTTGAAGAAGCTTTTTATACAACAGATCG
TGTAATGACTGTACCATTCCATAAATATGGGGAATACTTTCCTGGCACAGGAGACTTGAGGGATATTGGTGCTGGGAAAG
GAAAATACTATGCTGTCAATTTTCCAATGAGAGATGGTATAGATGATGAGTCATATGGGCGGATATTTAAGCCTATTATT
TCAAAAGTGATAGAGATGTATCAGCCTAGTGCTGTGGTATTACAGTGTGGTGCAGACTCATTATCTGGTGATAGACTTGG
TTGTTTCAATCTAACAGTCAAAGGTCATGCGAAATGTGTTGAAGTTGTAAAAACTTTTAACTTACTATCACTGATGCTTG
GAGGAGGTGGCTACACAATTTGTAATGTTGCTCGATGTTGGACATATGAGACTGCTGTTGCCCTTGATTGTGAGATTTCT
AATGAGTTGCCATATAATGATTACTTTGAGTATTTTGGACCGGACTTCAAACTGCATATTAGTCCTTCAAACATGACAAA
CCAGAACACTCCAGAATATATGGAAAAGATAAAAGAGCGTTTATTTGAAAATTTGCGCATGTTGCCTCATGCACCTGGTG
TCCAAATGCAAGCTATTCTGGAAGGTGCTGTTCATGAAGACAGTGGAGATGAAGATGGAGACGATCCAGACAAGAGAATT
TCTATTTGAGCATCGGACAAGCGGATAGCTTGTGATGAAGAATTTTTAGATTCTGAAGGTGAAGGAGAAGAAGGTTGTAG
AAATGTGGCTGATCATAAGAAAGGAGCAAAGAAAGCTAGAATTGAAGAAGATAAGAAGGAAACAGAGGACAAAAAAGCAG
ATGTT

Alignment

ORF - retro_ogar_2181 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.52 %
• Parental protein coverage: 94.19 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GTRRKVCYYYDGDVGNYYYGQGHPMKPHRIRMTHNLLLNYGLYRKMEIYRPHKANAEEMTKYHSDDYIKF
          G...KVCY.YDGD.GNYYYGQGHPMK.HRIRMTHNLLLNYGLYRKMEIYRPHKA.AEEMTKYHSD.YI.F
Retrocopy GSKKKVCYDYDGDIGNYYYGQGHPMKLHRIRMTHNLLLNYGLYRKMEIYRPHKATAEEMTKYHSDEYIQF

Parental  LRSIRPDNMSEYSKQMQRFNVGEDCPVFDGLFEFCQLSTGGSVASAVKLNKQQTDIAVNWAGGLHHAKKS
          LRSIRPDN.SEYSKQMQRFNVGED.P.FDGLFEFCQLST.GSVA.A.KLN.QQTD.AVNWAGGLHHAKKS
Retrocopy LRSIRPDNTSEYSKQMQRFNVGEDWPAFDGLFEFCQLSTCGSVAGAMKLNRQQTDMAVNWAGGLHHAKKS

Parental  EASGFCYVNDIVLAILELLKYHQRVLYIDIDIHHGDGVEEAFYTTDRVMTVSFHKYGEYFPGTGDLRDIG
          EASGFCYVNDIVLAILELLKYHQRV.Y.DIDIHHGDGVEEAFYTTDRVMTV.FHKYGEYFPGTGDLRDIG
Retrocopy EASGFCYVNDIVLAILELLKYHQRVIYVDIDIHHGDGVEEAFYTTDRVMTVPFHKYGEYFPGTGDLRDIG

Parental  AGKGKYYAVNYPLRDGIDDESYEAIFKPVMSKVMEMFQPSAVVLQCGSDSLSGDRLGCFNLTIKGHAKCV
          AGKGKYYAVN.P.RDGIDDESY..IFKP..SKV.EM.QPSAVVLQCG.DSLSGDRLGCFNLT.KGHAKCV
Retrocopy AGKGKYYAVNFPMRDGIDDESYGRIFKPIISKVIEMYQPSAVVLQCGADSLSGDRLGCFNLTVKGHAKCV

Parental  EFVKSFNLPMLMLGGGGYTIRNVARCWTYETAVALDTEIPNELPYNDYFEYFGPDFKLHISPSNMTNQNT
          E.VK.FNL..LMLGGGGYTI.NVARCWTYETAVALD.EI.NELPYNDYFEYFGPDFKLHISPSNMTNQNT
Retrocopy EVVKTFNLLSLMLGGGGYTICNVARCWTYETAVALDCEISNELPYNDYFEYFGPDFKLHISPSNMTNQNT

Parental  NEYLEKIKQRLFENLRMLPHAPGVQMQAIPEDAIPEESGDEDEEDPDKRISICSSDKRIACEEEFSDSDE
          .EY.EKIK.RLFENLRMLPHAPGVQMQAI.E.A..E.SGDED..DPDKRISI..SDKRIAC.EEF.DS..
Retrocopy PEYMEKIKERLFENLRMLPHAPGVQMQAILEGAVHEDSGDEDGDDPDKRISI*ASDKRIACDEEFLDSEG

Parental  EGEGGRKNSSNFKK-AKRVKTEDEKEKDPEEKKEV
          EGE.G..N....KK.AK....E..K......K..V
Retrocopy EGEEGCRNVADHKKGAKKARIEEDKKETEDKKADV

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_2181 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 9 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Ciona intestinalis	ENSCING00000002649	1 retrocopy	retro_cint_18,
Myotis lucifugus	ENSMLUG00000013837	1 retrocopy	retro_mluc_283,
Macaca mulatta	ENSMMUG00000009948	2 retrocopies	retro_mmul_1085, retro_mmul_2518,
Mus musculus	ENSMUSG00000028800	1 retrocopy	retro_mmus_153,
Otolemur garnettii	ENSOGAG00000005709	3 retrocopies	retro_ogar_2181 , retro_ogar_3022, retro_ogar_3313,
Pelodiscus sinensis	ENSPSIG00000004134	1 retrocopy	retro_psin_44,
Rattus norvegicus	ENSRNOG00000009568	3 retrocopies	retro_rnor_1091, retro_rnor_1098, retro_rnor_2457,
Sarcophilus harrisii	ENSSHAG00000008787	1 retrocopy	retro_shar_573,
Tursiops truncatus	ENSTTRG00000001613	1 retrocopy	retro_ttru_1236,