RetrogeneDB ID: retro_ogar_3022

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873698.1:3263075..3264447(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOGAG00000025058
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

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

Sequence

>retro_ogar_3022
ATGGCGTACAGTCAAGTAGGCGGCAAGAAGAAAGTTTGCTGCTACTACGATGGTGATATTGGAAATTATTATTACATGCA
AGGTCATCCCATGAAACTGCACAGAATCCGCATGACCCATAACTTGCTGTTAAATTATGGCTTATACAGAAAAATGGAAA
TATATAGGCCCCATAAAGCTACTGCCAAAGAAATGACAAAATACCACAGTGATAAGTGTATCAAATTTCTGTGGTCAATA
AAACCAGATAACATGTCTGAGTATAGTAAGCAGACGCAGAGATTTAATGTTGGAGAGGATTGTCCAGTGTTTGATGGACT
TTTTGAGTTTTGTCAGCTCTCAACCGGTGGCTCAGTTGCTGGGGCCGTGAAGTTTAACCGACAACAGACTGATATGGCTG
TTAATTGGGCTGGAGGATTACAGCTAAAAAATCAGAAGCATCAGGGTTCTGTTATGTTAACGATATTGTGCTTGCCATTC
TTGAATTACTAAAGTATCATCAGAGAGTCTTATATATTGATATAGATATCCATCATGGTGATGGTGTTGAAGAAGCTTTT
TATACAACAGATCGTGTAATGACTGTATCATTCCATAAATATGGGGAATACTTTCCTGGCACGGGAGACTTGAGGGATAT
TGGTGCTGGAAAAGGCAAATACTATGCTGTCAATTTTCCAGTGAGAGATGGTATGGATGATGAGTCATATGGGCAGATAT
TTAAGCCTATTATTTCAAAAGTGATGGAGATGTATCAGCCTAGTGCTGTCGTATTACAGGGTGGTGCAGACTCATTATCT
GGTAATAGACTTGATTGTTTCAATCTAACAGTCAAAGGTCATGCTAAATGTGTTGAAGTTGTAAAAACTTTTAACTTACC
TTACTGATGCTTGGAGGAGGTGGCTACACAATTTGTAATATTGCTCGATGTTGGACATAAGAGACTGCTGTTGGCCTTGA
TTGTGAGATTCCTAATAAGTTGCCATATAATGATTACTTTGAATATTTTGGACCAGACTTCAAACTGCATATTAGTCCTT
CAAATATGACAAACCAGAACACTCCAGAATATATGGAAAAGATAAAACAGTGTTTATTTGAAAATTTGCGCATGTTGCCT
CATGCACCTGGTGTCCAAATGCAAGCTATTCCAGAAGATGCTATTTGTGAAGACAGTGGAGATGAAGATGGAGAAGAGTC
AGACAAGAGAATTTCTATTCGAGCATCAGACAAGCGGATAGCTTGTGATGAAGAATTTTCAGATTCTGAAGATGAAGGAG
AAGGAGGTCGTAGAATTGTGGCTGATTATAAGAAAGGAGCAAAGAAAGCTAGTACTGAAGATAAGAAGGAAACAGAGGAC
AAAAAAAGCAGA

Alignment

ORF - retro_ogar_3022 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.78 %
• Parental protein coverage: 94.81 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAQTQ-GTRRKVCYYYDGDVGNYYYGQGHPMKPHRIRMTHNLLLNYGLYRKMEIYRPHKANAEEMTKYHS
          MA..Q.G...KVC.YYDGD.GNYYY.QGHPMK.HRIRMTHNLLLNYGLYRKMEIYRPHKA.A.EMTKYHS
Retrocopy MAYSQVGGKKKVCCYYDGDIGNYYYMQGHPMKLHRIRMTHNLLLNYGLYRKMEIYRPHKATAKEMTKYHS

Parental  DDYIKFLRSIRPDNMSEYSKQMQRFNVGEDCPVFDGLFEFCQLSTGGSVASAVKLNKQQTDIAVNWAGGL
          D..IKFL.SI.PDNMSEYSKQ.QRFNVGEDCPVFDGLFEFCQLSTGGSVA.AVK.N.QQTD.AVNWAGGL
Retrocopy DKCIKFLWSIKPDNMSEYSKQTQRFNVGEDCPVFDGLFEFCQLSTGGSVAGAVKFNRQQTDMAVNWAGGL

Parental  HHAKKSEASG-FCYVNDIVLAILELLKYHQRVLYIDIDIHHGDGVEEAFYTTDRVMTVSFHKYGEYFPGT
          ...K.....G.FCYVNDIVLAILELLKYHQRVLYIDIDIHHGDGVEEAFYTTDRVMTVSFHKYGEYFPGT
Retrocopy -QLKNQKHQG<FCYVNDIVLAILELLKYHQRVLYIDIDIHHGDGVEEAFYTTDRVMTVSFHKYGEYFPGT

Parental  GDLRDIGAGKGKYYAVNYPLRDGIDDESYEAIFKPVMSKVMEMFQPSAVVLQCGSDSLSGDRLGCFNLTI
          GDLRDIGAGKGKYYAVN.P.RDG.DDESY..IFKP..SKVMEM.QPSAVVLQ.G.DSLSG.RL.CFNLT.
Retrocopy GDLRDIGAGKGKYYAVNFPVRDGMDDESYGQIFKPIISKVMEMYQPSAVVLQGGADSLSGNRLDCFNLTV

Parental  KGHAKCVEFVKSFNLP-MLMLGGGGYTIRNVARCWTYETAVALDTEIPNELPYNDYFEYFGPDFKLHISP
          KGHAKCVE.VK.FNLP..LMLGGGGYTI.N.ARCWT.ETAV.LD.EIPN.LPYNDYFEYFGPDFKLHISP
Retrocopy KGHAKCVEVVKTFNLP<LLMLGGGGYTICNIARCWT*ETAVGLDCEIPNKLPYNDYFEYFGPDFKLHISP

Parental  SNMTNQNTNEYLEKIKQRLFENLRMLPHAPGVQMQAIPEDAIPEESGDEDEEDPDKRISICSSDKRIACE
          SNMTNQNT.EY.EKIKQ.LFENLRMLPHAPGVQMQAIPEDAI.E.SGDED.E..DKRISI..SDKRIAC.
Retrocopy SNMTNQNTPEYMEKIKQCLFENLRMLPHAPGVQMQAIPEDAICEDSGDEDGEESDKRISIRASDKRIACD

Parental  EEFSDSDEEGEGGRKNSSNFKK-AKRVKTEDEKEKDPEEKK
          EEFSDS..EGEGGR......KK.AK...TED.KE.......
Retrocopy EEFSDSEDEGEGGRRIVADYKKGAKKASTEDKKETEDKKSR

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_3022 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 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,