RetrogeneDB ID: retro_ogar_3313

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873775.1:208689..210008(+)
• Located in intron of: ENSOGAG00000002148

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_3313
ATGGCACAGACACAGGGCACAAGGAAGAAAGTCTGTTACTACTATGATGGGGATGTTGGAAATTATTATTATGGACAAGG
CCACCCAACGAAGCCTAACCGAATCTGCATGACTCACAATTTGCTACTTAACCATGGTCTCTACTGAAAAATGGAAATCT
ATCGCCCTCATAAAGCCAATGCTGAGGAAATAACCAAGTACCACAGTGATGACTACATTAAATTCTTGTGCTCCATCCAT
CCAGATAACATGTCTGAATACAGCAAGCAGATGCAGAGATTCAATGTTGGTGAGAACCGTCCAGTATTTGATGGCCTGTT
TGAGTTCTGTCAGTTGTCTACTAGTGGCTCTGTGGCAAATGCTGTGAAACTTAAGACAGACATCGCTGTGAATTGGGCTG
GGGCCTGCACCATGCAAAGAAGTCCAAGGCATCTGGCTTCTGTTACATCAATGATATTGTCTTGGCCATCCTGGAACTGC
TAAAGTATCACCAGAGGGTGCTATATATTGACAATGATATTCACTGTGACGATGGCGTGGAAGAGGCCTTCTATACCACA
GACCAGGTCGTGACTATGTCCTTTCATAAAAATGGAGAGTACTTCCCAGGAACTGGGGACCTACGGGATATTGGGGCTGG
CAAAGGCAAGTATTAGGCTGTGAACTATCTGCTCTAAGATGGGATTGATGACGAGTCCTATGAGGCCATTTTCAAGCTGG
TAATGTCCAAAGTAATGGAGATGTTCCAGCCCAGTGCAGTGGTCTTACATTGTGGCTCAGACTTCCAGTCTGAGTATCAG
TTAGGTTGCTTCAATCTGACCATCAAAGGTCATGCCAAGTGTGTGGAATATGTCAAAAGCTTCAACCTGCCTATGTTGAT
GCTGGGAGGAGGGGGTTATACCATTTGTAGTGTTGCCCAATGCTAGACATATGAAACAGCTGTGGCCCTGGACACAAAAA
ATCCCTAATGAGCTTCCATACAATGACTACTTTGAATACTTTGGTCCAGACTTCAACCTTCACATCAGCCCCTCCAATAT
GACTAACCAGAATACTAATGAGTATTTGGAGAAGATCAAACAGCGACTGTTTGAGAACTTCAGGATACTGCCCCATGCAC
CAGGGGTTCAGATTCAGGCAATTCCTGAGGATGCCATCCCAGAGGAAAGTAGTGATGAGGATGAAGAAGACCCTGACAAA
TTCATCTCCGTCTGTTCCTCTGACAAATGAATTGCCTGTGAGGAAGAGTTCTCTGACTCGGATGAGGAAGGAGAGTACAG
CCGAAGAACACTTCCAACTTCAAAAAAGCTAAGAGAGTC

Alignment

ORF - retro_ogar_3313 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.44 %
• Parental protein coverage: 91.91 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MAQTQGTRRKVCYYYDGDVGNYYYGQGHPMKPHRIRMTHNLLLNYGLYRKMEIYRPHKANAEEMTKYHSD
          MAQTQGTR.KVCYYYDGDVGNYYYGQGHP.KP.RI.MTHNLLLN.GLY.KMEIYRPHKANAEE.TKYHSD
Retrocopy MAQTQGTRKKVCYYYDGDVGNYYYGQGHPTKPNRICMTHNLLLNHGLY*KMEIYRPHKANAEEITKYHSD

Parental  DYIKFLRSIRPDNMSEYSKQMQRFNVGEDCPVFDGLFEFCQLSTGGSVASAVKLNKQQTDIAVNWAG-GL
          DYIKFL.SI.PDNMSEYSKQMQRFNVGE..PVFDGLFEFCQLST.GSVA.AVKL....TDIAVNWAG.GL
Retrocopy DYIKFLCSIHPDNMSEYSKQMQRFNVGENRPVFDGLFEFCQLSTSGSVANAVKL---KTDIAVNWAG<GL

Parental  HHAKKSEASGFCYVNDIVLAILELLKYHQRVLYIDIDIHHGDGVEEAFYTTDRVMTVSFHKYGEYFPGTG
          HHAKKS.ASGFCY.NDIVLAILELLKYHQRVLYID.DIH..DGVEEAFYTTD.V.T.SFHK.GEYFPGTG
Retrocopy HHAKKSKASGFCYINDIVLAILELLKYHQRVLYIDNDIHCDDGVEEAFYTTDQVVTMSFHKNGEYFPGTG

Parental  DLRDIGAGKGKYYAVNYPLRDGIDDESYEAIFKPVMSKVMEMFQPSAVVLQCGSDSLSGDRLGCFNLTIK
          DLRDIGAGKGKY.AVNY.L.DGIDDESYEAIFK.VMSKVMEMFQPSAVVL.CGSD..S...LGCFNLTIK
Retrocopy DLRDIGAGKGKY*AVNYLL*DGIDDESYEAIFKLVMSKVMEMFQPSAVVLHCGSDFQSEYQLGCFNLTIK

Parental  GHAKCVEFVKSFNLPMLMLGGGGYTIRNVARCWTYETAVALDT-EIPNELPYNDYFEYFGPDFKLHISPS
          GHAKCVE.VKSFNLPMLMLGGGGYTI..VA.C.TYETAVALDT..IPNELPYNDYFEYFGPDF.LHISPS
Retrocopy GHAKCVEYVKSFNLPMLMLGGGGYTICSVAQC*TYETAVALDT>KIPNELPYNDYFEYFGPDFNLHISPS

Parental  NMTNQNTNEYLEKIKQRLFENLRMLPHAPGVQMQAIPEDAIPEESGDEDEEDPDKRISICSSDKRIACEE
          NMTNQNTNEYLEKIKQRLFEN.R.LPHAPGVQ.QAIPEDAIPEES.DEDEEDPDK.IS.CSSDK.IACEE
Retrocopy NMTNQNTNEYLEKIKQRLFENFRILPHAPGVQIQAIPEDAIPEESSDEDEEDPDKFISVCSSDK*IACEE

Parental  EFSDSDEEGEGGR-KNSSNFKKAKRV
          EFSDSDEEGE..R.KN.SNFKKAKRV
Retrocopy EFSDSDEEGEYSR<KNTSNFKKAKRV

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_3313 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,