RetrogeneDB ID: retro_oana_79

Retrocopy location

• Organism: Platypus (Ornithorhynchus anatinus)
• Coordinates: Contig46555:5589..6771(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HDAC2
• Ensembl ID: ENSOANG00000003631
• Aliases: None
• Description: histone deacetylase 2 [Source:HGNC Symbol;Acc:4853]

Sequence

>retro_oana_79
ATGAAGCCGCAGCGAATACGCATGGCGCATGCCCTCGTCTTGAGTTACGATTTATATAGACACATGGAAATATTCAGGCC
GCACAAAGCTGTCGAACCTGAATTATTGGCTTTTCATGACAACGAGTACGTTAATTTTCTTTCTGGAGTGAGTCCTGATA
ATTATCGAGAATTTGTTTACCAATTAAAACGGTTTAATGTTGGAGAGGCTACGGATTGCCCGGTTTTCGACGGACTGTAT
GTGTTCCAGCAGTCATGTAGTGGTGCATCCATTGATGCTGCACATCGTTTAAATCACCAACAGGCAGATATTTGCGTGAA
TTGGTCCGGCGGATTGCACCATGCGAAAAGATCTGAAGCGTCCGGTTTTTGTTACCTGAATGATATTGTTCTAGGTATAC
TCGAATTGTTAAAATACCATGCAAGGGTAATGTATATCGACATTGACGTCCATCACGGAGACGGGGTTGAAGAGGCATTT
TACGTCACTCATAGGGTTATGACAGTGAGCTTCCATAAATTTGGCAATTTTTTTCCTGGCACCGGCGACGTCACCGATAT
TGGCGTGTCATCTGGCAAATATTACAGTGTAAACGTCCCCTTAAATGATGGAATGGATGATGAGAATTTTGTCGAATTGT
TTAAAGTTATAATTGGCAGGTGTGTGGATGTTTATCGCCCGGGGGCCATTGTGTTACAATGCGGTGCCGATTCGCTAACT
GGAGATCGTTTGGGCCGTTTCAACTTGAGCATAAAAGGGCACGCTAGTTGCGTGCAATTTGTGAGGAATTTGAATATTCC
CTTATTAGTACTTGGTGGTGGTGGCTATACAATTAGAAATGTAGCGCGGTGTTGGGCGTACGAGACTGGGGTTGTATTGA
ATAAGCACGAGGATATGTCGGATCAAATTTCCCTTAACGATTATTACGATTATTATGCACCTGATTTCCAATTGCATTTG
ACACCCTCAGCGATGCCAAATTATAATACCCCGGAACATTTGGAAAAACTTCGAATTAAAATACTTGAAAACTTGAGATA
TGTTGAAAAGGCCCCAGGAGTTCAATTTGCACATGTACCTCCAGATTTTTTGCACCATGACGATGATTCTGATGAAGAAA
AACAACTACAGGTTTTTGACGAAGGCGGAGGTTTGGCCGTTGGAGATAGATTTGGATCGAGT

Alignment

ORF - retro_oana_79 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.04 %
• Parental protein coverage: 91.63 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MKPHRIRMTHNLLLNYGLYRKMEIYRPHKATAEEMTKYHSDEYIKFLRSIRPDNMSEYSKQMQRFNVGE-
          MKP.RIRM.H.L.L.Y.LYR.MEI.RPHKA...E....H..EY..FL....PDN..E...Q..RFNVGE.
Retrocopy MKPQRIRMAHALVLSYDLYRHMEIFRPHKAVEPELLAFHDNEYVNFLSGVSPDNYREFVYQLKRFNVGEA

Parental  -DCPVFDGLFEFCQLSTGGSVAGAVKLNRQQTDMAVNWAGGLHHAKKSEASGFCYVNDIVLAILELLKYH
          .DCPVFDGL..F.Q...G.S...A..LN.QQ.D..VNW.GGLHHAK.SEASGFCY.NDIVL.ILELLKYH
Retrocopy TDCPVFDGLYVFQQSCSGASIDAAHRLNHQQADICVNWSGGLHHAKRSEASGFCYLNDIVLGILELLKYH

Parental  QRVLYIDIDIHHGDGVEEAFYTTDRVMTVSFHKYGEYFPGTGDLRDIGAGKGKYYAVNFPMRDGIDDESY
          .RV.YIDID.HHGDGVEEAFY.T.RVMTVSFHK.G..FPGTGD..DIG...GKYY.VN.P..DG.DDE..
Retrocopy ARVMYIDIDVHHGDGVEEAFYVTHRVMTVSFHKFGNFFPGTGDVTDIGVSSGKYYSVNVPLNDGMDDENF

Parental  GQIFKPIISKVMEMYQPSAVVLQCGADSLSGDRLGCFNLTVKGHAKCVEVVKTFNLPLLMLGGGGYTIRN
          ...FK.II......Y.P.A.VLQCGADSL.GDRLG.FNL..KGHA.CV..V...N.PLL.LGGGGYTIRN
Retrocopy VELFKVIIGRCVDVYRPGAIVLQCGADSLTGDRLGRFNLSIKGHASCVQFVRNLNIPLLVLGGGGYTIRN

Parental  VARCWTYETAVALDC--EIPNELPYNDYFEYFGPDFKLHISPSNMTNQNTPEYMEKIKQRLFENLRMLPH
          VARCW.YET.V.L............NDY..Y..PDF.LH..PS.M.N.NTPE..EK......ENLR....
Retrocopy VARCWAYETGVVLNKHEDMSDQISLNDYYDYYAPDFQLHLTPSAMPNYNTPEHLEKLRIKILENLRYVEK

Parental  APGVQMQAIPEDAVHEDSGDEDGEDPDKRISIRASDKRIACDEEFSDS
          APGVQ....P.D..H.D....D..D..K...........A....F..S
Retrocopy APGVQFAHVPPDFLHHD----DDSDEEKQLQVFDEGGGLAVGDRFGSS

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP007412_brain	0.00 RPM	62.08 RPM
SRP007412_cerebellum	0.00 RPM	38.11 RPM
SRP007412_heart	0.00 RPM	20.01 RPM
SRP007412_kidney	0.00 RPM	50.34 RPM
SRP007412_liver	0.00 RPM	5.79 RPM
SRP007412_testis	0.00 RPM	79.11 RPM

ChIP-Seq

Ornithorhynchus anatinus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_oana_79 retrocopy.

TSS

Ornithorhynchus anatinus was not studied using FANTOM5 data.

Lab

retro_oana_79 was not experimentally validated.

Homology

Retrocopy orthology:

Ornithorhynchus anatinus 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 10 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Ciona intestinalis	ENSCING00000002649	1 retrocopy	retro_cint_18,
Echinops telfairi	ENSETEG00000008468	1 retrocopy	retro_etel_488,
Myotis lucifugus	ENSMLUG00000003117	4 retrocopies	retro_mluc_1570, retro_mluc_225, retro_mluc_2548, retro_mluc_935,
Monodelphis domestica	ENSMODG00000017860	1 retrocopy	retro_mdom_597,
Ornithorhynchus anatinus	ENSOANG00000003631	1 retrocopy	retro_oana_79 ,
Pan troglodytes	ENSPTRG00000018519	1 retrocopy	retro_ptro_69,
Sorex araneus	ENSSARG00000000354	1 retrocopy	retro_sara_651,
Ictidomys tridecemlineatus	ENSSTOG00000012779	1 retrocopy	retro_itri_374,
Tarsius syrichta	ENSTSYG00000009363	4 retrocopies	retro_tsyr_1337, retro_tsyr_1355, retro_tsyr_681, retro_tsyr_765,
Tursiops truncatus	ENSTTRG00000015043	1 retrocopy	retro_ttru_462,