RetrogeneDB ID: retro_pvam_1339

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: scaffold_64566:376..1310(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HDAC1
• Ensembl ID: ENSPVAG00000013325
• Aliases: None
• Description: histone deacetylase 1 [Source:HGNC Symbol;Acc:4852]

Sequence

>retro_pvam_1339
GTCTTATATATTGATATTGATACCCATCATGGTGATGATGTTGAAGAAGCTTTTTATACAACAGATCGTATAATGACTGT
ATCCTTCCATACATACGGTGAATACTTCCCTGGAACAGGAGACTTGAGGGGTATTGGTGCAAGAAAAGACAAATACTATG
CTGTCCATTTTCCAGCAAGAGATGGTATAGATGATGAGTCATATGGGCAGATGTGTAAGCCTATTATCTCAAAAGGGATG
AAAACATATGAATCTAGTGCTGTCATGTTAGTGTGGTGCAGACTCTCTATCTGGTGATAGACTAGGTTGCTTCAATCTGA
TGATCGAAGGTCATGCTAAATATATAGAAGTTGTAAAAACTTTCATTTTACCATTTCTGATGCTTGGGGGAGGTGGATAC
AAAATCCATAATGTTGCTCAGTGTTAGACATAGGAGACTGAGTTGCCCTTGATTGTGAGATTCCCAATGAATTGCCATAT
AATGATTACTTTGAGTATTTTAGACCAAACTTCAAATTGCATATTAGTCCTTCAAACATGACAAACCAGAACACTCCAAA
ATATATGGAAAAAATAAAACAGCGTGTAGTTGAAAATTTATTCATGTTACCTTATGCAGCTAGTGTTCTAATGCAAGCTA
TTCCAGAAGGCGCTATTCATGAAGATAGTGGAGATGAAGATGGAGAAGATCTAGACAAGAGAATTTCTATTCGGGCATCA
GATAAACTGGTAGCTTGTGATGAAGAATTCTCAGATTCAGAGGATGAAGGAGAAGGAGATTGTAGAAATGTGGCTGATCA
TAAGAAAAGAGCAAAGAAAGCTAAAATCGAGGAAGACAAGAAGGAAACAGGACAAAAATGCGAATGTTAAGGAGGAAAAT
AAATCCAAGAATAATAGTGGAGAAAAAACAGATACCAAAGGAGCCAAATCAGAA

Alignment

ORF - retro_pvam_1339 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.35 %
• Parental protein coverage: 64.11 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  VLYIDIDIHHGDGVEEAFYTTDRVMTVSFHKYGEYFPGTGDLRDIGAGKGKYYAVNYPLRDGIDDESYEA
          VLYIDID.HHGD.VEEAFYTTDR.MTVSFH.YGEYFPGTGDLR.IGA.K.KYYAV..P.RDGIDDESY..
Retrocopy VLYIDIDTHHGDDVEEAFYTTDRIMTVSFHTYGEYFPGTGDLRGIGARKDKYYAVHFPARDGIDDESYGQ

Parental  IFKPVISKVMEMFQPSAVVLQ-CGSDSLSGDRLGCFNLTIKGHAKCVEFVKSFNLPMLMLGGGGYTIRNV
          ..KP.ISK.M.....S..V...CG.DSLSGDRLGCFNL.I.GHAK..E.VK.F.LP.LMLGGGGY.I.NV
Retrocopy MCKPIISKGMKTYE-SSAVML>CGADSLSGDRLGCFNLMIEGHAKYIEVVKTFILPFLMLGGGGYKIHNV

Parental  ARCWTYETA-VALDTEIPNELPYNDYFEYFGPDFKLHISPSNMTNQNTNEYLEKIKQRLFENLRMLPHAP
          A.C.T.ET..VALD.EIPNELPYNDYFEYF.P.FKLHISPSNMTNQNT..Y.EKIKQR..ENL.MLP.A.
Retrocopy AQC*T*ETE<VALDCEIPNELPYNDYFEYFRPNFKLHISPSNMTNQNTPKYMEKIKQRVVENLFMLPYAA

Parental  GVQMQAIPEDAIPEESGDEDEEDPDKRISICSSDKRIACEEEFSDSDEEGEGGRKNSSNFKK-AKRVKTE
          .V.MQAIPE.AI.E.SGDED.ED.DKRISI..SDK..AC.EEFSDS..EGEG...N....KK.AK..K.E
Retrocopy SVLMQAIPEGAIHEDSGDEDGEDLDKRISIRASDKLVACDEEFSDSEDEGEGDCRNVADHKKRAKKAKIE

Parental  DEKEKEPEEKKE-ITEEEKTKE---DKQEAKGVKEE
          ..K.KE...K.E...EE.K.K.....K...KG.K.E
Retrocopy EDK-KETGQKCE>VKEENKSKNNSGEKTDTKGAKSE

Legend:

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

Expression

RNA-Seq

Pteropus vampyrus was not studied using RNA-Seq expression data.

ChIP-Seq

Pteropus vampyrus was not studied using ChIP-Seq data.

EST

Pteropus vampyrus was not studied using EST data.

TSS

Pteropus vampyrus was not studied using FANTOM5 data.

Lab

retro_pvam_1339 was not experimentally validated.

Homology

Retrocopy orthology:

Pteropus vampyrus 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 12 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Ciona intestinalis	ENSCING00000002649	1 retrocopy	retro_cint_18,
Callithrix jacchus	ENSCJAG00000000970	2 retrocopies	retro_cjac_2490, retro_cjac_830,
Homo sapiens	ENSG00000116478	1 retrocopy	retro_hsap_826,
Gorilla gorilla	ENSGGOG00000011741	1 retrocopy	retro_ggor_676,
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,
Nomascus leucogenys	ENSNLEG00000002473	1 retrocopy	retro_nleu_259,
Pelodiscus sinensis	ENSPSIG00000004134	1 retrocopy	retro_psin_44,
Pteropus vampyrus	ENSPVAG00000013325	1 retrocopy	retro_pvam_1339 ,
Rattus norvegicus	ENSRNOG00000009568	3 retrocopies	retro_rnor_1091, retro_rnor_1098, retro_rnor_2457,
Sarcophilus harrisii	ENSSHAG00000008787	1 retrocopy	retro_shar_573,