RetrogeneDB ID: retro_pvam_32

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: GeneScaffold_1052:370498..370896(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DCK
• Ensembl ID: ENSPVAG00000004341
• Aliases: None
• Description: deoxycytidine kinase [Source:HGNC Symbol;Acc:2704]

Sequence

>retro_pvam_32
GAACGATCTGTGTGTAGTGACAGGTATATTTTTGCATCTGATTTGCATGAATCTGACCACATGAATGAAACAGAGTGGAC
AATTTATCAAGACTGGCATGACTGGATGAAATCCAGTTTGGCCAAAGCCTTTAACTGGATGGAATCATTTATCTTTGAGC
CACTCCAGAGAACTGCTTGAGTAGGACATATTTACTGGGAAAAAATGAGGAACAAGGCATTCTTGAATATTTAGAGAAGC
TTCACTATAAGCAAGAAAGTCGGCTCCTGCATATAACACAGAAAACCAACTTTGGGTATCTATAAGGAGTGCCTGTCTTA
ACACTGGATGCTAATAAAGACTTTAAAGACAAACATGACAGTCTGGATGAAAGAGTCAAAGAATTTTTGAGTACTTTA

Alignment

ORF - retro_pvam_32 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80. %
• Parental protein coverage: 51.54 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  ERSVYSDRYIFASNLYESDCMNETEWTIYQDWHDWLNN-QFGQSLELDGIIYLRATPEKCLSRIYLRGRN
          ERSV.SDRYIFAS.L.ESD.MNETEWTIYQDWHDW....QFGQSL.LDGIIYL.ATPE.CLSR.YL.G.N
Retrocopy ERSVCSDRYIFASDLHESDHMNETEWTIYQDWHDWMKS<QFGQSL*LDGIIYL*ATPENCLSRTYLLGKN

Parental  EEQGIPLEYLEKLHSKHESWLLHRTLKTNFDYLQEVPILTLDVNEDFKDKHDSLVERVKEFLSTL
          EEQGI.LEYLEKLH.K.ES.LLH.T.KTNF.YL..VP.LTLD.N.DFKDKHDSL.ERVKEFLSTL
Retrocopy EEQGI-LEYLEKLHYKQESRLLHITQKTNFGYL*GVPVLTLDANKDFKDKHDSLDERVKEFLSTL

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_32 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 8 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Felis catus	ENSFCAG00000022606	1 retrocopy	retro_fcat_1830,
Myotis lucifugus	ENSMLUG00000005844	1 retrocopy	retro_mluc_2007,
Mus musculus	ENSMUSG00000029366	1 retrocopy	retro_mmus_2735,
Oryctolagus cuniculus	ENSOCUG00000001265	1 retrocopy	retro_ocun_1247,
Pan troglodytes	ENSPTRG00000016139	1 retrocopy	retro_ptro_427,
Pteropus vampyrus	ENSPVAG00000004341	1 retrocopy	retro_pvam_32 ,
Rattus norvegicus	ENSRNOG00000003296	1 retrocopy	retro_rnor_1026,
Xenopus tropicalis	ENSXETG00000018331	1 retrocopy	retro_xtro_9,