RetrogeneDB ID: retro_pvam_1489

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: scaffold_9988:30789..31395(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPF1
• Ensembl ID: ENSPVAG00000003729
• Aliases: None
• Description: ribosome production factor 1 homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:30350]

Sequence

>retro_pvam_1489
CAACAGACTTCTCCCAATATTCTCATCATAACATCAGATAGACCTCATGGGAGAACAGTACGACTCTGTAAACAGCTATC
TACAGTTATACCAAACTCACATATTTATTACAGAAGAGGACTAGCTCAGAAAAAGATTATTTCACAGTGTATTGCCAGAG
ACTTCACAGATCTGATTGTTATTAATGAAGATCATAAAACACCAAATGGATTAATTTTGAGTCACTTACCAAGTGGCCCG
ACTACTTATTTTAAAATGAGTAATGTTTGTCTGTGTAGGAAATTAAGAGGCAAAGACTCCACAGAACACATACCTGAAAT
AATTCTGAATAATTTTACAACACGGTTGGGTCATTCTATTGGACAGATGTTTGCACCTATCTTTCCCAATAATCCTCAAT
TCATTAGAAGGCAGGTTGCCACATTTCACAATCAATGAGATTATACCTTCTTCAGATTTCACAGATACATACTCAAGAGT
GAAAAGAAAGTGGGAATTTAGGAACTTGGACCACATTTTACCTTAAAATTAAGATCTCTTCAGAAAGGAACCTTCGATTC
TAAATATGGAGAACATGAGTGGGTCCATATGCCCCGGGAAGTAGAA

Alignment

ORF - retro_pvam_1489 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.33 %
• Parental protein coverage: 58.45 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RQTSPKILITTSDRPHGRTVRLCEQLSTVIPNSHVYYRRGLALKKIIPQCISRDFTDLIVINEDRKTPNG
          .QTSP.ILI.TSDRPHGRTVRLC.QLSTVIPNSH.YYRRGLA.KKII.QCI.RDFTDLIVINED.KTPNG
Retrocopy QQTSPNILIITSDRPHGRTVRLCKQLSTVIPNSHIYYRRGLAQKKIISQCIARDFTDLIVINEDHKTPNG

Parental  LILSHLPSGPTAHFKMSSVRLRKEIKRRGKDPTEHIPEIILNNFTTRLGHSIGRMFASLFPHNPQFIGRQ
          LILSHLPSGPT..FKMS.V.L......RGKD.TEHIPEIILNNFTTRLGHSIG.MFA..FP.NPQFI.RQ
Retrocopy LILSHLPSGPTTYFKMSNVCLCRKL--RGKDSTEHIPEIILNNFTTRLGHSIGQMFAPIFPNNPQFIRRQ

Parental  VATFHNQRDYIFFRFHRYIFKSEKKVGIQELGPRFTLKLRSLQKGTFDSKYGEYEWVHKPREMD
          VATFHNQ.DY.FFRFHRYI.KSEKKVGI.ELGP.FTLKLRSLQKGTFDSKYGE.EWVH.PRE..
Retrocopy VATFHNQ*DYTFFRFHRYILKSEKKVGI*ELGPHFTLKLRSLQKGTFDSKYGEHEWVHMPREVE

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_1489 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 7 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Erinaceus europaeus	ENSEEUG00000001097	1 retrocopy	retro_eeur_17,
Myotis lucifugus	ENSMLUG00000016028	2 retrocopies	retro_mluc_681, retro_mluc_942,
Mus musculus	ENSMUSG00000028187	1 retrocopy	retro_mmus_3026,
Oryctolagus cuniculus	ENSOCUG00000014803	1 retrocopy	retro_ocun_1133,
Pteropus vampyrus	ENSPVAG00000003729	1 retrocopy	retro_pvam_1489 ,
Rattus norvegicus	ENSRNOG00000015969	1 retrocopy	retro_rnor_1372,
Tupaia belangeri	ENSTBEG00000013600	4 retrocopies	retro_tbel_1027, retro_tbel_2204, retro_tbel_2279, retro_tbel_63,