RetrogeneDB ID: retro_pvam_310

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: GeneScaffold_2469:578682..579214(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CYB5R3
• Ensembl ID: ENSPVAG00000014126
• Aliases: None
• Description: cytochrome b5 reductase 3 [Source:HGNC Symbol;Acc:2873]

Sequence

>retro_pvam_310
CCACCAAAACCAGTCTCCAGACAGGAAGACAAGGGCTTAGTAGACCTGGTCATCATGGTTTACTTCAAAGATGCCCATCC
CAAGTTGCACACTGGAAGAAAGATGTCCCAGTACCTAGAAAACATGATCATTGCAGTCATCATTGAGATCTAGACCCAAA
TGTGCTGCTAGTCTACCAGACAAAGGAAAGTTTGCTATCTGTCCAGACAAGAAATCTAACCCCAACATCAAGATGGTGAA
GTCTGTTGGCATCACTGTGGGAGGAACAGGCATCACTCGGATACTGCAATTGATCCACGCCATCACAAAAGACCTGGATG
ACCACACTGTGTGCCAGTTGCTCTTTGTCATTCAGGCTGAGAATGACATCCTGCTGCAGCTGGAGCTGGTGAAACTGAGG
AACGAACACTTTGCTTGCTTCAAGCTCTAGTATGTGGTAGACAGAGCCACTATGGCCTGGGACTACAGCTAGGGCTTTGT
GAGCAAGTTGATGATCCAGGACCAACTTCCACTCCCAAAGGAGGAGCCCATG

Alignment

ORF - retro_pvam_310 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.33 %
• Parental protein coverage: 59.14 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  PYTPVSSDDDKGFVDLVIKVYFKDTHPKFPAGGKMSQYVESLKIGDTIDF-RGPNGLLVYQ-GKGKFAIR
          P..PVS...DKG.VDLVI.VYFKD.HPK...G.KMSQY.E...I...I.....PN.LLVYQ..KGKFAI.
Retrocopy PPKPVSRQEDKGLVDLVIMVYFKDAHPKLHTGRKMSQYLENMIIAVIIEI<LDPNVLLVYQ<DKGKFAIC

Parental  PDKKSNPVIKTAKSVGMIAGGTGITPMLQVIRAIMKDPDDPTVCHLLFANQTEKDILLRPELEELRNEHS
          PDKKSNP.IK..KSVG...GGTGIT..LQ.I.AI.KD.DD.TVC.LLF..Q.E.DILL..EL..LRNEH.
Retrocopy PDKKSNPNIKMVKSVGITVGGTGITRILQLIHAITKDLDDHTVCQLLFVIQAENDILLQLELVKLRNEHF

Parental  ARFKLWYTVDKAPEAWDYSQGFVNEEMIRDHLPPPEEEPL
          A.FKL.Y.VD.A..AWDYS.GFV...MI.D.LP.P.EEP.
Retrocopy ACFKL*YVVDRATMAWDYS*GFVSKLMIQDQLPLPKEEPM

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_310 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 4 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000009549	1 retrocopy	retro_amel_1305,
Bos taurus	ENSBTAG00000016516	2 retrocopies	retro_btau_1244, retro_btau_1287,
Pteropus vampyrus	ENSPVAG00000014126	1 retrocopy	retro_pvam_310 ,
Tursiops truncatus	ENSTTRG00000015143	2 retrocopies	retro_ttru_408, retro_ttru_918,