RetrogeneDB ID: retro_pvam_928

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: scaffold_17120:6729..7047(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: POLR3K
• Ensembl ID: ENSPVAG00000000530
• Aliases: None
• Description: polymerase (RNA) III (DNA directed) polypeptide K, 12.3 kDa [Source:HGNC Symbol;Acc:14121]

Sequence

>retro_pvam_928
CTTCTCTTCTGCCTTGGCTGCAGGAACAGGGCTGATCATGGAGGAGGGATAGCGCTGTCACCATTTTGCCTGCAATACCT
GCCCTTATACTCACAACATCACCTGAAGGGTAACAAATCAGAAGTATTCAAAGATGAAAGTGAATGATGTACTGGCGGAG
CATCTGCCTAGGAGAATGTTAACTCTACTGCAGAGAGGTGTCCCAAATGTGAACATCCTTGTGCTTATTTTATGCAGCTC
CAGGCGCACTCTGCAGACTAGCCAATGACTACCTTCTGCAAGTGCTGTAATGCTCAGTGTGGACACCGCTGAAGGGAC

Alignment

ORF - retro_pvam_928 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.06 %
• Parental protein coverage: 99.07 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LLFCPGC-GNGLIVEEGQRCHRFACNTCPYVHNITRKVTNRKYPKLKEVDDVL-GGAAAWENVDSTAEPC
          LLFC.GC.G.GLI.EEG.RCH.FACNTCPY.HNIT..VTN.KY.K.K.V.DVL.GGA.A.ENV.STAE.C
Retrocopy LLFCLGC>GTGLIMEEG*RCHHFACNTCPYTHNIT*RVTNQKYSKMK-VNDVL<GGASA*ENVNSTAERC

Parental  PKCEHPRAYFMQLQTRSADEPMTTFYKCCNAQCGHRWRD
          PKCEHP.AYFMQLQ..SAD.PMTTF.KCCNAQCGHR.RD
Retrocopy PKCEHPCAYFMQLQAHSAD*PMTTFCKCCNAQCGHR*RD

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_928 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 11 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000019715	1 retrocopy	retro_cfam_1881,
Callithrix jacchus	ENSCJAG00000011568	1 retrocopy	retro_cjac_2660,
Echinops telfairi	ENSETEG00000009989	2 retrocopies	retro_etel_1166, retro_etel_1543,
Felis catus	ENSFCAG00000009110	2 retrocopies	retro_fcat_1978, retro_fcat_409,
Homo sapiens	ENSG00000161980	1 retrocopy	retro_hsap_1861,
Myotis lucifugus	ENSMLUG00000015593	3 retrocopies	retro_mluc_1565, retro_mluc_1943, retro_mluc_341,
Oryctolagus cuniculus	ENSOCUG00000013608	1 retrocopy	retro_ocun_145,
Otolemur garnettii	ENSOGAG00000002526	2 retrocopies	retro_ogar_1101, retro_ogar_254,
Pan troglodytes	ENSPTRG00000007525	1 retrocopy	retro_ptro_1241,
Pteropus vampyrus	ENSPVAG00000000530	1 retrocopy	retro_pvam_928 ,
Sus scrofa	ENSSSCG00000007970	1 retrocopy	retro_sscr_1141,