RetrogeneDB ID: retro_pvam_190

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: GeneScaffold_1783:157921..158434(-)
• Located in intron of: ENSPVAG00000002696

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSPVAG00000012305
• Aliases: None
• Description: None

Sequence

>retro_pvam_190
GCGGTGATGGCAGTGGAGCTGACGCTGCTGGAGAAGTCCCTGGGGCTGAGTAAAGGAAACAAATACAGTATTCGGGGTGA
GTGTCAGATTCCAGTTCTTAAAACGAAGAATAGACTAAGTCTAACAGGACTGACTACTATAACAGTCAAGCAAGCCAATA
AAGAATATTTGCTCGGGAGCACTAGAGAAGAAAAAGCAATAGTTCAACAATGGTTAGAATACAGAGTAACTCAAGTAGAT
GGACACTCTAATAAAGATGATATCCACATTCTGTTGAAGGATCTTAATTCACATCTTGAAGATAAAGTCTGCTTTACAGA
ATATAAATTTACCTTAGCAGATATCCTATTATACTATGGACTTCATCGCTTTATAGCTGACCTGAAAGTTCAAGAAAAGG
AGAAATATCTTAATGTACCTCGCTGGTTTTGTGATGTTCAGTATTATCCAGGCATCAGGCAATATCTGTCTAGTGTTGTC
TTCATGAAGAACAGACTATTTACTAGTTCCTAC

Alignment

ORF - retro_pvam_190 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.16 %
• Parental protein coverage: 98.86 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  AAATTELMLLEKSLGLSKGNKYSAQGERQIPVLQTNNGPSLTGLTTIAAHLVKQANKEYLLGSTAEEKAI
          A....EL.LLEKSLGLSKGNKYS..GE.QIPVL.T.N..SLTGLTTI....VKQANKEYLLGST.EEKAI
Retrocopy AVMAVELTLLEKSLGLSKGNKYSIRGECQIPVLKTKNRLSLTGLTTIT---VKQANKEYLLGSTREEKAI

Parental  VQQWLEYRVTRVDGYSNKDDIRILLKDSNSYLEDKVYLTGYNFTLADILLYYGLHR-IVDLTVQEKEKYL
          VQQWLEYRVT.VDG.SNKDDI.ILLKD.NS.LEDKV..T.Y.FTLADILLYYGLHR.I.DL.VQEKEKYL
Retrocopy VQQWLEYRVTQVDGHSNKDDIHILLKDLNSHLEDKVCFTEYKFTLADILLYYGLHRFIADLKVQEKEKYL

Parental  NVSRWFCHIQHYPGIRQHLSSVVFIKNRLYTNSH
          NV.RWFC..Q.YPGIRQ.LSSVVF.KNRL.T.S.
Retrocopy NVPRWFCDVQYYPGIRQYLSSVVFMKNRLFTSSY

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_190 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 10 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000017318	1 retrocopy	retro_amel_636,
Dasypus novemcinctus	ENSDNOG00000019203	1 retrocopy	retro_dnov_1550,
Erinaceus europaeus	ENSEEUG00000006156	1 retrocopy	retro_eeur_87,
Felis catus	ENSFCAG00000011622	1 retrocopy	retro_fcat_1075,
Macropus eugenii	ENSMEUG00000008960	1 retrocopy	retro_meug_1883,
Microcebus murinus	ENSMICG00000012636	1 retrocopy	retro_mmur_1404,
Myotis lucifugus	ENSMLUG00000007715	1 retrocopy	retro_mluc_1474,
Mustela putorius furo	ENSMPUG00000000588	1 retrocopy	retro_mputfur_486,
Pteropus vampyrus	ENSPVAG00000012305	2 retrocopies	retro_pvam_1374, retro_pvam_190 ,
Rattus norvegicus	ENSRNOG00000016390	5 retrocopies	retro_rnor_1682, retro_rnor_2013, retro_rnor_2132, retro_rnor_2133, retro_rnor_785,