RetrogeneDB ID: retro_pvam_215

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: GeneScaffold_1939:35113..35493(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: YIPF6
• Ensembl ID: ENSPVAG00000014526
• Aliases: None
• Description: Yip1 domain family, member 6 [Source:HGNC Symbol;Acc:28304]

Sequence

>retro_pvam_215
AATGCTGACAGCGAAAAAGACGGAGGGCCCCGGTTGGCAGAAATGTTGGTCATCATTTGGTTTGGGGCAGTTACCATCAT
CCTCAACTCGAAACTTCCTGGAGGAAACGTCCTTTTTTTCAGAGCCTCTGTACGCTGAGTTACTGCATACTTCCCTTCAC
AGGGGCCGGCAGTGCTGGTGGCCGGCTGGTGCTTTTGGCTGAGCTAGGACCGATAAACCGCATAGCCCGGCTTTTGGTGG
TGATCGTGATGTTCGCCTGGTCTCTAGTAGCTTCCGCAGCTGTCCTCGCCGACAGCCAGCCTCCAGCCCGCAAAGCCCTC
GCCTCCTGCCCCGCGTTCTTGTTCTATTTCGTCATCAGTTGGACGATTCTCACCTTCACG

Alignment

ORF - retro_pvam_215 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.66 %
• Parental protein coverage: 53.62 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SADSEKDGGPQFAEVFVIIWFGAVTITLNSKLLGGNI-SFFQSLCVLGYCILPLTVAMLVCRLVLL-AEH
          .ADSEKDGGP..AE..VIIWFGAVTI.LNSKL.GGN...FFQSLC.L.YCILP.T.A........L.AE.
Retrocopy NADSEKDGGPRLAEMLVIIWFGAVTIILNSKLPGGNV<PFFQSLCTLSYCILPFTGAGSAGGRLVLLAEL

Parental  GPINFMVRLLVVIVMFAWSIVASTAFLADSQPPNRKALAVYPVFLFYFVISWMILTFT
          GPIN...RLLVVIVMFAWS.VAS.A.LADSQPP.RKALA..P.FLFYFVISW.ILTFT
Retrocopy GPINRIARLLVVIVMFAWSLVASAAVLADSQPPARKALASCPAFLFYFVISWTILTFT

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_215 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Felis catus	ENSFCAG00000023551	1 retrocopy	retro_fcat_103,
Otolemur garnettii	ENSOGAG00000002223	1 retrocopy	retro_ogar_2677,
Pteropus vampyrus	ENSPVAG00000014526	1 retrocopy	retro_pvam_215 ,