RetrogeneDB ID: retro_pvam_406

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: GeneScaffold_2980:59740..60067(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CHURC1
• Ensembl ID: ENSPVAG00000011384
• Aliases: None
• Description: churchill domain containing 1 [Source:HGNC Symbol;Acc:20099]

Sequence

>retro_pvam_406
ATGTGTGGGGACTGCGTGGAGAAGAAATATCCAAACTAGGGTAACAACAGCCTGGAAGATGGATATTTCCTGCTGAACTT
TACAGAATGTACAGTGTGTAGTATGTGAGATTTTATGCTGATCACAAACAAATTTTTGAAAGTGGAAGATGAAGAAATAG
TTACTTATGATCATCTGTGTAAGAATTGTTATCACAGGAGGCATGAGTATACATTCAGTATCATGAATGAGTTTCAGGAG
TATACCATGCTGTGTCTGTTATGTGGCAAAGCTGATGATACCGTCAGTATTCTCCTTGATGACCCCTGACAAATGACTCT
GTTATTT

Alignment

ORF - retro_pvam_406 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.88 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MCGDCVEKEYPNRGNICLENGSFLLNFTGCAVCNKRDFMLITNKSLKEEDGEEIVTYDPDLCKNCHHVVA
          MCGDCVEK.YPN.GN..LE.G.FLLNFT.C.VC...DFMLITNK.LK.ED.EEIVTYD..LCKNC.H...
Retrocopy MCGDCVEKKYPN*GNNSLEDGYFLLNFTECTVCSM*DFMLITNKFLKVED-EEIVTYD-HLCKNCYH--R

Parental  RHEYTFSIMDEFQEYTMLCLLCGKAEDTISILPDDPRQMTLLF
          RHEYTFSIM.EFQEYTMLCLLCGKA.DT.SIL.DDP.QMTLLF
Retrocopy RHEYTFSIMNEFQEYTMLCLLCGKADDTVSILLDDP*QMTLLF

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_406 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 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Myotis lucifugus	ENSMLUG00000004300	1 retrocopy	retro_mluc_2068,
Monodelphis domestica	ENSMODG00000009664	1 retrocopy	retro_mdom_1775,
Mustela putorius furo	ENSMPUG00000006792	1 retrocopy	retro_mputfur_554,
Oryctolagus cuniculus	ENSOCUG00000001838	1 retrocopy	retro_ocun_997,
Pteropus vampyrus	ENSPVAG00000011384	1 retrocopy	retro_pvam_406 ,