RetrogeneDB ID: retro_pvam_390

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: GeneScaffold_2907:617977..618598(+)
• Located in intron of: ENSPVAG00000015191

Retrocopy information

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

Parental gene information

• Parental gene symbol: SLC25A40
• Ensembl ID: ENSPVAG00000007425
• Aliases: None
• Description: solute carrier family 25, member 40 [Source:HGNC Symbol;Acc:29680]

Sequence

>retro_pvam_390
GATGCCTTTTTGAAAATCATTCGAAACAAGAACATTAAATTCCTGTGGAGTGGAGTTTCCCTTACTTTAGTGATGGCAGT
TCCTGCCACAGTTATTTATTTTATATACTATGATCAATTAACTGCTCTTCTGAGATCTAAATTAGAAGAAAATAAAAGCT
GCATATCAATTGTTGCTGGAATTGTAGTGAGATTTGGTGCAGTAACTGCGATGAGTCAATTAAAATTGATTGGAACCAAG
ATGCAATCTAAAAAGTTTTCTTACAAGGAACCGCATCAATTTATCAGCAGGAAAGTATCTAAAGATGGTTGGATTTCCCT
TTGGAGGGGCTGGGCCTCCACTGTTTTTAGAGATGTAACATTCTCAGCAATGTACTGGTGTAACTATGAAGTTTTAAAGA
AGTGATTGTGTGAAAAATCTGATTTAGATGATCTAGCATTTATGATCAACTTTACTTCAGGAGCAAAGTCTGGTTCTTTT
GCAGCTGTTACAACTTTACCATTTGATGTGGTGAAAACACAAAAGCAGACTTAACTTTGGATGTAGGAAAGTCATAAAAT
GTCTATGCTTTCGTGTACATGTACCTGGGTTATAATGAACACTATTGCTAAGGATGGGTAT

Alignment

ORF - retro_pvam_390 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.04 %
• Parental protein coverage: 61.72 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  DAFWKIIRNEGIKSLWSGLPPTLVMAVPATVIYFTCYDQLTALLRSKLGENESHIPIVAGIVARFGAVTV
          DAF.KIIRN..IK.LWSG...TLVMAVPATVIYF..YDQLTALLRSKL.EN.S.I.IVAGIV.RFGAVT.
Retrocopy DAFLKIIRNKNIKFLWSGVSLTLVMAVPATVIYFIYYDQLTALLRSKLEENKSCISIVAGIVVRFGAVTA

Parental  ISPLELIRTKMQSKKFSYNELHQYVSKRVSEDGWISLWRGWAPTVLRDVPFSAMYWYNYEVLKKWLCEKS
          .S.L.LI.TKMQSKKFSY.E.HQ..S..VS.DGWISLWRGWA.TV.RDV.FSAMYW.NYEVLKK.LCEKS
Retrocopy MSQLKLIGTKMQSKKFSYKEPHQFISRKVSKDGWISLWRGWASTVFRDVTFSAMYWCNYEVLKK*LCEKS

Parental  GLYEPTFMINFTSGALSGSFAAVATLPFDVVKTQKQTQLWMYESHKISVPLHMSTWAIMKNIVVKNGF
          .L....FMINFTSGA.SGSFAAV.TLPFDVVKTQKQT.LWM.ESHK.S......TW.IM.N...K.G.
Retrocopy DLDDLAFMINFTSGAKSGSFAAVTTLPFDVVKTQKQT*LWM*ESHKMSMLSCTCTWVIM-NTIAKDGY

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_390 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Pteropus vampyrus	ENSPVAG00000007425	1 retrocopy	retro_pvam_390 ,