RetrogeneDB ID: retro_pvam_1415

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: scaffold_81952:117..591(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MXD1
• Ensembl ID: ENSPVAG00000001244
• Aliases: None
• Description: MAX dimerization protein 1 [Source:HGNC Symbol;Acc:6761]

Sequence

>retro_pvam_1415
ATGGTGTCGGCGGTTTAGATAAACATCCAGATGCTGCTGGAGGCGGCCGGCTGTCTGGAGCGGCAGGAGAGAGAAGCTAA
ACATGGTCACGCCTCCATCTTACCCTACAGTAACAAAGACAGAGATGCCTTAAAACAAAGGAACAAATCCAAGAAGAATA
ACAGCAGTAGCAGATCGACTCACAATGAAATGGAGAATAGTCGGTCCCATCTTCACTTGTGCCTGGAGAAGTCAAAGGGG
CTAGTACAGCTTGGGCCCAGATGAAACCAACACACCGCATTGAGTTTATGAACAAAAGCCAAATTGCACATAAAAAAACT
AGGTGATTGTGACAGAAAAGCCACTGTCTGAATAGACCAGCTTCAGCGAGAGCGGCAACATCTGAAGAGGCAGCTGGAGA
AACTGGGCATTGAGAGGATATGGAGAGACAGCGTCGGCTCCACGGGCTCCTTGGAGTGCTCAGACTCCGACAGG

Alignment

ORF - retro_pvam_1415 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.36 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 4
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAAAVRMNIQMLLEAADYLERREREAEHGYASMLPYNNKDRDALKRRSKSKKNNSSSRSTHNEMEKNRRA
          M..AV..NIQMLLEAA..LER.EREA.HG.AS.LPY.NKDRDALK.R.KSKKNNSSSRSTHNEME.N.R.
Retrocopy MVSAV*INIQMLLEAAGCLERQEREAKHGHASILPYSNKDRDALKQRNKSKKNNSSSRSTHNEME-NSRS

Parental  HLRLCLEKLKGLVPLGPESNRHTTLSLLTKAKLHIKKLEDCDRKAIHQIDQLQREQRHLKRQLEKLGIER
          HL.LCLEK.KGLV.LGP..N.HT.LSL.TKAKLHIKKL.DCDRKA...IDQLQRE..HLKRQLEKLGIER
Retrocopy HLHLCLEKSKGLVQLGPR*NQHTALSL*TKAKLHIKKLGDCDRKATV*IDQLQRERQHLKRQLEKLGIER

Parental  IRMDSIGSTVSSERSDSDR
          I..DS.GST.S.E.SDSDR
Retrocopy IWRDSVGSTGSLECSDSDR

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_1415 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 2 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000003047	1 retrocopy	retro_chof_1224,
Pteropus vampyrus	ENSPVAG00000001244	2 retrocopies	retro_pvam_1415 , retro_pvam_1430,