RetrogeneDB ID: retro_pvam_391

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: GeneScaffold_2907:1330584..1330968(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PFDN6
• Ensembl ID: ENSPVAG00000001910
• Aliases: None
• Description: prefoldin subunit 6 [Source:HGNC Symbol;Acc:4926]

Sequence

>retro_pvam_391
ATGGCTAAGCTGATCTAGAAGAAGCTACCGGGAAAAGTGGAGAAAAAACAGCCTCAAAAGGACTTGAGTAAATTCATGTC
AGGGTGGCAGAAGCTTGAAGCACGACTAACAGAAAATAATATCATGAAGGAGGAACTGGCCCTGCTGGCTGGGTTCAACG
TAGTTTTTAAACTTCTGGGCCCTGTGCTGGTCAAACAGGAGCTAGGGGAGGCTTGGGTTACAGTGAGGAAGAGGCTGGAC
TATATCACAGCTGAAATTAAGCGTTATGAATTCCAGTTCCGGGACCTCGAGTGGCAGTCAGAGCAACAGAGGAAGACCCT
TGCTCAGCAAAAGCAGGAGTTCCAGCAGGCCCAGGCAGCAAAAGCAGGGGATTCTGGGAAGGCC

Alignment

ORF - retro_pvam_391 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.4 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAELIQKKLQGEVEKYQQLQKDLSKSMSGRQKLEAQLTENNIVKEELALLDGSNVVFKLLGPVLVKQELG
          MA.LI.KKL.G.VEK..Q.QKDLSK.MSG.QKLEA.LTENNI.KEELALL.G.NVVFKLLGPVLVKQELG
Retrocopy MAKLI*KKLPGKVEK-KQPQKDLSKFMSGWQKLEARLTENNIMKEELALLAGFNVVFKLLGPVLVKQELG

Parental  EARATVGKRLDYITAEIKRYESQLRDLERQSEQQRETLAQLQQEFQRAQAAKAGASGKA
          EA..TV.KRLDYITAEIKRYE.Q.RDLE.QSEQQR.TLAQ..QEFQ.AQAAKAG.SGKA
Retrocopy EAWVTVRKRLDYITAEIKRYEFQFRDLEWQSEQQRKTLAQQKQEFQQAQAAKAGDSGKA

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_391 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 12 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000001576	2 retrocopies	retro_amel_221, retro_amel_824,
Bos taurus	ENSBTAG00000010723	1 retrocopy	retro_btau_619,
Canis familiaris	ENSCAFG00000000956	2 retrocopies	retro_cfam_1749, retro_cfam_1981,
Dipodomys ordii	ENSDORG00000013828	1 retrocopy	retro_dord_453,
Felis catus	ENSFCAG00000028199	1 retrocopy	retro_fcat_1784,
Macropus eugenii	ENSMEUG00000016778	1 retrocopy	retro_meug_1930,
Microcebus murinus	ENSMICG00000000922	1 retrocopy	retro_mmur_1520,
Mustela putorius furo	ENSMPUG00000002364	1 retrocopy	retro_mputfur_608,
Oryctolagus cuniculus	ENSOCUG00000010559	1 retrocopy	retro_ocun_711,
Otolemur garnettii	ENSOGAG00000028341	4 retrocopies	retro_ogar_1185, retro_ogar_2023, retro_ogar_3508, retro_ogar_85,
Ochotona princeps	ENSOPRG00000000983	1 retrocopy	retro_opri_12,
Pteropus vampyrus	ENSPVAG00000001910	1 retrocopy	retro_pvam_391 ,