RetrogeneDB ID: retro_pvam_686

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: GeneScaffold_683:82207..82624(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: EXOSC1
• Ensembl ID: ENSPVAG00000003372
• Aliases: None
• Description: exosome component 1 [Source:HGNC Symbol;Acc:17286]

Sequence

>retro_pvam_686
ATGAGAGAAACAGAGTCCCATTACTGTCAGATGTGGGGGCTATTGTAACCTGTAAGGTCTCTAGCATCAGTTTGCACTTT
GCCAAAGTACACATCCTGTATGTGGGGTCCATACTACTTAAGAACTTTTCTCCAGGAACTATTTGCAAGGAAGATATCTG
AGCTACTGAAAAAGACAAGGTTGAAATTTATGAGTTTCTATCCAGATGACATTGTTTTGGCCAAAGTGATCTCCTTAGGT
GACCCACAGTCCAACTATCTCCTGACCACTGCGGAAAATGAGCTAGGAGTGCTGGTGGCCCACAGTGAATCAGGTGTCCA
GATGGTTCTCATCAACTGGTGTGAGACACAGTGCCATAAGACCCACACTAAAGAATTCTGGAAAGTGGCCCAAGTACAGC
CTGAATTCTTTCAGACC

Alignment

ORF - retro_pvam_686 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.76 %
• Parental protein coverage: 71.79 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MRETESQ-LLPDVGAIVTCKVSSINSRFAKVHILYVGSTPLKNSFRGTIRKEDVRATE-KDKVEIYKSFR
          MRETES..LL.DVGAIVTCKVSSI...FAKVHILYVGS..LKN...GTI.KED..ATE.K.......SF.
Retrocopy MRETESH<LLSDVGAIVTCKVSSISLHFAKVHILYVGSILLKNFSPGTICKEDI*ATE>KTRLK-FMSFY

Parental  PGDIVLAKVISLGDAQSNYLLTTAENELGVVVAHSESGVQMVPISWCEMQCPKTHTKEFRKVARVQPEFL
          P.DIVLAKVISLGD.QSNYLLTTAENELGV.VAHSESGVQMV.I.WCE.QC.KTHTKEF.KVA.VQPEF.
Retrocopy PDDIVLAKVISLGDPQSNYLLTTAENELGVLVAHSESGVQMVLINWCETQCHKTHTKEFWKVAQVQPEFF

Parental  QT
          QT
Retrocopy QT

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_686 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 11 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000006477	1 retrocopy	retro_chof_2075,
Dasypus novemcinctus	ENSDNOG00000007983	1 retrocopy	retro_dnov_104,
Erinaceus europaeus	ENSEEUG00000005647	3 retrocopies	retro_eeur_270, retro_eeur_438, retro_eeur_464,
Macropus eugenii	ENSMEUG00000002246	2 retrocopies	retro_meug_1799, retro_meug_951,
Myotis lucifugus	ENSMLUG00000009228	1 retrocopy	retro_mluc_1563,
Mus musculus	ENSMUSG00000034321	1 retrocopy	retro_mmus_691,
Oryctolagus cuniculus	ENSOCUG00000011898	1 retrocopy	retro_ocun_173,
Otolemur garnettii	ENSOGAG00000016259	1 retrocopy	retro_ogar_2496,
Pteropus vampyrus	ENSPVAG00000003372	1 retrocopy	retro_pvam_686 ,
Rattus norvegicus	ENSRNOG00000048708	1 retrocopy	retro_rnor_899,
Ictidomys tridecemlineatus	ENSSTOG00000006615	1 retrocopy	retro_itri_1253,