RetrogeneDB ID: retro_pvam_480

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: GeneScaffold_3405:155257..156062(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DUSP5
• Ensembl ID: ENSPVAG00000016242
• Aliases: None
• Description: dual specificity phosphatase 5 [Source:HGNC Symbol;Acc:3071]

Sequence

>retro_pvam_480
GTACCCCGCCTGCCCGCGTTCGGCCTCCTCTAACCGGGATGTGAGGCTTTCTACTCAGAATCTCCTGACCGTCGTTTGGC
TCTAAAACCCATTTCTCAAGAGAAGATTGAAACCCAGAGGGCCCGCAGAAGCCAAGGTGGGGAACCAGTGCCCAGCATTA
GCCAAGGCCGGCCTGGGACCAGAGGAGCCCAGCCCATACCCGTCCTTCGGGTCCTCTACCCCGGAAGTGCCTACCCTGCA
TCCAGATGCGAGGTCCTGCCCACCTGCGCAGCATGGCCCTGCTGAATGTCTCACGGTGGACCTCCGAGGCCTGCACGACC
CACCTGCACTACAGATGGATCCCAAGAGAAGGAACCATATGCCTGACATTAGCTCCCACTTTCAAGAAACAATAGACTTA
ATCGACTGAGTCAGGGAGAGGGAGGGAAAGTCCTGGTCCAATGCGAGGTAGGGATCTCCCTGTTCACCTGGCACCTGTAT
GGCTTCCCTCAGGAAGAGAATCGCTTCCACCTGAGGGAGGCCTTCCATGACATCAAGCAGAAGAGTGTGATCTTACCCAG
CTGTGGCTTCATGAGCCCGCTCCTACAGTATAAATTTGAGATCCTGCCTTCCATGTCCATTCCCCAGGCTCCTTCCTGCC
AGCAGGAGGCAGCCAGCTCTTTACTTATATAGCCCATTTTCAGACACTGAGCCCTAATGCAGAGGGTTCTACTGTACATT
CCCTACTTCGGTGCTGTCACCAGTGCCCACCCACTCACGGGTCTCAGATTTCAGTGGGAGCTCCATAGTCACAGCGACAT
CCTGC

Alignment

ORF - retro_pvam_480 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.99 %
• Parental protein coverage: 70.05 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 7

Retrocopy - Parental Gene Alignment:

Parental  LPAGPRVYFLKGGYETFYSEYPECCVDVKPISQERIDTDRALISQYGKPVLSVSY-RPAYDQGGPVEILP
          .P..P....L..G.E.FYSE.P......KPISQE.I.T.RA..SQ.G.PV.S.S..RP......P...L.
Retrocopy VPRLPAFGLL*PGCEAFYSESPDRRLALKPISQEKIETQRARRSQGGEPVPSISQGRPGTRGAQPIPVLR

Parental  FLYLGSAYHASKCEFL-ANLHITALLNVSRRTSEACTSHLHYKWIPVEDS-HTADISSHFQEAIDFIDCV
          .LY.GSAY.AS.CE.L.A.L...ALLNVSR.TSEACT.HLHY.WIP.E...H..DISSHFQE.ID.ID.V
Retrocopy VLYPGSAYPASRCEVL<AHLRSMALLNVSRWTSEACTTHLHYRWIPREGT<HMPDISSHFQETIDLID*V

Parental  REK-GGKVLVHCEAGISR-SPTICMAYLMKT-RQFRLKDAFDYIKQRRSVVSPNFGFMGQLLQYESEILP
          RE..GGKVLV.CE.GIS..SP..CMA.L.K....F.L..AF..IKQ..SV..P..GFM..LLQY..EILP
Retrocopy RER<GGKVLVQCEVGISL>SPGTCMASLRKR<NRFHLREAFHDIKQK-SVILPSCGFMSPLLQYKFEILP

Parental  STPTPQAPSC-QGEAASS-SFIAHLQTLSPDVQGS-YCTFPTSVLAPVPTHSTVSELSRSPVATATSC
          S...PQAPSC.Q..A.S....IAH.QTLSP...GS.YCTFPTSVL.PVPTHS.VS..S.S...TATSC
Retrocopy SMSIPQAPSCQQEAASSL<TYIAHFQTLSPNAEGS<YCTFPTSVLSPVPTHSRVSDFSGSSIVTATSC

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_480 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 3 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000001858	1 retrocopy	retro_dnov_1665,
Myotis lucifugus	ENSMLUG00000013773	1 retrocopy	retro_mluc_1121,
Pteropus vampyrus	ENSPVAG00000016242	2 retrocopies	retro_pvam_1416, retro_pvam_480 ,