RetrogeneDB ID: retro_pvam_709

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: GeneScaffold_91:124414..125533(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MPP1
• Ensembl ID: ENSPVAG00000009226
• Aliases: None
• Description: membrane protein, palmitoylated 1, 55kDa [Source:HGNC Symbol;Acc:7219]

Sequence

>retro_pvam_709
GGAATCACTCAGAAGATGAATGAAAAGCAGTCCTGCACGGTGGCAAGAATTCTTCATGGTGGCATGATACGTAGACAAGT
CTCCCTTCACATTGGGGATGAGACCCTAGAAATCAATGGCAGAAATGTGACTAATCACTTGGTAAATCAGCTGCAGAAGG
CGATGCAAGAAACCAAAGGAATGAGCTCCTTAAAAGTAATTCCCAACCAGCAAAATCGTCTTCCTGCTACACTATTGATG
TTCATGAGAGCACAGGTTGACTATGACCTCAAAAAGGACAATCTGATTCCTTGCAAGAAGGCAGGACTGAAGTTTGTTAC
TAGGAACATTATCCAGATCATCAATAAAGATGACAGTAACTGGCGGCAAGAGCCGGTGAAAAATTCTTCTAATGAGTCAG
CAGGATTGATCCCTTCTCCCCAGCTGCAGGAATAGCGAGTGGCAAGTGTGGCTCAGTCTGCTCCAAGTGAAGTCCCGAGC
TGCAGTTCCTTCCAGAAGAAGTACAAAGACAGATACCAGACCAAGCACAGCTCAAATTTTGACCAATTAAATGTTGTTTC
GTATGAGGAAGTTGTTTGGCTCCCTGCCTTCAGGAGGAAGACTCTGGTGCTGATTGGAGCCAGTGGGGTGGGTCGCTGCC
ACATTAAAAATACCCTGCTTAGCCAGGACCCAGAGAAGTTCTCATATCCTGCTCCATATACAACACAGCTGCCCAAAAAG
AGTGAGAAAGATGAGAAGAAGTACCACTTCATCTCCACGAAGGAGATGACGAGGAGCATCTCTGCCAATGAGTTTTTGGA
TCTTGGCAGCTACCAGGGCAACATGTTTGGTACCAAATTCGAAACAATGCACCAGATTCATCAGCAGGACAAGATTGCAA
TCCTTGACATCAAGCCCCAGACCCCGAAGATTGTTAGGTCGGCAGAACTTTCACATGTCATTGTGTTTATCACGCCTACT
GATCTGGGCACTCAGATGGAAGCCCTGCAGTAGCTTCAGAAGGACTCGGTTTCCATCCGCAGCCAGTATGCTCACTACTT
TGACCTCTCACTGGTCAATAATAGCACTAATGAAACCCTTAAAAAATTGCAAAAAGGCTTTGACCGGGCGTGCAGTTCT

Alignment

ORF - retro_pvam_709 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.8 %
• Parental protein coverage: 80.26 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GITLKLNEKQSCTVARILHGGMIHRQGSLHVGDEILEINGTNVTNHSVDQLQKAMKETKGMISLKVIPNQ
          GIT.K.NEKQSCTVARILHGGMI.RQ.SLH.GDE.LEING.NVTNH.V.QLQKAM.ETKGM.SLKVIPNQ
Retrocopy GITQKMNEKQSCTVARILHGGMIRRQVSLHIGDETLEINGRNVTNHLVNQLQKAMQETKGMSSLKVIPNQ

Parental  QNRLPA-LQMFMRAQFDYDPKKDNLIPCKEAGLKFVTGDIIQIINKDDSNWWQGRVEGSAKESAGLIPSP
          QNRLPA.L.MFMRAQ.DYD.KKDNLIPCK.AGLKFVT..IIQIINKDDSNW.Q..V..S..ESAGLIPSP
Retrocopy QNRLPATLLMFMRAQVDYDLKKDNLIPCKKAGLKFVTRNIIQIINKDDSNWRQEPVKNSSNESAGLIPSP

Parental  ELQEWRVASVAQSAPSEAPSCSPFGKKKKYKDKYLAKHSSIFDQLDVVSYEEVVRLPAFKRKTLVLIGAS
          .LQE.RVASVAQSAPSE.PSCS.F...KKYKD.Y..KHSS.FDQL.VVSYEEVV.LPAF.RKTLVLIGAS
Retrocopy QLQE*RVASVAQSAPSEVPSCSSF--QKKYKDRYQTKHSSNFDQLNVVSYEEVVWLPAFRRKTLVLIGAS

Parental  GVGRSHIKNILLSRDPEKFAYPAPYTTRPPKKSEEDGKEYHFISTEEMTRGISANEFLEFGSYQGNMFGT
          GVGR.HIKN.LLS.DPEKF.YPAPYTT..PKKSE.D.K.YHFIST.EMTR.ISANEFL..GSYQGNMFGT
Retrocopy GVGRCHIKNTLLSQDPEKFSYPAPYTTQLPKKSEKDEKKYHFISTKEMTRSISANEFLDLGSYQGNMFGT

Parental  KFETVHQIHQQGKIAILDIEPQTLKIVRTAELSPFIVFIAPTDQGTQTEALQQLQKDSEAIRSQYAHYFD
          KFET.HQIHQQ.KIAILDI.PQT.KIVR.AELS..IVFI.PTD.GTQ.EALQ.LQKDS..IRSQYAHYFD
Retrocopy KFETMHQIHQQDKIAILDIKPQTPKIVRSAELSHVIVFITPTDLGTQMEALQ*LQKDSVSIRSQYAHYFD

Parental  LSLVNNGVDETLKKLQEAFEQACSS
          LSLVNN...ETLKKLQ..F..ACSS
Retrocopy LSLVNNSTNETLKKLQKGFDRACSS

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_709 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 4 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000004231	1 retrocopy	retro_dnov_977,
Felis catus	ENSFCAG00000006578	1 retrocopy	retro_fcat_1352,
Pteropus vampyrus	ENSPVAG00000009226	1 retrocopy	retro_pvam_709 ,
Tupaia belangeri	ENSTBEG00000011524	2 retrocopies	retro_tbel_4481, retro_tbel_564,