RetrogeneDB ID: retro_pvam_233

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: GeneScaffold_2048:100248..100905(-)
• Located in intron of: ENSPVAG00000013223

Retrocopy information

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

Parental gene information

• Parental gene symbol: NT5C3B
• Ensembl ID: ENSPVAG00000010634
• Aliases: None
• Description: 5'-nucleotidase, cytosolic IIIB [Source:HGNC Symbol;Acc:28300]

Sequence

>retro_pvam_233
GTGCAGGAGGTCGTGGGCATCCTCCACAGGGGCGGGGGGGACTGCTCACAGGTCATTTCTGATTTTGACATGACCTTGAG
CAGGTTTGCTTATAATGGAAAGTGATGCCCTTCTTCCTACAATATTCTGGATAACAGCGAGATCATCAGTGAGGAGTGCC
AGAAAGAGCTGAAAGCGCTCTTTCACCACTGTTACCCAGTTTAGATTGATCCACATGGGACTATCAAAGAGAAGTTACCT
CGTATGGTAGATTAGTGGACTAAAGCGCACAATCTCCCTTGTCAGCAGATATTCAGAGATTTTGAACAGCCCAGGTGCTT
AGAGAGTCCAGCACAATGCTTAGGGAGGGTTACAAGATGTTCTAAAACACCCTCTACCAAAACAACAGTCCCTTTTTCAT
CTTTTCCACGACCATTGGTGATAACCTGGAAGAAATGATCCCACGATGAAAGTGTTGCACCCCAGCATCCACATTGTGTC
TAACTACATGAATTTGGACGAAGATGGTTTCCTGCAGGCATTGAAGGGCCAGCTGGTATACAGAACAAGAACAGCTCCAT
GTGGGAGAACTCCAGTTACTTCCAGCAGCTTCAGGGCAAAATCAACATCCTCCGGCTGGGAGACTCCATAGGGGACCTCA
GAATGGCTGATGGGATG

Alignment

ORF - retro_pvam_233 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.54 %
• Parental protein coverage: 75.68 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  VQEIVGALRRGGGDRLQVISDFDMTLSRFAYNGKRCPSSHNILDNSKIISEECRKELKALLHHYYPIEID
          VQE.VG.L.RGGGD..QVISDFDMTLSRFAYNGK.CPSS.NILDNS.IISEEC.KELKAL.HH.YP..ID
Retrocopy VQEVVGILHRGGGDCSQVISDFDMTLSRFAYNGK*CPSSYNILDNSEIISEECQKELKALFHHCYPV*ID

Parental  PHWTIKEKLPHMVEWWTKAHSLLCQQ-KIQKFQIAQVVRESNAMLREGYKMFFNTLYQNSVPLFIFSAGI
          PH.TIKEKLP.MV..WTKAH.L.CQQ..IQ.F..AQV.RES..MLREGYKMF.NTLYQN..P.FIFS..I
Retrocopy PHGTIKEKLPRMVD*WTKAHNLPCQQ<DIQRF*TAQVLRESSTMLREGYKMF*NTLYQNNSPFFIFSTTI

Parental  GDILEEIIRQ-KQVFHPNIHVVSNYMDFDKDG-FLQGFKGQLIHTYNKNSTVCENSGYFQQLQGKTNILL
          GD.LEE.I.....V.HP.IH.VSNYM..D.DG.F..G..G......NKNS...ENS.YFQQLQGK.NIL.
Retrocopy GDNLEEMIPR<MKVLHPSIHIVSNYMNLDEDG<FPAGIEGPA-GIQNKNSSMWENSSYFQQLQGKINILR

Parental  LGDSMGDLTMADGV
          LGDS.GDL.MADG.
Retrocopy LGDSIGDLRMADGM

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_233 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 7 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000005754	1 retrocopy	retro_amel_1542,
Erinaceus europaeus	ENSEEUG00000013493	1 retrocopy	retro_eeur_413,
Felis catus	ENSFCAG00000023499	1 retrocopy	retro_fcat_1017,
Mustela putorius furo	ENSMPUG00000010759	2 retrocopies	retro_mputfur_1354, retro_mputfur_1594,
Pteropus vampyrus	ENSPVAG00000010634	1 retrocopy	retro_pvam_233 ,
Pteropus vampyrus	ENSPVAG00000013182	2 retrocopies	retro_pvam_148, retro_pvam_706,
Sorex araneus	ENSSARG00000006434	1 retrocopy	retro_sara_505,