RetrogeneDB ID: retro_pvam_106

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: GeneScaffold_1395:18191..18804(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SDCBP2
• Ensembl ID: ENSPVAG00000003014
• Aliases: None
• Description: syndecan binding protein (syntenin) 2 [Source:HGNC Symbol;Acc:15756]

Sequence

>retro_pvam_106
ATGGTGGCTCCTGTAACTGGTAATGATGTTGTATTCATAGAGCAGGAATTAAGCAAGGGATTCATGAAATCATTTTGTGT
AAGGATTGAGATGGAAAAATTGGGCTTCCTCTTAAATCAGTAGATAATGGTATATTTGTTCAGCTAGTCTAGGGAATTCT
CCAGCCTCATTAGTTGGTCTGAGATATGGGGACCAAGTACTCCAGATCAATGGAGAAAACTGTGCAGGCTAAAGCTCTGA
TAAATCACACAGAGTGCTCTAATGAGTTTTTAGAGAGATTACCATGACTATTCGTGACCAGCCTTTTGAACGTACAATTA
CTATGCATAAGGATAGTACTAGACATGTTGATTTTATCTTTAAAAATGGAAAAATAACATCCATGGTAGAAGATAGCTCT
GCAGCCAAAAACGGTCTTCTCACAGAACATGTCTGTGAAATTAATGGACAGAATGTCATTGAATTGAAGGACTCTAAAAT
TGCCAACATACTGTTGACATCTGGGACTGTAGTTACTACTACAATCATGCCTGCTTTTATCTTTGAACATATTATTAAAT
GGATAGTACCAAGCATTGTGAAAAGCCTAATGGACCACACCATTCCTGAGGTT

Alignment

ORF - retro_pvam_106 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 55.98 %
• Parental protein coverage: 70.89 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MVAPVSQNSLG-ARRAEIKPGVREIHLCKDERGKTGLRLRAIDKGLFVQLV-QANTPASLVGLRFGDQIL
          MVAPV..N......RA.IK.G..EI.LCKD..GK.GL.L...D.G.FVQLV...N.PASLVGLR.GDQ.L
Retrocopy MVAPVTGNDVV<IHRAGIKQGIHEIILCKD*DGKIGLPLKSVDNGIFVQLV<LGNSPASLVGLRYGDQVL

Parental  QIDGRDCAGWSTDKAHRVVKRASAEKIIMVVRDRPFQRTVTMHKDSKGHIGFVIKKGKVVSVVKGSSAAR
          QI.G..CAG.S.DK.HRV......E.I.M..RD.PF.RT.TMHKDS..H..F..K.GK..S.V..SSAA.
Retrocopy QINGENCAG*SSDKSHRVL**VFRE-ITMTIRDQPFERTITMHKDSTRHVDFIFKNGKITSMVEDSSAAK

Parental  NGLVTNHCMCEVNGQNVIGLKDKEVTEILAKAGNVVTLTIIPTVIFEHMVKKLSPTLLHHTMDHSIPDV
          NGL.T.H..CE.NGQNVI.LKD.....IL...G.VVT.TI.P..IFEH..K...P......MDH.IP.V
Retrocopy NGLLTEH-VCEINGQNVIELKDSKIANILLTSGTVVTTTIMPAFIFEHIIKWIVPSIVKSLMDHTIPEV

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_106 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
Microcebus murinus	ENSMICG00000014370	1 retrocopy	retro_mmur_127,
Pteropus vampyrus	ENSPVAG00000003014	1 retrocopy	retro_pvam_106 ,
Tursiops truncatus	ENSTTRG00000002740	2 retrocopies	retro_ttru_1733, retro_ttru_1902,