RetrogeneDB ID: retro_pvam_282

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: GeneScaffold_2328:15985..16285(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SMIM19
• Ensembl ID: ENSPVAG00000014829
• Aliases: None
• Description: small integral membrane protein 19 [Source:HGNC Symbol;Acc:25166]

Sequence

>retro_pvam_282
ATGGGTGGCAGTGGTTCTGTAGATTGCAGCATTCATGAGACCTGGAACGAAGCCAGAAATGTTTTCTTGGTAGTGATCCT
CTTCAGCTTTGGTCTCTTCATGTAGGCCAAGAGGAATAAAAAGAAAACTATGAGGATATTCAGTGTGCCACTTATAGTGG
AAACTTTGTCAGAGCCCAACTTTCATGACACAATAAGCAAAATTCTTTCAACACAGCAACTGGAAATGTATTCCATTTCA
AGGAAGTATAACTTTCAACAGCCACCAAACCAATCTGACAGTGTGCAGCTCTCCTTGGAA

Alignment

ORF - retro_pvam_282 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77. %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MGDDGSIDYSVHEAWNEATNVYLVVILVSFGLFMYAKRNKRKIMRIFSVPPTAETLSEPNFYDTISKIRL
          MG..GS.D.S.HE.WNEA.NV.LVVIL.SFGLFM.AKRNK.K.MRIFSVP...ETLSEPNF.DTISKI..
Retrocopy MGGSGSVDCSIHETWNEARNVFLVVILFSFGLFM*AKRNKKKTMRIFSVPLIVETLSEPNFHDTISKILS

Parental  RQQLEMYSISRKYDYQQPQNQADSVQLSLE
          .QQLEMYSISRKY..QQP.NQ.DSVQLSLE
Retrocopy TQQLEMYSISRKYNFQQPPNQSDSVQLSLE

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_282 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 6 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000005067	1 retrocopy	retro_amel_346,
Cavia porcellus	ENSCPOG00000002665	1 retrocopy	retro_cpor_1019,
Felis catus	ENSFCAG00000031243	1 retrocopy	retro_fcat_1312,
Pteropus vampyrus	ENSPVAG00000014829	1 retrocopy	retro_pvam_282 ,
Sorex araneus	ENSSARG00000008851	2 retrocopies	retro_sara_28, retro_sara_510,
Tupaia belangeri	ENSTBEG00000008608	1 retrocopy	retro_tbel_2485,