RetrogeneDB ID: retro_pvam_1095

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: scaffold_2841:2813..3123(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PPP1R14B
• Ensembl ID: ENSPVAG00000017120
• Aliases: None
• Description: protein phosphatase 1, regulatory (inhibitor) subunit 14B [Source:HGNC Symbol;Acc:9057]

Sequence

>retro_pvam_1095
CCCCCTGGGGCTGCAGGTGAGGGCCCAGTGAGGTGCCAAGAGAAAGTCATGGTCAAGGAAGACTGCAAGGAGCAAGGAAG
CACCTCACCGTGGAGGAATGGATCCTGGAGTAGCACACTCACCTCCATCACTGCCAGACATAGGGGATTCTAGAGCTAGA
AATTGAGGTAGATTAGCTCCTAGACATGGAGCGATATCTGGCTGCCAGGATCAGGGAGCTGCTAGTTGACTGTTACAAAC
CCCCTGGGGCCTTCATTTCTAGCTGTTGGGCAAGACCCAGGGCCTACAGAACCTGAGCACCCCCCAGAAG

Alignment

ORF - retro_pvam_1095 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.96 %
• Parental protein coverage: 72.11 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  PGGADDEGPVRRQGKVTVKYDRKE-LRKRLNLEEWILEQLTRLYDCQEEEIPELEIDVDELLDMESDDTR
          P.GA..EGPVR.Q.KV.VK.D.KE..RK.L..EEWILE..T.L..CQ...I.ELEI.VD.LLDME.....
Retrocopy PPGAAGEGPVRCQEKVMVKEDCKE<ARKHLTVEEWILE*HTHLHHCQT*GILELEIEVD*LLDMER--YL

Parental  AARVKELLVDCYKPTEAFISG-LLDKIRGMQKLSTPQK
          AAR..ELLVDCYKP..AFIS..LL.K..G.Q.LSTPQK
Retrocopy AARIRELLVDCYKPPGAFISS<LLGKTQGLQNLSTPQK

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_1095 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 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000018019	1 retrocopy	retro_amel_934,
Felis catus	ENSFCAG00000030667	1 retrocopy	retro_fcat_1417,
Mus musculus	ENSMUSG00000056612	5 retrocopies	retro_mmus_1045, retro_mmus_2245, retro_mmus_2624, retro_mmus_30, retro_mmus_3473,
Otolemur garnettii	ENSOGAG00000030926	2 retrocopies	retro_ogar_3158, retro_ogar_376,
Pteropus vampyrus	ENSPVAG00000017120	1 retrocopy	retro_pvam_1095 ,
Rattus norvegicus	ENSRNOG00000021151	2 retrocopies	retro_rnor_1262, retro_rnor_41,