RetrogeneDB ID: retro_pvam_748

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: scaffold_1056:241017..241344(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: LAMTOR2
• Ensembl ID: ENSPVAG00000010328
• Aliases: None
• Description: late endosomal/lysosomal adaptor, MAPK and MTOR activator 2 [Source:HGNC Symbol;Acc:29796]

Sequence

>retro_pvam_748
CCCAAGGCTCTGAGGTGGGTGCTAAACCAGGCCATCACTGCCGGCGTTCAGAACAACCTGCTACTGCATAGTGACAGAGC
CCTGGTGGCTACGCAGGTTACAGGGGTGGGGATGCTCAAGTCGCCACGGCCATCACCAGTAACATCTGGGCCATCCATGA
CCAGATGGGAACCAGGCGTTTAATAAAGACCATGCCGAACTCATCCTGATCGGCTGCATGGAGGGTCATGCAGCCATCAC
CCAGTGATCAACCTTCCATTGCGTATGTATGCCGAGGACACTGTGGGCTTTGGAATGCTCAAGGCCAAGGCCCAGTTTCA
GTGCGGT

Alignment

ORF - retro_pvam_748 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.41 %
• Parental protein coverage: 73.33 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  PKALTQVLSQANTGGVQSTLLLNNEGSLLA-YSGYGDTDARVTAAIASNIWAAYDR-NGNQAFNEDNLKF
          PKAL..VL.QA.T.GVQ..LLL.....L.A.Y.GY...DA.V..AI.SNIWA..D...GNQAFN.D....
Retrocopy PKALRWVLNQAITAGVQNNLLLHSDRALVA<YAGYRGGDAQVATAITSNIWAIHDQ<DGNQAFNKDHAEL

Parental  ILMDCMEGRVAITR-VANLLLCMYAKETVGFGMLKAKARCGTG
          IL..CMEG..AIT..V.NL.L.MYA..TVGFGMLKAKA....G
Retrocopy ILIGCMEGHAAITQ<VINLPLRMYAEDTVGFGMLKAKAQFQCG

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_748 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 8 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000009193	1 retrocopy	retro_ecab_629,
Felis catus	ENSFCAG00000028596	1 retrocopy	retro_fcat_872,
Myotis lucifugus	ENSMLUG00000023871	1 retrocopy	retro_mluc_237,
Mus musculus	ENSMUSG00000028062	1 retrocopy	retro_mmus_878,
Otolemur garnettii	ENSOGAG00000016953	2 retrocopies	retro_ogar_2919, retro_ogar_910,
Pteropus vampyrus	ENSPVAG00000010328	1 retrocopy	retro_pvam_748 ,
Rattus norvegicus	ENSRNOG00000019908	3 retrocopies	retro_rnor_1037, retro_rnor_2493, retro_rnor_847,
Tursiops truncatus	ENSTTRG00000013344	1 retrocopy	retro_ttru_1782,