RetrogeneDB ID: retro_pvam_92

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: GeneScaffold_131:56614..56870(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSPVAG00000003521
• Aliases: None
• Description: None

Sequence

>retro_pvam_92
ATGCCCAAAAATAAAGGTAAAGGAGGCAAAAACAAGTGCAGGGTAAGAATGAGAATAAATCTGAAAAAAAAAAAAAAAGA
GTTGGTGTATAAAGAGGATGAGTAAGGGTAAGCTCAGGTCATCAAAATGTTGAGGGAAAAGATTATTAGAAGCAATGTTT
TTTGATGGTATAAAAAGGTTATGCCATATCAAAGGAAAATTGAGAGAAATGATCTGAATAAATATCTCAGATATGGTATT
GGTTGACCTGCCAGAC

Alignment

ORF - retro_pvam_92 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.14 %
• Parental protein coverage: 56.43 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MPKNKGKGGKN--RRRGKNENESEKRELVFKEDGQEYAQVIKML-GNGRLEAMCFDGVKRLCHIRGKLRK
          MPKNKGKGGKN..R.R..........ELV.KED....AQVIKML.G...LEAM.FDG.KRLCHI.GKLR.
Retrocopy MPKNKGKGGKNKCRVRMRINLXXXXXELVYKEDE*G*AQVIKML>GKRLLEAMFFDGIKRLCHIKGKLRE

Parental  ----KTSDIILVGLRD
          ......SD..LV.L.D
Retrocopy MI*INISDMVLVDLPD

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_92 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 12 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000005371	1 retrocopy	retro_cjac_66,
Dipodomys ordii	ENSDORG00000011536	1 retrocopy	retro_dord_484,
Homo sapiens	ENSG00000173674	2 retrocopies	retro_hsap_1431, retro_hsap_350,
Gorilla gorilla	ENSGGOG00000012186	3 retrocopies	retro_ggor_1103, retro_ggor_363, retro_ggor_968,
Myotis lucifugus	ENSMLUG00000012977	2 retrocopies	retro_mluc_250, retro_mluc_3,
Monodelphis domestica	ENSMODG00000027820	1 retrocopy	retro_mdom_274,
Mus musculus	ENSMUSG00000067194	1 retrocopy	retro_mmus_264,
Otolemur garnettii	ENSOGAG00000008182	1 retrocopy	retro_ogar_128,
Pan troglodytes	ENSPTRG00000022504	1 retrocopy	retro_ptro_978,
Pteropus vampyrus	ENSPVAG00000003521	2 retrocopies	retro_pvam_780, retro_pvam_92 ,
Rattus norvegicus	ENSRNOG00000005736	1 retrocopy	retro_rnor_24,
Sus scrofa	ENSSSCG00000029864	1 retrocopy	retro_sscr_948,