RetrogeneDB ID: retro_ogar_2300

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873610.1:4030951..4031228(+)
• Located in intron of: ENSOGAG00000004964

Retrocopy information

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

Parental gene information

• Parental gene symbol: VAMP3
• Ensembl ID: ENSOGAG00000009797
• Aliases: None
• Description: vesicle-associated membrane protein 3 [Source:HGNC Symbol;Acc:12644]

Sequence

>retro_ogar_2300
CCTGCAGGTTCATGTGCTGCTGGGGCAGTAATTGAAGACTTCAGCAGACACAAAATCAAGTAGATGAGGTGGTGGACATA
ATGAGAGTTAACATGGAAAACATGTTGGAAAGAGACCAAAAACTCTTGAGTTAGACGACCGTGCAGATGCACTGCAGGCA
GGCGCCTCTCAGTTTGAAACAAGTGCTGCCAAGTTAAAGAGAAAATACTGGTGGAAGAATCGCAAGATGTGGGCCATAAG
GATTAGTGTTTTGGTTATCATCATCACCATCATCATT

Alignment

ORF - retro_ogar_2300 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.26 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  PAGSSAAA-GSNRRLQQTQNQVDEVVDIMRVNVDKVLERDQKLS-ELDDRADALQAGASQFETSAAKLKR
          PAGS.AA..GSN.RLQQTQNQVDEVVDIMRVN....LERDQKL..ELDDRADALQAGASQFETSAAKLKR
Retrocopy PAGSCAAG<GSN*RLQQTQNQVDEVVDIMRVNMENMLERDQKLL<ELDDRADALQAGASQFETSAAKLKR

Parental  KYWWKNCKMWAIGITVLVIIIIIII
          KYWWKN.KMWAI.I.VLVIII.III
Retrocopy KYWWKNRKMWAIRISVLVIIITIII

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Otolemur garnettii was not studied using RNA-Seq expression data.

ChIP-Seq

Otolemur garnettii was not studied using ChIP-Seq data.

EST

Otolemur garnettii was not studied using EST data.

TSS

Otolemur garnettii was not studied using FANTOM5 data.

Lab

retro_ogar_2300 was not experimentally validated.

Homology

Retrocopy orthology:

Otolemur garnettii 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 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Monodelphis domestica	ENSMODG00000005770	1 retrocopy	retro_mdom_273,
Mus musculus	ENSMUSG00000028955	1 retrocopy	retro_mmus_1851,
Otolemur garnettii	ENSOGAG00000009797	1 retrocopy	retro_ogar_2300 ,
Otolemur garnettii	ENSOGAG00000026745	1 retrocopy	retro_ogar_3369,
Procavia capensis	ENSPCAG00000004825	1 retrocopy	retro_pcap_389,
Tarsius syrichta	ENSTSYG00000007733	6 retrocopies	retro_tsyr_1027, retro_tsyr_1435, retro_tsyr_1634, retro_tsyr_1757, retro_tsyr_524, retro_tsyr_968,