RetrogeneDB ID: retro_ogar_2955

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873689.1:1613544..1614069(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PSMD14
• Ensembl ID: ENSOGAG00000004933
• Aliases: None
• Description: proteasome (prosome, macropain) 26S subunit, non-ATPase, 14 [Source:HGNC Symbol;Acc:16889]

Sequence

>retro_ogar_2955
GACAGACTTCTTAGATTTGGAGGAGGCATACCTGGTTTGGGCCAAGGGCCACCTATGGATGCTCCTGCCGTGGACACAGC
AGAACAAGTCTCTATCTCTTCACTGGCACTGTTAAAAATGTTAAAACATGGCTGTGCTGGAGTTCCAATGGAAGTTATGG
GTCTGATGCTTGGAGAATTTGTTGGTGATTACACGGTCAAAGTGATTGATGGGTTTGCCATGCCACAGTCAGGAACAGGT
GTCAGTGTAGAGGCAGTTGATCCAGTGTTCCAAGCCAAGAAGTTAGATAATTTGTAGCAGACAGGGAGGCCTGAGATGGT
TGTTGGTTGGTATCACAGTCACCCTGGCTTTGGTTGTTGGCTTTATGGTGTGGATATCAGCACTCAGCAGAGCTTTGAAG
CCTTGTCAGAGAGAGCTGTGGCAGTGGTTGTGGATCCTATTCAGAGTGTAAAAGGAAAAGTTGTTATTGATGCCTTCAGA
TTGATCAATGCTAATATGATGGTCTTAGGACATGAACCCAGACAA

Alignment

ORF - retro_ogar_2955 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88. %
• Parental protein coverage: 56.49 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  DRII-LGEETTSLGEGPPTDAPAVDTAEQVYISSLALLKMLKHGRAGVPMEVMGLMLGEFVDDYTVRVID
          DR....G.....LG.GPP.DAPAVDTAEQV.ISSLALLKMLKHG.AGVPMEVMGLMLGEFV.DYTV.VID
Retrocopy DRLLRFGGGIPGLGQGPPMDAPAVDTAEQVSISSLALLKMLKHGCAGVPMEVMGLMLGEFVGDYTVKVID

Parental  VFAMPQSGTGVSVEAVDPVFQAKMLDMLKQTGRPEMVVGWYHSHPGFGCWLSGVDINTQQSFEALSERAV
          .FAMPQSGTGVSVEAVDPVFQAK.LD.L.QTGRPEMVVGWYHSHPGFGCWL.GVDI.TQQSFEALSERAV
Retrocopy GFAMPQSGTGVSVEAVDPVFQAKKLDNL*QTGRPEMVVGWYHSHPGFGCWLYGVDISTQQSFEALSERAV

Parental  AVVVDPIQSVKGKVVIDAFRLINANMMVLGHEPRQ
          AVVVDPIQSVKGKVVIDAFRLINANMMVLGHEPRQ
Retrocopy AVVVDPIQSVKGKVVIDAFRLINANMMVLGHEPRQ

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_2955 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 9 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000002556	1 retrocopy	retro_chof_2387,
Callithrix jacchus	ENSCJAG00000005572	1 retrocopy	retro_cjac_1434,
Gorilla gorilla	ENSGGOG00000015747	1 retrocopy	retro_ggor_1710,
Mus musculus	ENSMUSG00000026914	1 retrocopy	retro_mmus_701,
Otolemur garnettii	ENSOGAG00000004933	2 retrocopies	retro_ogar_2955 , retro_ogar_3213,
Pongo abelii	ENSPPYG00000012881	1 retrocopy	retro_pabe_2100,
Pan troglodytes	ENSPTRG00000012575	1 retrocopy	retro_ptro_1636,
Rattus norvegicus	ENSRNOG00000004911	1 retrocopy	retro_rnor_1271,
Tupaia belangeri	ENSTBEG00000014118	1 retrocopy	retro_tbel_3917,