RetrogeneDB ID: retro_ogar_2315

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873611.1:4963634..4963927(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SPCS1
• Ensembl ID: ENSOGAG00000004106
• Aliases: None
• Description: signal peptidase complex subunit 1 homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:23401]

Sequence

>retro_ogar_2315
ATTGCACTCCTGGGCTTGGTAGGCCTGCCAGGCCGTACACAGTACCAGATCTAGCCTGTGTGGTCACTGAGGCTCAGTTG
CACTCAACCCACAGCCTACTGGCTGCACTCTGCTGTCCACCTCAGCAGGTTATGCTGGAGCACCTGTGCTTGCTGCCCAT
GCAGATAGACTACAGGGGCCAGAAGCTAGCTGAGCAGATGTTTCAGAGAATTCTTTTTTTTTTTTCTTCTGCAATGGTTA
GATTTATCTATGAACCATTTGGGTGGACGGTCTATATAATTATGGCTGGATTT

Alignment

ORF - retro_ogar_2315 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.73 %
• Parental protein coverage: 59.76 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  IVFSGLAGSPGDTEYRT-RAPTTANSQSPSSCSLPLALCCSPPGPVMLEHLSSLPTQMDYKGQKLAEQMF
          I...GL.G.PG.T.Y....A......Q..S..SL..ALCC.PP..VMLEHL..LP.Q.DY.GQKLAEQMF
Retrocopy IALLGLVGLPGRTQYQI<LACVVTEAQLHSTHSLLAALCC-PPQQVMLEHLCLLPMQIDYRGQKLAEQMF

Parental  QGI--ILFSAIVGFIYGYVAEQFGWTVYIVMAGF
          Q.I.....SA.V.FIY....E.FGWTVYI.MAGF
Retrocopy QRIXXXXXSAMVRFIY----EPFGWTVYIIMAGF

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_2315 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 15 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000008426	1 retrocopy	retro_amel_1899,
Canis familiaris	ENSCAFG00000008927	1 retrocopy	retro_cfam_2079,
Equus caballus	ENSECAG00000023559	1 retrocopy	retro_ecab_86,
Erinaceus europaeus	ENSEEUG00000007914	1 retrocopy	retro_eeur_25,
Homo sapiens	ENSG00000114902	1 retrocopy	retro_hsap_294,
Gorilla gorilla	ENSGGOG00000028027	1 retrocopy	retro_ggor_332,
Microcebus murinus	ENSMICG00000014061	1 retrocopy	retro_mmur_292,
Myotis lucifugus	ENSMLUG00000000744	1 retrocopy	retro_mluc_2104,
Macaca mulatta	ENSMMUG00000017370	1 retrocopy	retro_mmul_549,
Otolemur garnettii	ENSOGAG00000004106	3 retrocopies	retro_ogar_2119, retro_ogar_2315 , retro_ogar_2788,
Pongo abelii	ENSPPYG00000013798	1 retrocopy	retro_pabe_380,
Pan troglodytes	ENSPTRG00000015011	1 retrocopy	retro_ptro_241,
Tarsius syrichta	ENSTSYG00000006854	2 retrocopies	retro_tsyr_1359, retro_tsyr_599,
Tursiops truncatus	ENSTTRG00000008576	1 retrocopy	retro_ttru_806,
Vicugna pacos	ENSVPAG00000007380	1 retrocopy	retro_vpac_269,