RetrogeneDB ID: retro_ogar_2671

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873646.1:3727094..3727379(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SEC61B
• Ensembl ID: ENSOGAG00000004168
• Aliases: None
• Description: Sec61 beta subunit [Source:HGNC Symbol;Acc:16993]

Sequence

>retro_ogar_2671
CCTGGCCCGACCCCCAGTGGCACTAACGTGGGCTCTTCAGGACGCTCTCCCAGCAAAGCAGTGGCTGCCCGGGCTGCAGG
ATCCCCTGTCCAGCAAAGGAAAAATGCCAACTGTGAAACAAGGAGTGCCGGCCGCACAACCTCAGCAGGCACTGGGGGCA
TGTGGCTGTTCTACACGGAAGATTCACCTGGGCTCAAAGCTGGCCCTGTTCCAGTATTGGTTATGAGTCTTCTGTTCATC
ACTTCTGTATTTATGTTGTACATTTAGGGCAAGTACACTCGTTCA

Alignment

ORF - retro_ogar_2671 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.53 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  PGPTPSGTNVGSSGRSPSKAVAARAAGSTVRQRKNASCGTRSAGRTTSAGTGGMWRFYTEDSPGLKVGPV
          PGPTPSGTNVGSSGRSPSKAVAARAAGS.V.QRKNA.C.TRSAGRTTSAGTGGMW.FYTEDSPGLK.GPV
Retrocopy PGPTPSGTNVGSSGRSPSKAVAARAAGSPVQQRKNANCETRSAGRTTSAGTGGMWLFYTEDSPGLKAGPV

Parental  PVLVMSLLFIASVFMLHIWGKYTRS
          PVLVMSLLFI.SVFML.I.GKYTRS
Retrocopy PVLVMSLLFITSVFMLYI*GKYTRS

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_2671 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 12 parental genes, and 23 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000002457	3 retrocopies	retro_btau_1053, retro_btau_360, retro_btau_791,
Equus caballus	ENSECAG00000026930	1 retrocopy	retro_ecab_711,
Echinops telfairi	ENSETEG00000005293	4 retrocopies	retro_etel_1777, retro_etel_1889, retro_etel_483, retro_etel_695,
Gorilla gorilla	ENSGGOG00000004205	1 retrocopy	retro_ggor_708,
Macropus eugenii	ENSMEUG00000000321	1 retrocopy	retro_meug_1921,
Microcebus murinus	ENSMICG00000011121	4 retrocopies	retro_mmur_1037, retro_mmur_1631, retro_mmur_435, retro_mmur_543,
Myotis lucifugus	ENSMLUG00000001097	1 retrocopy	retro_mluc_2170,
Macaca mulatta	ENSMMUG00000010661	1 retrocopy	retro_mmul_86,
Mus musculus	ENSMUSG00000053317	2 retrocopies	retro_mmus_1377, retro_mmus_2679,
Nomascus leucogenys	ENSNLEG00000017055	1 retrocopy	retro_nleu_2844,
Otolemur garnettii	ENSOGAG00000004168	3 retrocopies	retro_ogar_1132, retro_ogar_2671 , retro_ogar_823,
Pongo abelii	ENSPPYG00000019441	1 retrocopy	retro_pabe_680,