RetrogeneDB ID: retro_ogar_1870

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873570.1:5388662..5389130(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CHMP2A
• Ensembl ID: ENSOGAG00000005628
• Aliases: None
• Description: charged multivesicular body protein 2A [Source:HGNC Symbol;Acc:30216]

Sequence

>retro_ogar_1870
GTTCGCACTCGGCACTATGTGGGTGAGTTTGTGTTGATGTGGGCCAACATCCAGGCTGTGTCCCTCAAGATCCAGATACT
CAAGTCCAACAACTCAATGGCACAAGCCACGAAAGGTGTCACCAAGGCCATGGGCACCATGAACAGACAGCTGAAATTGC
CCCAGATTTAGAAGATCGTGATGGGGTTTGAGTGGCAAGCAGAGATCATGGACATGAAGGAGGAGATGATGAATGATGCC
ATAGATGATGCCATGGGTGATAAAGAAGATGAAGAGGAGAGTGGTGCTGTTGTATCCCAGGTCCTGGATGAGCTGGGACT
GAGCCTGACAGATGAGCTGTCAATCCTCCCCTCAACTGGAGGCTCACTCAGTGTGGCTGCTGGTGGGAAACAAGCAGAAG
CTATAGCCTCAGCCCTGACTGATGCTGATGCAGACCTAGAGGAGCCGCTCAACAACCTGTGGAGGGAC

Alignment

ORF - retro_ogar_1870 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.82 %
• Parental protein coverage: 70.27 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VRTRRYVRKFVLMRANIQAVSLKIQTLKSNNSMAQAMKGVTKAMGTMNRQLKLPQIQKIMMEFERQAEIM
          VRTR.YV..FVLM.ANIQAVSLKIQ.LKSNNSMAQA.KGVTKAMGTMNRQLKLPQI.KI.M.FE.QAEIM
Retrocopy VRTRHYVGEFVLMWANIQAVSLKIQILKSNNSMAQATKGVTKAMGTMNRQLKLPQI*KIVMGFEWQAEIM

Parental  DMKEEMMNDAIDDAMGDEEDEEESDAVVSQVLDELGLSLTDELSNLPSTGGSLSVAAGGKKAEAAASALA
          DMKEEMMNDAIDDAMGD.EDEEES.AVVSQVLDELGLSLTDELS.LPSTGGSLSVAAGGK.AEA.ASAL.
Retrocopy DMKEEMMNDAIDDAMGDKEDEEESGAVVSQVLDELGLSLTDELSILPSTGGSLSVAAGGKQAEAIASALT

Parental  DADADLEERLKNLRRD
          DADADLEE.L.NL.RD
Retrocopy DADADLEEPLNNLWRD

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_1870 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 4 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Macropus eugenii	ENSMEUG00000013531	1 retrocopy	retro_meug_1308,
Mus musculus	ENSMUSG00000033916	1 retrocopy	retro_mmus_1039,
Otolemur garnettii	ENSOGAG00000005628	2 retrocopies	retro_ogar_1870 , retro_ogar_2753,
Pongo abelii	ENSPPYG00000010511	1 retrocopy	retro_pabe_196,