RetrogeneDB ID: retro_ogar_348

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873520.1:42202313..42202844(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOGAG00000030434
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: TPD52
• Ensembl ID: ENSOGAG00000016601
• Aliases: None
• Description: tumor protein D52 [Source:HGNC Symbol;Acc:12005]

Sequence

>retro_ogar_348
ATGGATTGTAGAGAGATGGACTTACATGAGGACTACCAGTCCCCGTTTGATTTTGATACAGGAGTGAACAAAAGCTATCT
CTACTTGTCTCCTAGTGGAAATTCATCTCCACCCGGATCACCTGCTCTTCAGAAATTTGGTCTGCTGAGGACAGATCCAG
CCCCTGAGGAAGGAGAGGATGTTGCTGCCACCGTCAGTCCTACAGACGACCTATCAGAAGAGGAGCGAGAAGAGCTGAGA
CGAGAACTGGCAAAGGTTGAAGAAGAAATTCAGACTCTGTCTCAAGTGTTAGCAGCAAAAGAGAAGCACCTAGCAGGGAT
CAAGCGGAAACTTGGAATCGGTTCACTACAAGAATTAAAACAGAATATTGCCAAAGGATGGCAAGATGTGGCGGCAACAT
CTGCATACAAGAAGACATCTGAAGCATTGTCTCAGGCTGGACAGAAGGCTTCCGCTGCCTTTTCATCCGTTGGCTCCGTC
ATCACCAAAAAGCTGGAAGATATCAAAAACTCCCCAACCTTGAAATCATTT

Alignment

ORF - retro_ogar_348 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.83 %
• Parental protein coverage: 71.66 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MDCREMDLYEDYQSPFDFDTGVNKSYLYLSPSGNSSPPGSPTLQKFGLLRTDPVPEEGEDVAATISTPDN
          MDCREMDL.EDYQSPFDFDTGVNKSYLYLSPSGNSSPPGSP.LQKFGLLRTDP.PEEGEDVAAT.S..D.
Retrocopy MDCREMDLHEDYQSPFDFDTGVNKSYLYLSPSGNSSPPGSPALQKFGLLRTDPAPEEGEDVAATVSPTDD

Parental  LSEEEREELRRELAKVEEEIQTLSQVLAAKEKHLAEIKRKLGISSLQELKQNIAKGWQDVTATSAYKKTS
          LSEEEREELRRELAKVEEEIQTLSQVLAAKEKHLA.IKRKLGI.SLQELKQNIAKGWQDV.ATSAYKKTS
Retrocopy LSEEEREELRRELAKVEEEIQTLSQVLAAKEKHLAGIKRKLGIGSLQELKQNIAKGWQDVAATSAYKKTS

Parental  ETLSQAGQKASAAFSSVGSVITKKLEDVKLQAFSHSF
          E.LSQAGQKASAAFSSVGSVITKKLED.K......SF
Retrocopy EALSQAGQKASAAFSSVGSVITKKLEDIKNSPTLKSF

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_348 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 7 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000001357	1 retrocopy	retro_chof_1370,
Dasypus novemcinctus	ENSDNOG00000017379	2 retrocopies	retro_dnov_1294, retro_dnov_1451,
Mus musculus	ENSMUSG00000027506	1 retrocopy	retro_mmus_3221,
Oryctolagus cuniculus	ENSOCUG00000008247	1 retrocopy	retro_ocun_325,
Otolemur garnettii	ENSOGAG00000013689	1 retrocopy	retro_ogar_3142,
Otolemur garnettii	ENSOGAG00000016601	2 retrocopies	retro_ogar_1677, retro_ogar_348 ,
Tursiops truncatus	ENSTTRG00000000088	1 retrocopy	retro_ttru_1888,