RetrogeneDB ID: retro_ogar_3142

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873728.1:2169999..2170375(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TPD52L2
• Ensembl ID: ENSOGAG00000013689
• Aliases: None
• Description: tumor protein D52-like 2 [Source:HGNC Symbol;Acc:12007]

Sequence

>retro_ogar_3142
GATACCAGTATGAATACTCTTAACAGAGGTCTGCTGTCTGACTCCATGACTGATGTCCCTGTCGACAGAGATGTGGCTGC
CTGTACTTGTGCTGTTGAGAGTCTAGTGGATGCTGAAGAGGAGCTCAAGATTGAGCTCATGAAGGTGGAAAAGGAAACTG
TTACCCTGTGCCAGGTCTTGGCAGCAAAGAGAAGCACTTCAGTGAGCTCAAGAAAAGGTGGAGCCTCTCCACTTTGTGGG
GGCATGAGGCAGAGCCTGTCCAGGAGCTGGCATAATGTGCCAAGTCTCTAACACCTATGCAAAAACTTATGAGAAACTCT
GAGAGTGGAATGAGAAAGTGTAAGAAGACTCAAGAAACTCTCCCACAAGCAGGACT

Alignment

ORF - retro_ogar_3142 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.02 %
• Parental protein coverage: 55.02 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  DINLNSPNKGLLSDSMTDVPVDTAVAARTLADEGLTEAEEEELRAELTKVEEEIVTLRQVLAAK-ERHCG
          D...N..N.GLLSDSMTDVPVD..VAA.T.A.E.L..AEEE.L..EL.KVE.E.VTL.QVLAAK.E.H..
Retrocopy DTSMNTLNRGLLSDSMTDVPVDRDVAACTCAVESLVDAEEE-LKIELMKVEKETVTLCQVLAAK<EKHFS

Parental  ELRRRLGLSTL-GGLKQNLSRSWHDV-QVSNAYVKTSEKLGEWNEKVTQSDLYKKTQET
          EL..R..LSTL.GG..Q.LSRSWH.V.QVSN.Y.KT.EKL.EWNEKV........T..T
Retrocopy ELKKRWSLSTL>GGMRQSLSRSWHNV>QVSNTYAKTYEKL*EWNEKV*EDSRNSPTSRT

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_3142 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 5 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000003663	1 retrocopy	retro_acar_36,
Dasypus novemcinctus	ENSDNOG00000014930	1 retrocopy	retro_dnov_1582,
Equus caballus	ENSECAG00000021789	1 retrocopy	retro_ecab_69,
Otolemur garnettii	ENSOGAG00000013689	1 retrocopy	retro_ogar_3142 ,
Otolemur garnettii	ENSOGAG00000016601	2 retrocopies	retro_ogar_1677, retro_ogar_348,