RetrogeneDB ID: retro_ogar_1052

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873534.1:16726055..16726578(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TTC1
• Ensembl ID: ENSOGAG00000016342
• Aliases: None
• Description: tetratricopeptide repeat domain 1 [Source:HGNC Symbol;Acc:12391]

Sequence

>retro_ogar_1052
ACTAAACTAAAGGAGGAGGGAAATGAGCAGTTTACGAAAGGAGATTATATAGAAGCTGAAAGTTCTTATAGTCGAGCCCT
AGAGATGTGCCCGTCCCGTTTCCAAAAAGACAGATCTATTCTGTTTTCAAATAGAGCTGCCGCAAGGATGAAACAGGGTA
AGAAAGAGATGGCCATTAAGGACTGCAGCAAAGCAATTCGGTTAAACCCCAACTATATCAGGGCAATATTGAGGAGAGCG
GAGTTGTATGAGAAAATGGACAAACTAGATGAAGCCCTAGAAGATTATAAATCTATATTAGAAAAGGATCCATCAATACA
CCAAGCAAGAGAAGCTTGTATGAGATTACCTAAGCAAATCGAAGAACGAAATGAAAGACTGAAAGAAGATATGTCAGGTA
AACTAAAAGATCTTGGGAATTCTCCGACCGTTTGGGCTCTCCACAGAAAATTTCCAGATCAAACAGGATTCCTCCACTGG
CTCCTACTCCATTAATTTTGTTCAAAATCCAAATAATAACAGG

Alignment

ORF - retro_ogar_1052 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.22 %
• Parental protein coverage: 60.07 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  TKLKEEGNEQFKKGDYIEAESSYSRALETCPSCFQKDRSILFSNRAAARMKQDKKEMAIKDCSKAIQLNP
          TKLKEEGNEQF.KGDYIEAESSYSRALE.CPS.FQKDRSILFSNRAAARMKQ.KKEMAIKDCSKAI.LNP
Retrocopy TKLKEEGNEQFTKGDYIEAESSYSRALEMCPSRFQKDRSILFSNRAAARMKQGKKEMAIKDCSKAIRLNP

Parental  NYIRAILRRAELYEKTDKLDEALEDYKSILEKDPSIHQAREACMRLPKQIEERNERLKEEMLGKLKD-LG
          NYIRAILRRAELYEK.DKLDEALEDYKSILEKDPSIHQAREACMRLPKQIEERNERLKE.M.GKLKD.LG
Retrocopy NYIRAILRRAELYEKMDKLDEALEDYKSILEKDPSIHQAREACMRLPKQIEERNERLKEDMSGKLKD>LG

Parental  NLVLRPFGLSTENFQIKQDSSTGSYSINFVQNPNNNR
          ...LRPFGLSTENFQIKQDSSTGSYSINFVQNPNNNR
Retrocopy --ILRPFGLSTENFQIKQDSSTGSYSINFVQNPNNNR

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_1052 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
Echinops telfairi	ENSETEG00000019397	1 retrocopy	retro_etel_1659,
Myotis lucifugus	ENSMLUG00000003057	2 retrocopies	retro_mluc_1351, retro_mluc_2408,
Otolemur garnettii	ENSOGAG00000016342	1 retrocopy	retro_ogar_1052 ,
Tupaia belangeri	ENSTBEG00000004641	1 retrocopy	retro_tbel_3250,
Vicugna pacos	ENSVPAG00000012031	1 retrocopy	retro_vpac_498,