RetrogeneDB ID: retro_ogar_2801

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873665.1:140426..140664(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: APOC1
• Ensembl ID: ENSOGAG00000028159
• Aliases: None
• Description: apolipoprotein C-I [Source:HGNC Symbol;Acc:607]

Sequence

>retro_ogar_2801
GTGAGGCTCATGCTATCACTCCTGATCCTAGTGTGGGTCTGTCAATGGATTTAGAAGGCCCAGCCCCAGCCCAGGCGGCT
CCGGACTTCTCTGGCACCTTGAATAAGCTGAAGGAATTTGAAACGCCATGGAGGACAAAGCCTAGGAAGTCATTGACTGC
ATGAAACAGAGCAACATTTCTACCAAGACCAGGAATTGGTTTTCAGAGGCATTTGAGAAAGTGAAAGAGAAACTTAAA

Alignment

ORF - retro_ogar_2801 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.85 %
• Parental protein coverage: 98.75 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MRLMLSLPVLVLV-LAMVLEGPAPAQGTMDLDFTRH-LKEFG-NTMGDKAREVIDRIKQSDIPAKTRNWF
          .RLMLSL..LV.V.L.M.LEGPAPAQ...D...T...LKEF..N.M.DKA.EVID..KQS.I..KTRNWF
Retrocopy VRLMLSLLILVWV<LSMDLEGPAPAQAAPDFSGTLNKLKEFE<NAMEDKA*EVIDCMKQSNISTKTRNWF

Parental  SETFQKVKEKLK
          SE.F.KVKEKLK
Retrocopy SEAFEKVKEKLK

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_2801 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
Ailuropoda melanoleuca	ENSAMEG00000012737	1 retrocopy	retro_amel_582,
Canis familiaris	ENSCAFG00000004615	1 retrocopy	retro_cfam_530,
Otolemur garnettii	ENSOGAG00000028159	1 retrocopy	retro_ogar_2801 ,
Rattus norvegicus	ENSRNOG00000018426	1 retrocopy	retro_rnor_204,
Tupaia belangeri	ENSTBEG00000007093	2 retrocopies	retro_tbel_1243, retro_tbel_2226,