RetrogeneDB ID: retro_ogar_1089

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873535.1:8758183..8758949(-)
• Located in intron of: ENSOGAG00000016195

Retrocopy information

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

Parental gene information

• Parental gene symbol: RABGGTB
• Ensembl ID: ENSOGAG00000007665
• Aliases: None
• Description: Rab geranylgeranyltransferase, beta subunit [Source:HGNC Symbol;Acc:9796]

Sequence

>retro_ogar_1089
GAACATGCAGATTACATCGCCTCCTATGGCTCTAAGAAAGATGATTATGAATACCGCCTGTCTGAATATTTGAGAATGAG
TGGCATCTATTGGGGTCTGACAGTGATGGCTCTAATGGGACAGCTTGATCACATGAATAGAGAAGAAATTCTGACATTTA
TTAAGTCATGCCAACATGAGTGTGGTAGAATAAGTGGTTAGTATTGGATATGATCCTCATCTTGTATACACTCTGAGTGC
TGTCCAGATTCTTACTCTGTATGATAGTATTAATGTTATTGACATAAACAAAATTGTGGAATATGTTTAAAGTCTACAGA
AAGAAGATGGTTCTTTTGCTGGAAACATATGGGGAGAAATTGATATAAGCTTCTCTTTCTGTGCAGTGGCTACTTTGGCT
CTTTTGGGGAAGCTTGATGCTATTAATGTGGAAAAGGCAATTGAATTTGTTTTATCCTGCATGAACTTTGTTGGTGGATT
TGGTTGCAGACCAGGTGCCGAATCCCATGCTGGGCAGATCTATTGTTGCACAGGATTCCTGGCTATTACTAGTCAGTTGC
ATCACGTAAATTCTGATTTACTTGGTTGGTGGCTTTGTGAATGACAGTTACCCTCAGGCGGACTCAATGGAAGGCCAGAG
AAGTTACCAGATGTATGCTAGTCATGGTGGGTGTTGGCATCTCTAAAGATAATTGGAAGGCTTCATTGGATTGATAGAGA
GAAACTTCGTAGTTTTATTTTAGCATGTCAAGATGAAGAAATGGGG

Alignment

ORF - retro_ogar_1089 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.41 %
• Parental protein coverage: 77.27 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KHADYIASYGSKKDDYEYCMSEYLRMSGIYWGLTVMDLMGQLDRMNREEILTFIKSCQHECGGISA-SIG
          .HADYIASYGSKKDDYEY..SEYLRMSGIYWGLTVM.LMGQLD.MNREEILTFIKSCQHECG.IS..SIG
Retrocopy EHADYIASYGSKKDDYEYRLSEYLRMSGIYWGLTVMALMGQLDHMNREEILTFIKSCQHECGRISG>SIG

Parental  HDPHLLYTLSAVQILTLYDSINVIDVNKVVEYVQSLQKEDGSFAGDIWGEIDTRFSFCAVATLALLGKLD
          .DPHL.YTLSAVQILTLYDSINVID.NK.VEYV.SLQKEDGSFAG.IWGEID..FSFCAVATLALLGKLD
Retrocopy YDPHLVYTLSAVQILTLYDSINVIDINKIVEYV*SLQKEDGSFAGNIWGEIDISFSFCAVATLALLGKLD

Parental  AINVEKAIEFVLSCMNFDGGFGCRPGSESHAGQIYCCTGFLAITSQLHQVNSDLLGWWLCERQLPSGGLN
          AINVEKAIEFVLSCMNF.GGFGCRPG.ESHAGQIYCCTGFLAITSQLH.VNSDLLGWWLCE.QLPSGGLN
Retrocopy AINVEKAIEFVLSCMNFVGGFGCRPGAESHAGQIYCCTGFLAITSQLHHVNSDLLGWWLCE*QLPSGGLN

Parental  GRPEKLPDVCYSWWVLASLKIIGRLHWIDREKLRSFILACQDEETG
          GRPEKLPDVC.SWWVLASLKIIGRLHWIDREKLRSFILACQDEE.G
Retrocopy GRPEKLPDVC*SWWVLASLKIIGRLHWIDREKLRSFILACQDEEMG

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_1089 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 8 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000011052	1 retrocopy	retro_acar_155,
Canis familiaris	ENSCAFG00000020392	1 retrocopy	retro_cfam_2104,
Choloepus hoffmanni	ENSCHOG00000009456	2 retrocopies	retro_chof_1851, retro_chof_260,
Mus musculus	ENSMUSG00000038975	1 retrocopy	retro_mmus_1030,
Otolemur garnettii	ENSOGAG00000007665	1 retrocopy	retro_ogar_1089 ,
Sorex araneus	ENSSARG00000007392	1 retrocopy	retro_sara_207,
Ictidomys tridecemlineatus	ENSSTOG00000021824	1 retrocopy	retro_itri_484,
Tursiops truncatus	ENSTTRG00000014126	3 retrocopies	retro_ttru_1391, retro_ttru_1767, retro_ttru_214,