RetrogeneDB ID: retro_ogar_2988

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873693.1:2733237..2733881(+)
• Located in intron of: ENSOGAG00000029308

Retrocopy information

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

Parental gene information

• Parental gene symbol: NUDT5
• Ensembl ID: ENSOGAG00000005816
• Aliases: None
• Description: nudix (nucleoside diphosphate linked moiety X)-type motif 5 [Source:HGNC Symbol;Acc:8052]

Sequence

>retro_ogar_2988
ATGAAAAACCAAGAACCGACAGATTCTTCTTAGAATGCCAAACAATGTATTATTTCACAGAAATTAATTTCAGAAGGAAA
ATGGTTCAAGCTTGAAAAAACAACTTACATGGATCCTGCTGGTAAAACCAGAACCTGGGAAACCAGTGAAGCACACAACC
AGGAAGGGGCAGTCTGCTGATGGGGTAGTGGTCATCCCTGTGTTGCAGAGAACTTTTCATTACAAGTGAATCGTAATGAA
ACAACCACTGATGGACAGCTACTGCTTAGAGTTCCCTGCAATCTCATAGATGATTAACGCCCAGGAGCAGCTGCTCTCCA
AGAGCTTCAAGAGGAAACTGGCTACAAGGGTGATGTTGTTGAATGTTCTCCAGCTTTCTGTATGGACCCAAGTTTGTTAA
ACTGTACCACACACACTGTGATGGCAACCGTTAATGGGGATGATGCAGAAATCATACAACCCAAGCCAAAGCTGGGGGTG
GAGAATTTGTAGAAGTAATTTCTTTACCAAAGAATGACCTGGTGAAGAGAATTGATGCTCTGGTAGCTGAAGAGCATCTC
ATAGTGGATGCTAGAATCTACTCTTCCTCTCTGCTGCTGAAACATGCAAACATGAAGCCTTTTGAAGGGCCCTTTCTGAA
ATTT

Alignment

ORF - retro_ogar_2988 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.33 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MENQEATDSAQNGRQCIISEELISEGKWVKLEKTTYMDPTGKTSLNRTWET-VKRMTRKGQSADGVAVIP
          M.NQE.TDS..N..QCIIS..LISEGKW.KLEKTTYMDP.GKT...RTWET.VK..TRKGQSADGV.VIP
Retrocopy MKNQEPTDSS*NAKQCIISQKLISEGKWFKLEKTTYMDPAGKT---RTWET>VKHTTRKGQSADGVVVIP

Parental  VLQRTLHYECIILVKQFRPPMGGYCLEFPA-GLIDDDESPEAAALRELEEETGYKGDVAECSPAVCMDPG
          VLQRT.HY..I.......P.M..YCLEFPA..LIDD...P.AAAL.EL.EETGYKGDV.ECSPA.CMDP.
Retrocopy VLQRTFHYK*IVMKQ---PLMDSYCLEFPA<NLIDD*R-PGAAALQELQEETGYKGDVVECSPAFCMDPS

Parental  LSNCTTHIVTVTINGDDAENVRPKP-KPGDGEFVEVISLPKNDLLKRIDALVAEEHLTVDARVYSYALAL
          L.NCTTH.V..T.NGDDAE...PKP.K.G.GEFVEVISLPKNDL.KRIDALVAEEHL.VDAR.YS..L.L
Retrocopy LLNCTTHTVMATVNGDDAEIIQPKP<KAGGGEFVEVISLPKNDLVKRIDALVAEEHLIVDARIYSSSLLL

Parental  KHANTKPFEVPFLKF
          KHAN.KPFE.PFLKF
Retrocopy KHANMKPFEGPFLKF

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_2988 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 18 parental genes, and 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000019509	2 retrocopies	retro_btau_1326, retro_btau_1438,
Canis familiaris	ENSCAFG00000004794	2 retrocopies	retro_cfam_435, retro_cfam_612,
Equus caballus	ENSECAG00000023658	1 retrocopy	retro_ecab_647,
Echinops telfairi	ENSETEG00000006403	1 retrocopy	retro_etel_946,
Felis catus	ENSFCAG00000025093	1 retrocopy	retro_fcat_350,
Homo sapiens	ENSG00000165609	1 retrocopy	retro_hsap_3580,
Gorilla gorilla	ENSGGOG00000006325	1 retrocopy	retro_ggor_2415,
Loxodonta africana	ENSLAFG00000012052	1 retrocopy	retro_lafr_226,
Myotis lucifugus	ENSMLUG00000010453	2 retrocopies	retro_mluc_1263, retro_mluc_2073,
Macaca mulatta	ENSMMUG00000017141	1 retrocopy	retro_mmul_1828,
Nomascus leucogenys	ENSNLEG00000012298	1 retrocopy	retro_nleu_2838,
Oryctolagus cuniculus	ENSOCUG00000009308	1 retrocopy	retro_ocun_862,
Otolemur garnettii	ENSOGAG00000005816	2 retrocopies	retro_ogar_2071, retro_ogar_2988 ,
Pongo abelii	ENSPPYG00000002091	2 retrocopies	retro_pabe_2949, retro_pabe_3040,
Pan troglodytes	ENSPTRG00000002294	1 retrocopy	retro_ptro_2427,
Rattus norvegicus	ENSRNOG00000017741	1 retrocopy	retro_rnor_1672,
Sus scrofa	ENSSSCG00000011113	1 retrocopy	retro_sscr_143,
Tursiops truncatus	ENSTTRG00000007394	2 retrocopies	retro_ttru_209, retro_ttru_495,