RetrogeneDB ID: retro_ogar_978

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873532.1:28484567..28485101(+)
• Located in intron of: ENSOGAG00000007765

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSOGAG00000012225
• Aliases: None
• Description: None

Sequence

>retro_ogar_978
AAATCCCAAATCAGATACCCAGTGGAATCATTCTTCCACTTTTTCCTCATAAACCACTCCTTTCTTACAATTACAGTCTA
TTTTCTCTGTGAATTGCTCTGCAGCAGTTTTATTGCTTAGATGGTGATAATTATCTTGTTATCATGTGACTTTTGGATAG
TGAAGAATGTCACAAGTAGACTAATGGTTGGCCTATGTTGGTAGAATCATACTGAGGAAAATGAAAAGAGCCTCGGGTTG
TTTGAGCCCAAGAAGGCATCCTCTTAAGAGAGTAAAACTATTTCAGAGGCTGAATCAGGAATCTTTTGGTTAGGATTTAT
GCCTGCCTAGTGAGTGCTATGGGTGGTATTTGCCTTTCATGTCCTATTCTTCAGAGTAAAATGGTTGGCAGTGGTTATCA
TGGGTGTGGTGCTCCAAGGTGCCAACTTATATGGTTACATCAGCGTTAAGTGGGCAGAAGAAAGAATTACACCAGCACAG
TTACTTTGTATTTGGGTAAACAGTTTTTAAAAACAATATCCTGCAGATGATCAG

Alignment

ORF - retro_ogar_978 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.21 %
• Parental protein coverage: 85.85 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  KSKIRHPVASFFHLFFRVS----AIIVYLLCELLSSSFIACMVTIILLLSCDFWAVKNVTGRLMVGLRWW
          KS.IR.PV.SFFH.FF........I.VY.LCELL.SSFIA.MV.II.LLSCDFW.VKNVT.RLMVGL.W.
Retrocopy KSQIRYPVESFFH-FFLINHSFLTITVYFLCELLCSSFIA*MV-IIILLSCDFWIVKNVTSRLMVGLCW*

Parental  NHIDEDGKSHWVFESRKESSQENKTASEAESRIFWLGLI-ACPVLWVIFAFSALFSFRVKWLAVVLMGVV
          NH..E..KS...FE..K.SS.E.KT.SEAES.IFWLG...A..VLWV.FAF..LF.FRVKWLAVV.MGVV
Retrocopy NHTEENEKSLGLFEPKKASS*ESKTISEAESGIFWLGFMPA**VLWVVFAFHVLF-FRVKWLAVVIMGVV

Parental  LQGANLYGYIRCK-VGSRKNFTNMATSYLGKQFL-RQNTGDDQ
          LQGANLYGYI..K.VG.RKN.T...T.YLGKQFL..Q...DDQ
Retrocopy LQGANLYGYISVK<VGRRKNYTSTVTLYLGKQFL>KQYPADDQ

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_978 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 15 parental genes, and 27 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000005330	1 retrocopy	retro_cpor_184,
Dasypus novemcinctus	ENSDNOG00000007609	2 retrocopies	retro_dnov_1041, retro_dnov_1390,
Homo sapiens	ENSG00000171928	1 retrocopy	retro_hsap_2278,
Homo sapiens	ENSG00000175106	1 retrocopy	retro_hsap_1625,
Loxodonta africana	ENSLAFG00000003854	1 retrocopy	retro_lafr_465,
Myotis lucifugus	ENSMLUG00000002825	1 retrocopy	retro_mluc_1484,
Macaca mulatta	ENSMMUG00000019203	5 retrocopies	retro_mmul_1032, retro_mmul_2125, retro_mmul_278, retro_mmul_600, retro_mmul_748,
Nomascus leucogenys	ENSNLEG00000014658	2 retrocopies	retro_nleu_1961, retro_nleu_2008,
Oryctolagus cuniculus	ENSOCUG00000000498	1 retrocopy	retro_ocun_759,
Otolemur garnettii	ENSOGAG00000012225	1 retrocopy	retro_ogar_978 ,
Pan troglodytes	ENSPTRG00000007790	1 retrocopy	retro_ptro_20,
Pan troglodytes	ENSPTRG00000008796	1 retrocopy	retro_ptro_996,
Rattus norvegicus	ENSRNOG00000050649	1 retrocopy	retro_rnor_636,
Ictidomys tridecemlineatus	ENSSTOG00000000642	6 retrocopies	retro_itri_1415, retro_itri_1841, retro_itri_310, retro_itri_473, retro_itri_711, retro_itri_782,
Tarsius syrichta	ENSTSYG00000008082	2 retrocopies	retro_tsyr_2000, retro_tsyr_530,