RetrogeneDB ID: retro_ogar_3026

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873699.1:348257..349014(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SEPHS1
• Ensembl ID: ENSOGAG00000007807
• Aliases: None
• Description: selenophosphate synthetase 1 [Source:HGNC Symbol;Acc:19685]

Sequence

>retro_ogar_3026
CTCCTTGGAGTCAGTAATGAAATCATTAATAGAGAAAGGGATAAAGTGTGTCCTTGGTTACAGAGGGTCTGACAGATGCA
TGAGAGGAAGCAGGGACATCTTTAGGTGGCCAAACAGTATTAACTCCTGGATTATTTGGGGAGGAGTCTCTTTAAATGTC
TACCAGCCTAGCGAATCTACCATGCCAGATAACACAGCTGGTGCAGCACCAGGGCATGTTGGGTGTTGAAGAAGCCCCCG
GGCACACAAGCCCCAGTCTCTGTGCTCCAGTTGCTGGGTATTGCTGAAAAATAGAATAAAGTTAAAGTAGTTTTCACCCA
AGAGGAGTTGACACGCCAAGAAGCAATGATGACCATGGCAAGGCTTAACAGAATACCTGCAGGACTTGTGCCCACATTCA
ACGCCCACGAGGCCGCCAATATCACAGGCTTCCGAATTTGGGGTCATGTGGAGAACCTGGCTAAGCAGCAGAGAAATTAG
GTATCCTTTGTAATCCACAACCTTCCTGTACTGCCCAAGATGGCTGGTGTAGCAAGGCCTGTGGACACCTGCTTGCCCCG
TGCCCAGGACTTCCTGGAGACATAAGAAGTCCTGCTGATATGTTTATCACTGAGCAAGCAGCTCTGTCCTATGCAGAGGC
AAAGTCCCCTGAACATGGTAAAGGTCACCAAGTATGGATTATTGGCATTGCAGAGAAGGGCAATGTACAGCCAGAATCAT
AGACAAACCCTGGATCAGGGAAGTTGCACCAAGAGTC

Alignment

ORF - retro_ogar_3026 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.84 %
• Parental protein coverage: 65.05 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  LLGVSNKMTDRERDKVMP-LIIQGFKDAAEEAGTSVTGGQTVLNP-WIVLGGVSTTVCQPNEFIMPDN--
          LLGVSN....RERDKV.P.L...G..DA.EEAGTS..GGQTVL.P.WI..GGVS..V.QP.E..MPDN..
Retrocopy LLGVSNEIINRERDKVCP<LVTEGLTDA*EEAGTSL-GGQTVLTP<WIIWGGVSLNVYQPSESTMPDNTA

Parental  -AVPGDV-LVLTKPLGTQVAVAVHQWLDIPEKWNKIKLVVTQEDVELAYQEAMMNMARLNRTAAGLMHTF
          .A.PG.V..VL.KP.GTQ..V.V.Q.L.I.EK.NK.K.V.TQE..EL..QEAMM.MARLNR..AGL..TF
Retrocopy GAAPGHV<WVLKKPPGTQAPVSVLQLLGIAEK*NKVKVVFTQE--ELTRQEAMMTMARLNRIPAGLVPTF

Parental  NAHAATDITGFGILGHAQNLAKQQRNEVSFVIHNLPVLAKMAAV-SKACGNMFGLMHGTCPETSGGLLIC
          NAH.A..ITGF.I.GH..NLAKQQRN.VSFVIHNLPVL.KMA.V.SKACG.......G............
Retrocopy NAHEAANITGFRIWGHVENLAKQQRN*VSFVIHNLPVLPKMAGV<SKACGHLLAPCPGLPGDIRSPADMF

Parental  LPREQAARFCAEIKSPKYGEGHQAWIIGIVEKGN-RTARIIDKPRIIEVAPQV
          .....A....AE.KSP..G.GHQ.WIIGI.EKGN..TARIIDKP.I.EVAP.V
Retrocopy ITEQAALSY-AEAKSPEHGKGHQVWIIGIAEKGN<CTARIIDKPWIREVAPRV

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_3026 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 10 parental genes, and 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000009494	2 retrocopies	retro_cjac_166, retro_cjac_2219,
Dipodomys ordii	ENSDORG00000014119	1 retrocopy	retro_dord_792,
Equus caballus	ENSECAG00000014281	1 retrocopy	retro_ecab_77,
Homo sapiens	ENSG00000086475	3 retrocopies	retro_hsap_2196, retro_hsap_3860, retro_hsap_4705,
Macaca mulatta	ENSMMUG00000021233	4 retrocopies	retro_mmul_1607, retro_mmul_2495, retro_mmul_2647, retro_mmul_922,
Mus musculus	ENSMUSG00000026662	1 retrocopy	retro_mmus_248,
Nomascus leucogenys	ENSNLEG00000012205	7 retrocopies	retro_nleu_1868, retro_nleu_2211, retro_nleu_234, retro_nleu_2668, retro_nleu_2873, retro_nleu_3004, retro_nleu_327,
Otolemur garnettii	ENSOGAG00000007807	1 retrocopy	retro_ogar_3026 ,
Pan troglodytes	ENSPTRG00000002303	3 retrocopies	retro_ptro_1135, retro_ptro_1669, retro_ptro_3126,
Rattus norvegicus	ENSRNOG00000018125	1 retrocopy	retro_rnor_59,