RetrogeneDB ID: retro_ogar_1938

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873576.1:5444976..5445426(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ATP5G3
• Ensembl ID: ENSOGAG00000027578
• Aliases: None
• Description: ATP synthase, H+ transporting, mitochondrial Fo complex, subunit C3 (subunit 9) [Source:HGNC Symbol;Acc:843]

Sequence

>retro_ogar_1938
AGTCCTCCAGCTGTGCCACCCAAAGAGTATAAGATGTTTGCCATAGCCAAGCTTGCCTGCACCTTGCTCTGATCCAAGCT
GGATCCAGAGTTGCATAGAGACCAATTTCTGCAGCAGTGTTATCTCAACCAGAGGCTGGGACTGGAGAGGGCTCTGCAGT
ATTTAATAATCGTGCTCAGAATGGTGTGTCGTAGCTAATCCAAAGGCAGTTTCAGATCAGTGGAATCAGCGGAGACATTG
ATACCAAATGTATTGATACAACTGCAGCAGTAGGAGCGACTAGTTCTGGTACTGGTACTGGAACAATCTTTGTAAGCCTT
ATCCTTGGTTGTGTCAGAAACCCTTCCCTGAAGCAAAGGCTGTTCGTATAAAATATCCTGGAATTTGCCTTGTCTGAAGC
TAAGGTTCTCTTTTTTTCCAATGGTTGGTTTTCTTGATTTGTTTGCCATG

Alignment

ORF - retro_ogar_1938 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.39 %
• Parental protein coverage: 99.35 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  SPPAAPPEECKMFACARLACTP-ALIRAGSRVAYRPISASVLSRPEARTGEGSAVFNG-AQNGVSQLIRR
          SPPA.PP.E.KMFA.A.LACT..ALI.AGSRVA.RPISA.VLS.PEA.TGEGSAVFN..AQNGVS.LI.R
Retrocopy SPPAVPPKEYKMFAIAKLACTL<ALIQAGSRVA*RPISAAVLSQPEAGTGEGSAVFNNRAQNGVS*LIQR

Parental  GFQTSAISRDIDTAAKFIGAGAATVGVAGSGAGIGTVFGSLIIGYARNPSLKQQLFSYAILGFALSEAMG
          .FQ.S.IS.DIDT..K.I...AA.VG...SG.G.GT.F.SLI.G..RNPSLKQ.LF...IL.FALSEA..
Retrocopy QFQISGISGDIDT--KCIDTTAA-VGATSSGTGTGTIFVSLILGCVRNPSLKQRLFV*NILEFALSEAKV

Parental  LFCL-MVAFLILFAM
          LF...MV.FL.LFAM
Retrocopy LFFS>MVGFLDLFAM

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_1938 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 19 parental genes, and 35 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000012367	1 retrocopy	retro_amel_1829,
Canis familiaris	ENSCAFG00000013366	2 retrocopies	retro_cfam_4, retro_cfam_5,
Choloepus hoffmanni	ENSCHOG00000012592	3 retrocopies	retro_chof_189, retro_chof_2561, retro_chof_508,
Callithrix jacchus	ENSCJAG00000008207	3 retrocopies	retro_cjac_279, retro_cjac_38, retro_cjac_4183,
Cavia porcellus	ENSCPOG00000006194	1 retrocopy	retro_cpor_479,
Dasypus novemcinctus	ENSDNOG00000010440	2 retrocopies	retro_dnov_235, retro_dnov_396,
Loxodonta africana	ENSLAFG00000010768	1 retrocopy	retro_lafr_120,
Myotis lucifugus	ENSMLUG00000012822	1 retrocopy	retro_mluc_23,
Macaca mulatta	ENSMMUG00000003954	1 retrocopy	retro_mmul_148,
Monodelphis domestica	ENSMODG00000009520	3 retrocopies	retro_mdom_1070, retro_mdom_295, retro_mdom_545,
Mustela putorius furo	ENSMPUG00000013986	1 retrocopy	retro_mputfur_818,
Oryctolagus cuniculus	ENSOCUG00000012164	1 retrocopy	retro_ocun_949,
Otolemur garnettii	ENSOGAG00000003611	4 retrocopies	retro_ogar_142, retro_ogar_1620, retro_ogar_166, retro_ogar_2415,
Otolemur garnettii	ENSOGAG00000011713	3 retrocopies	retro_ogar_1847, retro_ogar_2767, retro_ogar_531,
Otolemur garnettii	ENSOGAG00000027578	1 retrocopy	retro_ogar_1938 ,
Rattus norvegicus	ENSRNOG00000001596	1 retrocopy	retro_rnor_1106,
Sorex araneus	ENSSARG00000006733	1 retrocopy	retro_sara_82,
Ictidomys tridecemlineatus	ENSSTOG00000013572	4 retrocopies	retro_itri_1091, retro_itri_1236, retro_itri_324, retro_itri_438,
Tupaia belangeri	ENSTBEG00000012159	1 retrocopy	retro_tbel_54,