RetrogeneDB ID: retro_ogar_863

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873529.1:13984999..13985816(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSOGAG00000003220
• Aliases: None
• Description: None

Sequence

>retro_ogar_863
TTTTTTCACAAGATGGCCGCGCCGGTAGTAACAGCTAATGATCCTCCCGCCAATGCCGGCCCAGCCCGGGTGGCGGCTCC
AGCTTCAACCCTGGCCCCAGCGCCAACGCCAGTTCCAGCGCGAGTTGCGGCTCCTGCTTCTTCTTCAGACCTGGCAGCGG
CAGCGGCTACAAATGCAGCTCTGGGTCAGACCCTGGCGTCAGCGCAAGCCCCAGCCCACACCCTGGCGCCCACATTGACT
GGTCCGGCCCTTCCAGGGCCCTTCCCTGGCGGCTGTGTGGTCAAACTTCACCCAGTCATTTTGGCCTCCATCGTGGACAG
CTATGAACGAGGAAATGAGGAAGCTGCCCATGTTATCGGAACCCTGTTGGGAACCGTTGACAAGCACTCAGTTGAGGTCA
CCAACTGCTTGTCAGTGCTGCACAATGAGTCAGAAGATGAAGTGGCTTGTTGACCTGGAATTTGCTATGAACATGTATGA
ATTGCACAAAAAAGTCTCTCCAAATGAGCTCATCCTGGGCTGGTGTGCTACAGGCCATGATATCACAGAACACTCTGTGC
TGATCCATGAGTACTCCAGCCTGGAGGCCCCAACCCCATTCACCTCACTGTGGACACAAGTCTCCAGAATGACCACATGA
GTATCAAAGCTGAATCTCAGCACTTTCATGGGTGTCCCTGGGAGGACCGTGGAAGTGATGTTCACACCTCTAACAGTGAA
ATACGCATATTACAACACTGAATGAGTTGGAGCTGACCGAGTGATTGGACTCTCAAGGGACTTGCAGGAAGTAGGAGGGG
CATCAGCTCGGACCCAG

Alignment

ORF - retro_ogar_863 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.42 %
• Parental protein coverage: 73.99 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  FFHKMAAPAVTASDPPANPGPAPAAAPALAPASTPAPAPTPAPAPAAAPASSSDPAAAAATATAPGQTPA
          FFHKMAAP.VTA.DPPAN.GPA..A....APAST.APAPTP.PA..AAPASSSD.AAAAAT..A.GQT.A
Retrocopy FFHKMAAPVVTANDPPANAGPARVA----APASTLAPAPTPVPARVAAPASSSDLAAAAATNAALGQTLA

Parental  SAQAPSQTPAPALTGPALPGPFPGGRVVKLHPVILASIVDSYERRNEGAARVIGTLLGTVDKHSVEVTNC
          SAQAP..T.AP.LTGPALPGPFPGG.VVKLHPVILASIVDSYER.NE.AA.VIGTLLGTVDKHSVEVTNC
Retrocopy SAQAPAHTLAPTLTGPALPGPFPGGCVVKLHPVILASIVDSYERGNEEAAHVIGTLLGTVDKHSVEVTNC

Parental  FSVPHNESEDEVA-VDMEFAKNMYELHKKVSPNELILGWYATGHDITEHSVLIHEYYSREA-PNPIHLTV
          .SV.HNESEDEVA.VD.EFA.NMYELHKKVSPNELILGW.ATGHDITEHSVLIHEY.S.EA.PNPIHLTV
Retrocopy LSVLHNESEDEVA>VDLEFAMNMYELHKKVSPNELILGWCATGHDITEHSVLIHEYSSLEA<PNPIHLTV

Parental  DTSLQNGRMSIKA-YVSTLMGVPGRTMGVMFTPLTVKYAYYDTERIGVDLIMKTCFSPNRVIGLSSDLQ
          DTSLQN..MSIKA...ST.MGVPGRT..VMFTPLTVKYAYY.TE..G.D...........V.G.S...Q
Retrocopy DTSLQNDHMSIKA>NLSTFMGVPGRTVEVMFTPLTVKYAYYNTE*VGADRVIGLSRDLQEVGGASARTQ

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_863 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 16 parental genes, and 25 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000004861	1 retrocopy	retro_btau_527,
Canis familiaris	ENSCAFG00000006884	1 retrocopy	retro_cfam_1339,
Callithrix jacchus	ENSCJAG00000011903	1 retrocopy	retro_cjac_1416,
Erinaceus europaeus	ENSEEUG00000001226	1 retrocopy	retro_eeur_130,
Echinops telfairi	ENSETEG00000002717	2 retrocopies	retro_etel_1583, retro_etel_35,
Homo sapiens	ENSG00000175390	3 retrocopies	retro_hsap_2106, retro_hsap_2512, retro_hsap_4321,
Gorilla gorilla	ENSGGOG00000011702	5 retrocopies	retro_ggor_1566, retro_ggor_1567, retro_ggor_1568, retro_ggor_1589, retro_ggor_1590,
Myotis lucifugus	ENSMLUG00000000825	1 retrocopy	retro_mluc_2356,
Macaca mulatta	ENSMMUG00000015010	1 retrocopy	retro_mmul_412,
Oryctolagus cuniculus	ENSOCUG00000004225	1 retrocopy	retro_ocun_1488,
Otolemur garnettii	ENSOGAG00000003220	3 retrocopies	retro_ogar_3041, retro_ogar_859, retro_ogar_863 ,
Otolemur garnettii	ENSOGAG00000014868	1 retrocopy	retro_ogar_388,
Otolemur garnettii	ENSOGAG00000016843	1 retrocopy	retro_ogar_1236,
Pongo abelii	ENSPPYG00000003512	1 retrocopy	retro_pabe_175,
Pan troglodytes	ENSPTRG00000003326	1 retrocopy	retro_ptro_197,
Pteropus vampyrus	ENSPVAG00000015764	1 retrocopy	retro_pvam_371,