RetrogeneDB ID: retro_ogar_3010

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873696.1:145877..146710(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSOGAG00000025948
• Aliases: None
• Description: None

Sequence

>retro_ogar_3010
TGTGCTCGACCACACAAGGCTGATGGGTGTGTTGTGGAACCAAAGAGAGCTGTATCTAGAGAGGATTCTGTAAAGCCTGG
TGCCCATCTCACAGTGAAGAAAATTTTTGTTGGTGGTATTAAAGAAGATACAGAAGAATATATTTGAGAGACTACTTTGA
AAAGTATGGCAGGATTGAAACCACAGAAGTTATGGAAGGCAGGCAGAGTGGAAAAAAGAGAGGATCTGCTTTGGTAACTT
TTGATGATCATGATACTGTTGATAAAATTGTTATTCAGAAAGACCCCACTATTAATGGGCATAATTGTGAAGTGAAAAAG
GCCCTTTCTAAACAAGAGATGCAGTCTGCTGAATCATAAAGAGGTCGTGGAGGTGGATCTGGCAACTTTAGGGGTCAGGG
AGGAAACTTTGGAGGTGGTGGAAACTTTGGTGGGAGAGGAGGATATGGTGGTGGAGCTGGTGGCAGCAGAGGTAGTTATG
GAGGAGGTGATGGTGGATATAATGGATTTGGAGGTGATGGTGGGAACTATGGTGGTGGTCCTGGTTACAGTAGTAGAGGG
GGCTATGTTGGTGGTGGACCAGGATAAGGAAACCAAGGTGGTGGATGTGGTGGTGGAGAAGGATATGATGGTTACAATGA
AGGAGGAAATTTTGGAGGTGGTAACTATGGTGGTGGTGGGAACTATGATGATTTTGGAAATTATAGTGGACAACAGCAAT
CAAGTTATGGACCTATGAAAAGGGGCAGTGTTGGTGGAAGAAGCTCAGGCAATCCATATGGTGGTGGTTATGGATCTGGT
GGTGGAAGTGGTGGATATGGTAGCAGAAGGTTC

Alignment

ORF - retro_ogar_3010 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.97 %
• Parental protein coverage: 82.32 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  CVEPHKADGRVVEPKRAVSREDSVKPGAHLTVKKIFVGSIKEDTEEY-HLRDYFEKYGKIKTIEVVEDRQ
          C..PHKADG.VVEPKRAVSREDSVKPGAHLTVKKIFVG.IKEDTEEY..LRDYFEKYG.I.T.EV.E.RQ
Retrocopy CARPHKADGCVVEPKRAVSREDSVKPGAHLTVKKIFVGGIKEDTEEY<YLRDYFEKYGRIETTEVMEGRQ

Parental  SGKKRGFAFATFDDHDTVDKIVVQKSHTINGHNCEVKKALSKQEMQSAGLQRGHEGGSGNFMGWGGNFGG
          SGKKRG.A..TFDDHDTVDKIV.QK..TINGHNCEVKKALSKQEMQSA...RG..GGSGNF.G.GGNF.G
Retrocopy SGKKRGSALVTFDDHDTVDKIVIQKDPTINGHNCEVKKALSKQEMQSAES*RGRGGGSGNFRGQGGNF-G

Parental  GGGNFDRGGNLGGRGGYGGGGGGSRGSYGGGDGGYNGFGGDGGNYGSGPGYSSRGGYGGGGPGYGNQGGG
          GGGNF...G..GG.GG..GG..GS.G...GG..G..G.GG...NYG.GPGYSSRGGY.GGGPG.GNQGGG
Retrocopy GGGNF---GGRGGYGGGAGGSRGSYGGGDGGYNGFGGDGG---NYGGGPGYSSRGGYVGGGPG*GNQGGG

Parental  YGGGGGYEGYNEGGSF-GGNYGGSGNYNDFGNYSGQQQSNYGPMKGGSFGGRSLGSPYGGGYGSGGGIGG
          .GGG.GY.GYNEGG.F.GGNYGG.GNY.DFGNYSGQQQS.YGPMK.GS.GGRS.G.PYGGGYGSGGG.GG
Retrocopy CGGGEGYDGYNEGGNFGGGNYGGGGNYDDFGNYSGQQQSSYGPMKRGSVGGRSSGNPYGGGYGSGGGSGG

Parental  YGSRRF
          YGSRRF
Retrocopy YGSRRF

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_3010 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 37 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000011920	4 retrocopies	retro_amel_1407, retro_amel_557, retro_amel_715, retro_amel_765,
Ficedula albicollis	ENSFALG00000003215	1 retrocopy	retro_falb_15,
Gallus gallus	ENSGALG00000009250	1 retrocopy	retro_ggal_10,
Monodelphis domestica	ENSMODG00000019803	1 retrocopy	retro_mdom_1590,
Oryctolagus cuniculus	ENSOCUG00000002743	2 retrocopies	retro_ocun_994, retro_ocun_995,
Otolemur garnettii	ENSOGAG00000002501	4 retrocopies	retro_ogar_2717, retro_ogar_2791, retro_ogar_437, retro_ogar_693,
Otolemur garnettii	ENSOGAG00000015353	3 retrocopies	retro_ogar_1384, retro_ogar_3077, retro_ogar_3189,
Otolemur garnettii	ENSOGAG00000025948	3 retrocopies	retro_ogar_1685, retro_ogar_3010 , retro_ogar_3175,
Otolemur garnettii	ENSOGAG00000028132	7 retrocopies	retro_ogar_1869, retro_ogar_1924, retro_ogar_2222, retro_ogar_2590, retro_ogar_3215, retro_ogar_600, retro_ogar_814,
Otolemur garnettii	ENSOGAG00000029707	3 retrocopies	retro_ogar_1721, retro_ogar_205, retro_ogar_2321,
Otolemur garnettii	ENSOGAG00000030251	2 retrocopies	retro_ogar_3509, retro_ogar_385,
Pelodiscus sinensis	ENSPSIG00000003011	1 retrocopy	retro_psin_16,
Sarcophilus harrisii	ENSSHAG00000018255	1 retrocopy	retro_shar_518,
Tarsius syrichta	ENSTSYG00000012949	2 retrocopies	retro_tsyr_1480, retro_tsyr_2122,
Xenopus tropicalis	ENSXETG00000001806	1 retrocopy	retro_xtro_11,
Xiphophorus maculatus	ENSXMAG00000000439	1 retrocopy	retro_xmac_2,