RetrogeneDB ID: retro_ogar_2911

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873679.1:555931..556523(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: JOSD1
• Ensembl ID: ENSOGAG00000007520
• Aliases: None
• Description: Josephin domain containing 1 [Source:HGNC Symbol;Acc:28953]

Sequence

>retro_ogar_2911
ATGAGTTGCCCACCAAGGACAGGAGACAGGGCCACATCTGAGCTGCCCTGGGCAGCACCTCACAGATCCACCATGAGAAA
GAGCACAGGGAGCTCTATGCCCACCATGCCCTCAATGACGTCCTCCAGGATGGTGATGCCTCCACCCAGGAAACACTCCA
TGAAGTGTCTGGAGGTCGTCTCCAAACACCATGATGAATGGTGACACCACACGAGAAGAGCATGCTGGGAAATGGAAGCT
ATGATGTGATGTCATGGCAGCATTTCAAACCAAGGGCTATGATGCTGTTGGTGGGACAAGCACAGGGATGTAGGTGTCAT
TGCTCTCACTAAGGTCATGGGCCTCATCACGAATCTGTCCTCCAGCCTATTCTGGGGTCCACCGAAGTCACCTCTCAAAA
GGCACCACTGGATCTGTGTTGGAGAGGTAGAGGGGACTTCTGTAACATCGACTCCAAACTCCAGATGGCTGAGTGCATGG
GAGACAGAGCAAGCTCAGGACATCTGGAAAACATCATTTGCCAAGAGAAAGCTGTGAACTGCTGGTGGTACCAGAAGCTG
TAGAGGCCCATCAGAGTTGGAGGACTGATGTG

Alignment

ORF - retro_ogar_2911 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.68 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  MSCVPWKGDKAKSESLELPQAAP-PQIYHEKQRRELCALHALNNVFQDSNAFTREALQEIF--QRLSPNT
          MSC.P..GD.A.S...ELP.AAP..QI.HEK..REL.A.HALN.V.QD..A.T.E.L.E........P..
Retrocopy MSCPPRTGDRATS---ELPWAAP<SQIHHEKEHRELYAHHALNDVLQDGDASTQETLHEVSGGRLQTP**

Parental  MVTPHKKSMLGNGNYDV-NVIMAALQTKGYEAV-WWDKRRDVSVIALTNVMGFIMNLPSSLCWGPLKLPL
          MVTPH.KSMLGNG.YDV..V..A..QTKGY.AV.WWDK.RDV.VIALT.VMG.I.NL.SSL.WGP.K.PL
Retrocopy MVTPHEKSMLGNGSYDV<DVMAA-FQTKGYDAV<WWDKHRDVGVIALTKVMGLITNLSSSLFWGPPKSPL

Parental  KRQHWICVREVGGA-YYNLDSKLKMPEWIGG-ESELRKFLKHHLRGKNCELLLVVPETVEAHQSWRTDV
          KR.HWICV.EV.G....N.DSKL.M.E..G...S.LR...KHHL....CE.LLVVPE.VEAHQSWRTDV
Retrocopy KRHHWICVGEVEGT<FCNIDSKLQMAECMGD<QSKLRTSGKHHLPRESCE-LLVVPEAVEAHQSWRTDV

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_2911 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 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000010171	1 retrocopy	retro_btau_1508,
Canis familiaris	ENSCAFG00000001379	1 retrocopy	retro_cfam_1500,
Choloepus hoffmanni	ENSCHOG00000001723	2 retrocopies	retro_chof_1576, retro_chof_233,
Equus caballus	ENSECAG00000015546	1 retrocopy	retro_ecab_251,
Felis catus	ENSFCAG00000002821	1 retrocopy	retro_fcat_565,
Macropus eugenii	ENSMEUG00000002899	2 retrocopies	retro_meug_1507, retro_meug_531,
Microcebus murinus	ENSMICG00000011798	1 retrocopy	retro_mmur_1202,
Myotis lucifugus	ENSMLUG00000003764	1 retrocopy	retro_mluc_1868,
Mus musculus	ENSMUSG00000022426	1 retrocopy	retro_mmus_3014,
Otolemur garnettii	ENSOGAG00000007520	3 retrocopies	retro_ogar_1462, retro_ogar_2911 , retro_ogar_3487,
Pteropus vampyrus	ENSPVAG00000010148	1 retrocopy	retro_pvam_181,
Rattus norvegicus	ENSRNOG00000014440	2 retrocopies	retro_rnor_2954, retro_rnor_906,
Sarcophilus harrisii	ENSSHAG00000015931	1 retrocopy	retro_shar_643,
Ictidomys tridecemlineatus	ENSSTOG00000024999	1 retrocopy	retro_itri_193,
Tarsius syrichta	ENSTSYG00000008846	1 retrocopy	retro_tsyr_1076,