RetrogeneDB ID: retro_ogar_3110

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873720.1:2185169..2185611(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: UBE2D3
• Ensembl ID: ENSOGAG00000012860
• Aliases: None
• Description: ubiquitin-conjugating enzyme E2D 3 [Source:HGNC Symbol;Acc:12476]

Sequence

>retro_ogar_3110
GCACTGAAACAGATTAATAAGGAATTTAGTGATCTGGCCCGTGACCCTCCAGCACAATGTTCTTCTGCAGGTCCAGTTGG
GCATGATATGCTTCAGCAGCAAGCCACAATTATGGGACCCAATGACAGCCCATATCGGGGTGGTGTATTCTTTTTGGCAA
TTCATTTTCCTACAGACTACCCCTTCAAACCACCTAAGATGGCATTTGCAACAAGAATTTATCATCCAAATATTAACAAT
CATGGCAGCGTTTGTCTCAATATTCTAAGACCACAGTGGTCTCCTGCTTCAACTACTTCTAAAGTTCTTTTATCCATTTG
TTCACTGTTAATGTGATCCAAGCCCAAATGACCCCCTAGTGCCAGAGATTGCACAGATCTATAAAACAGACAGTGATAAG
TACAACAGAATATCTCAGAAATGGACTCAAAAGTATGCCATG

Alignment

ORF - retro_ogar_3110 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.38 %
• Parental protein coverage: 98.65 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  AISRISQELSDLARDPPAQCS-AGPVGDDMFHWQATIMGPNDSPYQGGVFFLTIHFPTDYPFKPPKVAFT
          A...I..E.SDLARDPPAQCS.AGPVG.DM...QATIMGPNDSPY.GGVFFL.IHFPTDYPFKPPK.AF.
Retrocopy ALKQINKEFSDLARDPPAQCSSAGPVGHDMLQQQATIMGPNDSPYRGGVFFLAIHFPTDYPFKPPKMAFA

Parental  TRIYHPNINSNGSICLDILRSQWSPALTISKVLLSICSLL-CDPNPDDPLVPEIARIYKTDRDKYNRLAR
          TRIYHPNIN..GS.CL.ILR.QWSPA.T.SKVLLSICSLL.CDP.P.DPLVPEIA.IYKTD.DKYNR...
Retrocopy TRIYHPNINNHGSVCLNILRPQWSPASTTSKVLLSICSLL>CDPSPNDPLVPEIAQIYKTDSDKYNRISQ

Parental  EWTEKYAM
          .WT.KYAM
Retrocopy KWTQKYAM

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_3110 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 38 retrocopies.

Species	Parental gene accession	Retrocopies number
Ciona intestinalis	ENSCING00000018711	2 retrocopies	retro_cint_19, retro_cint_29,
Ciona savignyi	ENSCSAVG00000006136	1 retrocopy	retro_csav_18,
Erinaceus europaeus	ENSEEUG00000010820	1 retrocopy	retro_eeur_84,
Erinaceus europaeus	ENSEEUG00000014658	3 retrocopies	retro_eeur_263, retro_eeur_566, retro_eeur_591,
Echinops telfairi	ENSETEG00000001291	3 retrocopies	retro_etel_1218, retro_etel_1998, retro_etel_36,
Gorilla gorilla	ENSGGOG00000001368	2 retrocopies	retro_ggor_1156, retro_ggor_2321,
Ornithorhynchus anatinus	ENSOANG00000005415	1 retrocopy	retro_oana_51,
Otolemur garnettii	ENSOGAG00000007527	3 retrocopies	retro_ogar_2029, retro_ogar_2566, retro_ogar_626,
Otolemur garnettii	ENSOGAG00000012860	6 retrocopies	retro_ogar_1124, retro_ogar_3047, retro_ogar_3048, retro_ogar_3110 , retro_ogar_544, retro_ogar_599,
Otolemur garnettii	ENSOGAG00000014956	4 retrocopies	retro_ogar_1343, retro_ogar_2512, retro_ogar_2682, retro_ogar_3443,
Pongo abelii	ENSPPYG00000014967	1 retrocopy	retro_pabe_91,
Pteropus vampyrus	ENSPVAG00000015438	1 retrocopy	retro_pvam_234,
Sus scrofa	ENSSSCG00000024306	1 retrocopy	retro_sscr_783,
Sus scrofa	ENSSSCG00000029822	4 retrocopies	retro_sscr_1016, retro_sscr_672, retro_sscr_673, retro_sscr_918,
Tupaia belangeri	ENSTBEG00000000270	5 retrocopies	retro_tbel_1336, retro_tbel_145, retro_tbel_1837, retro_tbel_262, retro_tbel_3134,