RetrogeneDB ID: retro_ogar_2029

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873582.1:9267125..9267703(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOGAG00000029077
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: UBE2E1
• Ensembl ID: ENSOGAG00000007527
• Aliases: None
• Description: ubiquitin-conjugating enzyme E2E 1 [Source:HGNC Symbol;Acc:12477]

Sequence

>retro_ogar_2029
ATGTTGGATAATGATTCAAGGACCAGCACCAGCTCCTCCTCATCTTCATCCTCCAACCAGCAAATGGAGAAAGAAACAGA
CACCCCAAGAAAAAGGAGAGTAAAGTCAGCCTGAGCAAAAACTCTAAATTCTTCTCCACCAGAGCCAGGAGGATTCAGAA
GGAATTAGCAGACATCACTGTAGACCCCCCACCTAACTGCAGTGCTGGTCCCAAAGGCAATAACATTTATGGATGGAGAG
CAACCATTTCAGGGCATCCAGGATCTGTGTATGAGGGTGGTGTATTCTTCCCTGATATAACTTTTACACCAGAATATCCC
TTCAAGCCTCCAAAGGTTACATTTCGGACAAGAATCTGTCACTGTAATATTAACAGTCAAGGTGTTATTTGCTTTGACAT
ATTGAAAGATAATTGGAGTCCAGCACTAACCATTTCTAAAGTTCTCCTTTCTATCTGCTCACTTCTTACAGATTGTAATC
CTGCTGACCTGTCGGTAGGAAGTATTACTACTCAGTATATGACCAACAGAGCGGAACATGAGGGGATGGCCAGACAGTGG
GCCAAGAGACATGCTACC

Alignment

ORF - retro_ogar_2029 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.08 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSDDDSRASTSSSSSSSSNQQTEKETNTP-KKKESKVSMSKNSKLLSTSAKRIQKELADITLDPPPNCSA
          M.D.DSR.STSSSSSSSSNQQ.EKET.TP.KKKESKVS.SKNSK..ST.A.RIQKELADIT.DPPPNCSA
Retrocopy MLDNDSRTSTSSSSSSSSNQQMEKETDTP<KKKESKVSLSKNSKFFSTRARRIQKELADITVDPPPNCSA

Parental  GPKGDNIYEWRSTILGPPGSVYEGGVFFLDITFTPEYPFKPPKVTFRTRIYHCNINSQGVICLDILKDNW
          GPKG.NIY.WR.TI.G.PGSVYEGGVFF.DITFTPEYPFKPPKVTFRTRI.HCNINSQGVIC.DILKDNW
Retrocopy GPKGNNIYGWRATISGHPGSVYEGGVFFPDITFTPEYPFKPPKVTFRTRICHCNINSQGVICFDILKDNW

Parental  SPALTISKVLLSICSLLTDCNPADPLVGSIATQYMTNRAEHDRMARQWTKRYAT
          SPALTISKVLLSICSLLTDCNPAD..VGSI.TQYMTNRAEH..MARQW.KR.AT
Retrocopy SPALTISKVLLSICSLLTDCNPADLSVGSITTQYMTNRAEHEGMARQWAKRHAT

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_2029 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 12 parental genes, and 27 retrocopies.

Species	Parental gene accession	Retrocopies number
Ciona intestinalis	ENSCING00000006860	1 retrocopy	retro_cint_33,
Cavia porcellus	ENSCPOG00000002251	2 retrocopies	retro_cpor_1036, retro_cpor_52,
Gorilla gorilla	ENSGGOG00000008393	1 retrocopy	retro_ggor_76,
Loxodonta africana	ENSLAFG00000004150	1 retrocopy	retro_lafr_320,
Macropus eugenii	ENSMEUG00000014517	1 retrocopy	retro_meug_2089,
Mus musculus	ENSMUSG00000021774	3 retrocopies	retro_mmus_2493, retro_mmus_2600, retro_mmus_537,
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,
Pan troglodytes	ENSPTRG00000014693	1 retrocopy	retro_ptro_68,
Rattus norvegicus	ENSRNOG00000008794	3 retrocopies	retro_rnor_1632, retro_rnor_2291, retro_rnor_2343,
Sarcophilus harrisii	ENSSHAG00000001416	1 retrocopy	retro_shar_712,