RetrogeneDB ID: retro_ogar_1343

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873543.1:2216471..2217072(-)
• Located in intron of: ENSOGAG00000012787

Retrocopy information

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

Parental gene information

• Parental gene symbol: UBE2E3
• Ensembl ID: ENSOGAG00000014956
• Aliases: None
• Description: ubiquitin-conjugating enzyme E2E 3 [Source:HGNC Symbol;Acc:12479]

Sequence

>retro_ogar_1343
GTGTCCACTGAGGCACAAAGAGTTGATGACAGTCCGAGCACTAGTGGAAGAAGTTCCCATGGAGACCAACGTGAAAGTGT
TCAGCAAGAACCAGAAAGAGAGCAAGTTCAGCCCAAGAAAAAGGAGGGAAAACTATCCAGCAAAACTGCTGCTAAATTGT
CAACTAGTGCTGAAAGGATTCAGAAGGAACTTGCAGAAATTACACCGGATCCTCCTCCCAACTGTAGTGCTGGACCCAAA
GGAAACGACATTTATGAATGGAGGTCAACTATATTGAGACCCCCCAGGATCTGTCTGTGAAGGAGGGGTGTTCTTTCTTG
ACATTACCTTTTCACCAGACTATCCATTTAAGCCCCCTAAGGTTACCTTCCAAACAAGAATCCATCACTGTAATATTAAC
AGCCAAGGCATGATCTATCTAGACATCCTAAATGACAACTGAAGTCCAGCCCTAACCATTTCTAAGGTTCTCCTCTCTAT
CTGCTCCCTTACAGATTGCAACCATGCTGACCCTTTGGTGGGCAGCATTGCCACACAGTACATGACCAACAGAGCAGAAC
ATGACCAGATGGCCAGGCAGTGGACCAAGCAGTACGCCACA

Alignment

ORF - retro_ogar_1343 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.92 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSSDRQRSDDESPSTSSGSSDADQRDPAAPEPEEQEERKPSATQQKKNTKLSSKTTAKLSTSAKRIQKEL
          .S...QR.DD.SPSTS..SS..DQR.....EPE..E...P.....KK..KLSSKT.AKLSTSA.RIQKEL
Retrocopy VSTEAQRVDD-SPSTSGRSSHGDQRESVQQEPE-REQVQP----KKKEGKLSSKTAAKLSTSAERIQKEL

Parental  AEITLDPPPNCSAGPKGDNIYEWRSTIL-GPPGSVYEGGVFFLDITFSSDYPFKPPKVTFRTRIYHCNIN
          AEIT.DPPPNCSAGPKG..IYEWRSTIL..PPGSV.EGGVFFLDITFS.DYPFKPPKVTF.TRI.HCNIN
Retrocopy AEITPDPPPNCSAGPKGNDIYEWRSTIL>DPPGSVCEGGVFFLDITFSPDYPFKPPKVTFQTRIHHCNIN

Parental  SQGVICLDILKDNWSPALTISKVLLSICSLLTDCNPADPLVGSIATQYLTNRAEHDRIARQWTKRYAT
          SQG.I.LDIL.DN.SPALTISKVLLSICSL.TDCN.ADPLVGSIATQY.TNRAEHD..ARQWTK.YAT
Retrocopy SQGMIYLDILNDN*SPALTISKVLLSICSL-TDCNHADPLVGSIATQYMTNRAEHDQMARQWTKQYAT

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_1343 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 19 parental genes, and 46 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000014163	3 retrocopies	retro_cfam_2076, retro_cfam_2161, retro_cfam_27,
Choloepus hoffmanni	ENSCHOG00000007325	3 retrocopies	retro_chof_1756, retro_chof_2077, retro_chof_2358,
Ciona intestinalis	ENSCING00000006860	1 retrocopy	retro_cint_33,
Callithrix jacchus	ENSCJAG00000011559	3 retrocopies	retro_cjac_3194, retro_cjac_3911, retro_cjac_3967,
Equus caballus	ENSECAG00000007233	1 retrocopy	retro_ecab_196,
Echinops telfairi	ENSETEG00000019324	2 retrocopies	retro_etel_314, retro_etel_848,
Homo sapiens	ENSG00000170035	1 retrocopy	retro_hsap_4653,
Macaca mulatta	ENSMMUG00000008069	2 retrocopies	retro_mmul_1382, retro_mmul_1834,
Monodelphis domestica	ENSMODG00000010301	2 retrocopies	retro_mdom_1679, retro_mdom_1688,
Mus musculus	ENSMUSG00000027011	4 retrocopies	retro_mmus_2814, retro_mmus_3123, retro_mmus_3416, retro_mmus_3571,
Nomascus leucogenys	ENSNLEG00000006290	1 retrocopy	retro_nleu_2068,
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	ENSPPYG00000012987	1 retrocopy	retro_pabe_3614,
Rattus norvegicus	ENSRNOG00000004544	1 retrocopy	retro_rnor_1236,
Tupaia belangeri	ENSTBEG00000009932	2 retrocopies	retro_tbel_1986, retro_tbel_3294,
Tarsius syrichta	ENSTSYG00000002281	5 retrocopies	retro_tsyr_1393, retro_tsyr_1809, retro_tsyr_1842, retro_tsyr_1942, retro_tsyr_457,
Tursiops truncatus	ENSTTRG00000001361	1 retrocopy	retro_ttru_1056,