RetrogeneDB ID: retro_ogar_1935

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873575.1:7228845..7229215(-)
• Located in intron of: ENSOGAG00000005281

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPL11
• Ensembl ID: ENSOGAG00000032741
• Aliases: None
• Description: ribosomal protein L11 [Source:HGNC Symbol;Acc:10301]

Sequence

>retro_ogar_1935
GATCAAGGTGAAAGGAGAACCCCACGTGGGAACTTGGCGTCCACAAGGCCAGCCTCAGTCTCTGTGTGGCCGAGAGTGAG
AACTGACTGGCCCAGGTGGTCAGGCACTGGGGCAGCTCACAGGCCAGACCCTGTGTTCTCCAAGGCTAGATTTACCATCA
GATCCTTTGGCATCAGCAGAAATGAAAGGATTGCTGTCCCCTGCCCAGAGAGGCCCAGGCAGGAGAAATCCTGGAGCAAG
GCCTAAAGGTGTAGGAGCATGAGTTAAGGAAAAATAACTTCTCAGACGCTGGAAACTCTGGTTTGGAATCCAGGGATGTA
TCGATCTGCATATCGACTATGCTGTAAGCATCAGTCTGTTCAGCTTGGAC

Alignment

ORF - retro_ogar_1935 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.49 %
• Parental protein coverage: 70.79 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  DQGE-KENPMRELRIRKLCLNICVGESGDRLTRAAK-VLEQLTGQT-PVFSKARYTVRSFGIRRNEKIAV
          DQGE.KENP..EL...K..L..CV.ES...L.......L.QLTGQT.PVFSKAR.T.RSFGI.RNE.IAV
Retrocopy DQGE<KENPTWELGVHKASLSLCVAESEN*LAQVVR<ALGQLTGQT<PVFSKARFTIRSFGISRNERIAV

Parental  HCTVRGAKAEEILEKGLKVR-EYELRKNNFSDTGNFG-FGIQEHIDLGIKYDPSIGIYGLD
          .C..R....E....K....R.E.ELRKNNFSD.GN.G.FGIQ..IDL.I.Y..SI....LD
Retrocopy PCPER-PRQEKSWSKA*RCR<EHELRKNNFSDAGNSG<FGIQGCIDLHIDYAVSISLFSLD

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_1935 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 17 parental genes, and 53 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000005058	1 retrocopy	retro_acar_165,
Ailuropoda melanoleuca	ENSAMEG00000009704	3 retrocopies	retro_amel_1123, retro_amel_1754, retro_amel_234,
Canis familiaris	ENSCAFG00000013232	2 retrocopies	retro_cfam_1059, retro_cfam_543,
Cavia porcellus	ENSCPOG00000008432	2 retrocopies	retro_cpor_261, retro_cpor_788,
Equus caballus	ENSECAG00000021136	3 retrocopies	retro_ecab_471, retro_ecab_669, retro_ecab_926,
Felis catus	ENSFCAG00000028651	2 retrocopies	retro_fcat_1069, retro_fcat_1877,
Gorilla gorilla	ENSGGOG00000014628	6 retrocopies	retro_ggor_1192, retro_ggor_1325, retro_ggor_1690, retro_ggor_2204, retro_ggor_533, retro_ggor_603,
Macropus eugenii	ENSMEUG00000013738	3 retrocopies	retro_meug_488, retro_meug_517, retro_meug_633,
Myotis lucifugus	ENSMLUG00000008868	3 retrocopies	retro_mluc_1271, retro_mluc_1345, retro_mluc_2321,
Macaca mulatta	ENSMMUG00000002445	3 retrocopies	retro_mmul_2039, retro_mmul_2415, retro_mmul_2462,
Monodelphis domestica	ENSMODG00000012828	1 retrocopy	retro_mdom_641,
Mus musculus	ENSMUSG00000059291	3 retrocopies	retro_mmus_144, retro_mmus_146, retro_mmus_78,
Ornithorhynchus anatinus	ENSOANG00000000321	1 retrocopy	retro_oana_49,
Otolemur garnettii	ENSOGAG00000032741	6 retrocopies	retro_ogar_1325, retro_ogar_1935 , retro_ogar_1963, retro_ogar_2322, retro_ogar_2630, retro_ogar_569,
Rattus norvegicus	ENSRNOG00000026260	9 retrocopies	retro_rnor_1735, retro_rnor_2287, retro_rnor_2314, retro_rnor_2690, retro_rnor_271, retro_rnor_2725, retro_rnor_668, retro_rnor_795, retro_rnor_919,
Sarcophilus harrisii	ENSSHAG00000006767	1 retrocopy	retro_shar_638,
Tursiops truncatus	ENSTTRG00000016115	4 retrocopies	retro_ttru_1525, retro_ttru_1779, retro_ttru_476, retro_ttru_911,