RetrogeneDB ID: retro_ogar_1142

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873536.1:26515442..26516238(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOGAG00000033012
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSOGAG00000027672
• Aliases: None
• Description: None

Sequence

>retro_ogar_1142
GACCCAGATGTATTAGCAGATATCTGCTGGGCTGTTTCCTATCTTACTGACGGTCCAAATGAACAGGTTGAAATGGCTAT
GAAAGCAGGAGTTGTGCCCCAACTTGTGAAGCATATGAAAGCTACCAAATTGCCAACTGTTACTCCTGCACTAAGAGTCA
TAGGGAATATTGTCACTGGGACAGATAAAGAGACTCGGGTTGTAATTGATGAAAGTACTTACTGTCTTTCCCAGCCTGCT
GACCAAACCCCAAACCAACATTCAAAAGGAAGCCAGACGGACGACGTCAAACATCACAGCTGGCCGTCAGGACCAGATAC
AGCAAGTTGTGAATCATGGACTAGGCCCACAACTTGGTGGTGTTCTCTCTAAGGCAGACTTTAGGACACAAAAGGAAGCT
GTATAGGCTGCGACCAACTATACAAGTGGTGGAACAGTTGAACTGATTGTACACCTCGTTCACTGTGGCATTATAGAACT
GCTGATGGACCTCTTCACTGCAAAAGATATCAAAATTATTCTGGTTATTCTGCATGCCATTTCAAATATCTTTCAGACTG
CCGAGAAACTAGGTGAAAATGTCAAACTTGGCATAATGATTGAAGAATGCAGAGGTTTAGATAAAACTGAAGCTCTACAA
AACCATGAAAATGAGTCTGTGTACAAGGCTTTGTTAAGCTTGACTGAGAAGTATTTCTTGGTAGAGGAAGAGGAGGATCC
AAATGTAGTACCAGAAACTACCCCTGAAGGCTGCACCTTCCAAGTTCAGGATGGGACTCCTGGGCCTTTTAACTTT

Alignment

ORF - retro_ogar_1142 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.48 %
• Parental protein coverage: 55.72 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  DPEVLADTCWAISYLTDGPNERIEMVVKTGVVPQLVKLLGATELPIVTPALRAIGNIVTGTDEQTQVVID
          DP.VLAD.CWA.SYLTDGPNE..EM..K.GVVPQLVK...AT.LP.VTPALR.IGNIVTGTD..T.VVID
Retrocopy DPDVLADICWAVSYLTDGPNEQVEMAMKAGVVPQLVKHMKATKLPTVTPALRVIGNIVTGTDKETRVVID

Parental  AGA-LTVFP-SLLTNPKTNIQKEATWTMSNITAGRQDQIQQVVNHGLVPLLVGVLSKADFKTQKEAVWAV
          ....L..FP.SLLT.P.TNIQKEA..T.SNITAGRQDQIQQVVNHGL.P.L.GVLSKADF.TQKEAV.A.
Retrocopy EST<LLSFP<SLLTKPQTNIQKEARRTTSNITAGRQDQIQQVVNHGLGPQLGGVLSKADFRTQKEAV*AA

Parental  TNYTSGGTVEQIVYLVHCGIIEPLYLVMLRFKKCKLNINHQRAVEISIFKAAEKLGETEKLSIMIEECGS
          TNYTSGGTVE.IV.LVHCGIIE.L.......K..K.......A....IF..AEKLGE..KL.IMIEEC..
Retrocopy TNYTSGGTVELIVHLVHCGIIE-LLMDLFTAKDIKIILVILHAIS-NIFQTAEKLGENVKLGIMIEECRG

Parental  ADKIEALQNHENESAYKASLNLIEKYFSVEEEEDQNVVPETTSEGYTFQVQDETPGTFNF
          .DK.EALQNHENES.YKA.L.L.EKYF.VEEEED.NVVPETT.EG.TFQVQD.TPG.FNF
Retrocopy LDKTEALQNHENESVYKALLSLTEKYFLVEEEEDPNVVPETTPEGCTFQVQDGTPGPFNF

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_1142 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 24 parental genes, and 60 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000018411	3 retrocopies	retro_amel_1161, retro_amel_1318, retro_amel_440,
Bos taurus	ENSBTAG00000012225	1 retrocopy	retro_btau_1830,
Canis familiaris	ENSCAFG00000011598	2 retrocopies	retro_cfam_648, retro_cfam_90,
Cavia porcellus	ENSCPOG00000026318	1 retrocopy	retro_cpor_46,
Dasypus novemcinctus	ENSDNOG00000019151	6 retrocopies	retro_dnov_1184, retro_dnov_1811, retro_dnov_2161, retro_dnov_2279, retro_dnov_379, retro_dnov_693,
Equus caballus	ENSECAG00000020573	2 retrocopies	retro_ecab_1017, retro_ecab_1123,
Echinops telfairi	ENSETEG00000004445	2 retrocopies	retro_etel_346, retro_etel_347,
Felis catus	ENSFCAG00000001936	2 retrocopies	retro_fcat_1176, retro_fcat_921,
Homo sapiens	ENSG00000182481	1 retrocopy	retro_hsap_2950,
Gorilla gorilla	ENSGGOG00000027535	2 retrocopies	retro_ggor_2044, retro_ggor_2609,
Myotis lucifugus	ENSMLUG00000027946	7 retrocopies	retro_mluc_1034, retro_mluc_1258, retro_mluc_1414, retro_mluc_288, retro_mluc_50, retro_mluc_52, retro_mluc_993,
Macaca mulatta	ENSMMUG00000018256	3 retrocopies	retro_mmul_1140, retro_mmul_1635, retro_mmul_1947,
Monodelphis domestica	ENSMODG00000003897	1 retrocopy	retro_mdom_271,
Mus musculus	ENSMUSG00000018362	1 retrocopy	retro_mmus_229,
Nomascus leucogenys	ENSNLEG00000001749	3 retrocopies	retro_nleu_1052, retro_nleu_1634, retro_nleu_208,
Oryctolagus cuniculus	ENSOCUG00000015913	4 retrocopies	retro_ocun_1765, retro_ocun_1916, retro_ocun_426, retro_ocun_690,
Otolemur garnettii	ENSOGAG00000011924	1 retrocopy	retro_ogar_2991,
Otolemur garnettii	ENSOGAG00000027672	7 retrocopies	retro_ogar_1044, retro_ogar_1142 , retro_ogar_1757, retro_ogar_2008, retro_ogar_464, retro_ogar_477, retro_ogar_936,
Otolemur garnettii	ENSOGAG00000031106	3 retrocopies	retro_ogar_1289, retro_ogar_3237, retro_ogar_353,
Pongo abelii	ENSPPYG00000008569	1 retrocopy	retro_pabe_3501,
Pteropus vampyrus	ENSPVAG00000004976	2 retrocopies	retro_pvam_1321, retro_pvam_1333,
Rattus norvegicus	ENSRNOG00000015329	1 retrocopy	retro_rnor_42,
Sarcophilus harrisii	ENSSHAG00000011391	1 retrocopy	retro_shar_165,
Vicugna pacos	ENSVPAG00000001855	3 retrocopies	retro_vpac_124, retro_vpac_162, retro_vpac_163,