RetrogeneDB ID: retro_ogar_2416

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873620.1:5681862..5682266(-)
• Located in intron of: ENSOGAG00000031381

Retrocopy information

• Ensembl ID: ENSOGAG00000026421
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RPL32
• Ensembl ID: ENSOGAG00000028498
• Aliases: None
• Description: ribosomal protein L32 [Source:HGNC Symbol;Acc:10336]

Sequence

>retro_ogar_2416
ATGGCTACCCTCAGACCCCTTGTGAAGACGAAGATAGTCAAAAAGAGGATCAAGAAGTTTATCCGGCACCAATCAGACCG
ATATGTCAAAATTAAGTGTAACTGGCGGAAACCCAGAGGTATTGATAACAAGGTTCAGAGAAGATTCAAGGGCCAGATCT
TGATGTCCAACATTGATTACGGGACCTTAAGAAAACAAAGCATATGCTGCCCAGTGGTTTCCAGAAGTTCCTCATCCACA
GCCTCAAGGAGCTGGAAGTGCTGCTGACCTGCAACAAATCTTACTGTGCAGAGATTGCTCACAATGTTTCCTCCAAGAAC
CGCAAAGCCATTGTGGAAAGAGCAGCCCAGCTGGCCATCAGAGTCACCAATCCCAATGCCCGGCTGCGCAGCGAAGAAAA
TCAA

Alignment

ORF - retro_ogar_2416 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.5 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAALRPLVKPKIVKKRTKKFIRHQSDRYVKIKRNWRKPRGIDNRVRRRFKGQILMPNIGYGSN-KKTKHM
          MA.LRPLVK.KIVKKR.KKFIRHQSDRYVKIK.NWRKPRGIDN.V.RRFKGQILM.NI.YG...KKTKHM
Retrocopy MATLRPLVKTKIVKKRIKKFIRHQSDRYVKIKCNWRKPRGIDNKVQRRFKGQILMSNIDYGTL<KKTKHM

Parental  LPSGFRKFLVHNVKELEVLLMCNKSYCAEIAHNVSSKNRKAIVERAAQLAIRVTNPNARLRSEENE
          LPSGF.KFL.H..KELEVLL.CNKSYCAEIAHNVSSKNRKAIVERAAQLAIRVTNPNARLRSEEN.
Retrocopy LPSGFQKFLIHSLKELEVLLTCNKSYCAEIAHNVSSKNRKAIVERAAQLAIRVTNPNARLRSEENQ

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_2416 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 13 parental genes, and 121 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000014763	3 retrocopies	retro_acar_104, retro_acar_125, retro_acar_67,
Ailuropoda melanoleuca	ENSAMEG00000004583	26 retrocopies	retro_amel_1004, retro_amel_1041, retro_amel_1059, retro_amel_112, retro_amel_1274, retro_amel_1284, retro_amel_13, retro_amel_1394, retro_amel_1450, retro_amel_150, retro_amel_1651, retro_amel_168, retro_amel_1766, retro_amel_1827, retro_amel_1897, retro_amel_274, retro_amel_275, retro_amel_44, retro_amel_573, retro_amel_658, retro_amel_71, retro_amel_776, retro_amel_781, retro_amel_871, retro_amel_892, retro_amel_923,
Bos taurus	ENSBTAG00000015283	10 retrocopies	retro_btau_1102, retro_btau_1391, retro_btau_1568, retro_btau_1645, retro_btau_1728, retro_btau_1764, retro_btau_377, retro_btau_623, retro_btau_631, retro_btau_654,
Choloepus hoffmanni	ENSCHOG00000013534	27 retrocopies	retro_chof_1131, retro_chof_1164, retro_chof_1181, retro_chof_1234, retro_chof_1461, retro_chof_152, retro_chof_1821, retro_chof_1957, retro_chof_2022, retro_chof_205, retro_chof_2090, retro_chof_2146, retro_chof_2242, retro_chof_2265, retro_chof_2301, retro_chof_2410, retro_chof_2509, retro_chof_2527, retro_chof_2606, retro_chof_276, retro_chof_286, retro_chof_313, retro_chof_554, retro_chof_585, retro_chof_607, retro_chof_758, retro_chof_913,
Equus caballus	ENSECAG00000007201	4 retrocopies	retro_ecab_1115, retro_ecab_26, retro_ecab_369, retro_ecab_698,
Loxodonta africana	ENSLAFG00000032737	1 retrocopy	retro_lafr_14,
Macaca mulatta	ENSMMUG00000001340	6 retrocopies	retro_mmul_106, retro_mmul_117, retro_mmul_126, retro_mmul_79, retro_mmul_93, retro_mmul_95,
Mustela putorius furo	ENSMPUG00000017189	4 retrocopies	retro_mputfur_121, retro_mputfur_76, retro_mputfur_8, retro_mputfur_85,
Otolemur garnettii	ENSOGAG00000028498	24 retrocopies	retro_ogar_129, retro_ogar_1321, retro_ogar_1340, retro_ogar_1360, retro_ogar_1425, retro_ogar_1524, retro_ogar_160, retro_ogar_1683, retro_ogar_1766, retro_ogar_1833, retro_ogar_2032, retro_ogar_2412, retro_ogar_2416 , retro_ogar_2515, retro_ogar_3247, retro_ogar_3384, retro_ogar_545, retro_ogar_56, retro_ogar_571, retro_ogar_776, retro_ogar_870, retro_ogar_891, retro_ogar_924, retro_ogar_973,
Pongo abelii	ENSPPYG00000013391	2 retrocopies	retro_pabe_135, retro_pabe_98,
Rattus norvegicus	ENSRNOG00000010746	4 retrocopies	retro_rnor_179, retro_rnor_27, retro_rnor_278, retro_rnor_327,
Sarcophilus harrisii	ENSSHAG00000012782	1 retrocopy	retro_shar_580,
Sus scrofa	ENSSSCG00000027637	9 retrocopies	retro_sscr_1001, retro_sscr_1054, retro_sscr_107, retro_sscr_1081, retro_sscr_165, retro_sscr_76, retro_sscr_793, retro_sscr_957, retro_sscr_989,