RetrogeneDB ID: retro_ogar_400

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873520.1:71937246..71937641(-)
• Located in intron of: ENSOGAG00000004560

Retrocopy information

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

Parental gene information

• Parental gene symbol: SEC11C
• Ensembl ID: ENSOGAG00000002570
• Aliases: None
• Description: SEC11 homolog C (S. cerevisiae) [Source:HGNC Symbol;Acc:23400]

Sequence

>retro_ogar_400
GGATTGGACATCTTTGGAGATCTGAGGAAGATAGACAAGTATCAACTCTATTAGCAGGTGTTAAACTTTGCCATGATCAT
GTCTTCTGCACTCATGATATAGAAAGGCCTGATTGTGCTCACTGGCAGTGAGATCCCACCCAAGGTGGTGCTGAGTGGCA
GTATGGAGCTGGCCCTTCACATGGGAGACCTTCTGTTCCTCACACATTTCTGGGAAAACCCCATTAGAGCTGGTGAAGTT
GTTTTTTAGTTGAAGGACAAGACATTTCAATGGTTCACAGACTAATCAAAGTTTATGAAAATGATAATGGAGAAATCAAA
TTTCTGACCAAATGAGATAATAATAAAGTTATTGATAGAGTTTTATATAAAGAAGGTCAGAACTGGCTCAAAAAG

Alignment

ORF - retro_ogar_400 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.61 %
• Parental protein coverage: 69.27 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GLDIFGDLRKMNKRQLYYQVLNFAMIVSSALMIWKGLIVLTGSESPIVVVLSGSMEPAFHRGDLLFLTNF
          GLDIFGDLRK..K.QLY.QVLNFAMI.SSALMI.KGLIVLTGSE.P..VVLSGSME.A.H.GDLLFLT.F
Retrocopy GLDIFGDLRKIDKYQLY*QVLNFAMIMSSALMI*KGLIVLTGSEIPPKVVLSGSMELALHMGDLLFLTHF

Parental  REDPIRAGEIVVF-KVEGRDIPIVHRVIKVHEKDNGDIKFLTKGDNNEVDDRGLYKEGQNWLEK
          .E.PIRAGE.VVF..VEG.DI..VHR.IKV.E.DNG.IKFLTK.DNN.V.DR.LYKEGQNWL.K
Retrocopy WENPIRAGE-VVF<LVEGQDISMVHRLIKVYENDNGEIKFLTK*DNNKVIDRVLYKEGQNWLKK

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_400 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 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000017024	3 retrocopies	retro_ecab_1009, retro_ecab_455, retro_ecab_989,
Echinops telfairi	ENSETEG00000005115	2 retrocopies	retro_etel_1081, retro_etel_1139,
Felis catus	ENSFCAG00000006501	1 retrocopy	retro_fcat_1815,
Microcebus murinus	ENSMICG00000016052	1 retrocopy	retro_mmur_271,
Monodelphis domestica	ENSMODG00000020427	2 retrocopies	retro_mdom_1517, retro_mdom_377,
Oryctolagus cuniculus	ENSOCUG00000009204	2 retrocopies	retro_ocun_738, retro_ocun_895,
Otolemur garnettii	ENSOGAG00000002570	1 retrocopy	retro_ogar_400 ,
Otolemur garnettii	ENSOGAG00000007281	1 retrocopy	retro_ogar_3315,
Pteropus vampyrus	ENSPVAG00000002950	2 retrocopies	retro_pvam_620, retro_pvam_869,
Sus scrofa	ENSSSCG00000004912	1 retrocopy	retro_sscr_775,
Tupaia belangeri	ENSTBEG00000014804	1 retrocopy	retro_tbel_2357,
Tursiops truncatus	ENSTTRG00000007676	5 retrocopies	retro_ttru_1278, retro_ttru_1508, retro_ttru_1780, retro_ttru_1916, retro_ttru_490,