RetrogeneDB ID: retro_ogar_2597

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873637.1:41956..42337(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MED6
• Ensembl ID: ENSOGAG00000001311
• Aliases: None
• Description: mediator complex subunit 6 [Source:HGNC Symbol;Acc:19970]

Sequence

>retro_ogar_2597
CTCACTGCAGTGCGTGGTATTCAATCAGCTTTTGATGAAGCTATGTCATCCTGTTGATACCATCTTTCCAAAGGGTATTG
GTGGCACTTCAAAGACCATGAAGAGCAAGATAAAGTTAAACCTAAAGCCAAAAGGAAAGAATAACCAAGCTCTATTTTTC
AGAGACAACGTGTGGATGCTTAACTTGTAGACCTCAGACAAAAATTTCCACCCAGATTTGGGGAGCAAAAGTCTGGAGAA
AAGCCTGTCACAGTGGATCAGACAATGAAGGAGACAGAACCTATACCAGAAACAATAAAATCTGAAGAGAAGGAGACCAC
AAAGAATGTCCAACAGACAGTGAACGTTAAAGGCCCCCCTGGGAAACGGATGAGACTTCAG

Alignment

ORF - retro_ogar_2597 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.34 %
• Parental protein coverage: 50.2 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LTAVHGIQSAFDEAVSYCRYHPSKGYWWHFKDHEEQDKVKPKAKRKEEPSSIFQRQRVDALLVDLRQKFP
          LTAV.GIQSAFDEA.S.C.YH.SKGYWWHFKDHEEQDKVKPKAKRKE.PSSIFQRQRVDA.LVDLRQKFP
Retrocopy LTAVRGIQSAFDEAMSSC*YHLSKGYWWHFKDHEEQDKVKPKAKRKE*PSSIFQRQRVDA*LVDLRQKFP

Parental  PRFVQQKSGEKPVPVDQTKKETEPIPETIKSEEKETTKNVQQTVNVKGPPGKRMRLQ
          PRF..QKSGEKPV.VDQT.KETEPIPETIKSEEKETTKNVQQTVNVKGPPGKRMRLQ
Retrocopy PRFGEQKSGEKPVTVDQTMKETEPIPETIKSEEKETTKNVQQTVNVKGPPGKRMRLQ

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_2597 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 7 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Felis catus	ENSFCAG00000013091	1 retrocopy	retro_fcat_1612,
Myotis lucifugus	ENSMLUG00000017357	1 retrocopy	retro_mluc_265,
Monodelphis domestica	ENSMODG00000007174	3 retrocopies	retro_mdom_1190, retro_mdom_524, retro_mdom_625,
Otolemur garnettii	ENSOGAG00000001311	1 retrocopy	retro_ogar_2597 ,
Ochotona princeps	ENSOPRG00000008957	1 retrocopy	retro_opri_820,
Sorex araneus	ENSSARG00000002553	1 retrocopy	retro_sara_495,
Tupaia belangeri	ENSTBEG00000002302	1 retrocopy	retro_tbel_2272,