RetrogeneDB ID: retro_ogar_2381

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873618.1:25825..26179(+)
• Located in intron of: ENSOGAG00000011996

Retrocopy information

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

Parental gene information

• Parental gene symbol: TMCO1
• Ensembl ID: ENSOGAG00000011784
• Aliases: None
• Description: transmembrane and coiled-coil domains 1 [Source:HGNC Symbol;Acc:18188]

Sequence

>retro_ogar_2381
GAGAGGCAAGAAGAAAAACTAAAGAATAACAACAGAGATCTGTCAATGGTTCAAATGAAATCCATGTTTGCAATTGGCTT
TTGTTTTACTGCCCTAATGGGAATGTTCAATTCTATATTTGATGGTAGAATTGTGGCAAAGCTCCCATTCACCCCTCTTT
CTTACATTCAAGGACTGTCTCATGGAAACCTGCTGGGAGATGACACCACAGACTGTTCCTTCATCTTCCTGTAAATTCTC
TGAACTATGTCAATTTGGCAGAACATTCAGATTCTTGGCCTTGCTCCTTCATGAGCTGCCCTAAGCAGGTAAGGTGGATT
TCTTGGCCCTCCACCTCCTTCTGAGAAATTCTCC

Alignment

ORF - retro_ogar_2381 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.63 %
• Parental protein coverage: 63.1 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ERQEEKLKNNNRDLSMVRVLNITSCLFCFLILVEV-HIIFDGRVVAKLPFTPLSYIQGLSHRNLLGDDTT
          ERQEEKLKNNNRDLSMV.........FCF..L......IFDGR.VAKLPFTPLSYIQGLSH.NLLGDDTT
Retrocopy ERQEEKLKNNNRDLSMVQMKSMFAIGFCFTALMGMFNSIFDGRIVAKLPFTPLSYIQGLSHGNLLGDDTT

Parental  DCSFIFLYILCTMSIRQNIQKILGLAPSRAATKQAGGFLGPPPPSGKFS
          DCSFIFL.IL.TMSI.QNIQ.ILGLAPS.AA....GGFLGPPPPS.KFS
Retrocopy DCSFIFL*IL*TMSIWQNIQ-ILGLAPS*AALSR*GGFLGPPPPSEKFS

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_2381 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 4 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Macropus eugenii	ENSMEUG00000011045	2 retrocopies	retro_meug_894, retro_meug_997,
Monodelphis domestica	ENSMODG00000001335	2 retrocopies	retro_mdom_1319, retro_mdom_334,
Otolemur garnettii	ENSOGAG00000011784	1 retrocopy	retro_ogar_2381 ,
Sarcophilus harrisii	ENSSHAG00000016602	1 retrocopy	retro_shar_790,