RetrogeneDB ID: retro_ogar_2175

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873599.1:3970069..3970714(+)
• Located in intron of: ENSOGAG00000002883

Retrocopy information

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

Parental gene information

• Parental gene symbol: RAB5C
• Ensembl ID: ENSOGAG00000009456
• Aliases: None
• Description: RAB5C, member RAS oncogene family [Source:HGNC Symbol;Acc:9785]

Sequence

>retro_ogar_2175
ATGGCTAATCGAGGTGCAACAAGACCCAACGGACCGAATACTGGAAATAAAATATGCCAATTCAAACTAGTACTTCTGGG
AGAGTCTGCTGTTGGTAAATCAAGCCTAGTGCTTCGTTTTGTGAAAGGCCAATTTCATGAATTTCAAGAAAGTACCATTG
GGGCTGCTTTTCTAACCCGAACTGTGTGTCTTGATGATACTACAGTAAAATTTGAAATATGAGATACAGCTGGTCAGGAA
TGATACCATAGCTAAGCACCAATGTACTACAGAGGAGCACAAGCAGCCATAGTTGTAGGTGATATCACCAACGAGGAGTC
CTTTGCAAGAGCAAAAAATTGGGTTAAAGAGCTTCAGAGACAAGCAAGTCCTAACACTGTAACAGCTTTATCAGGAAACA
AGGCTGACCTAGCAAATAAAAGAGCTGTAGATTGCCAGGAAGCACAATCTTATGCAGATGATAACAGTTTATTATTCATG
GAGACATCTGCCAAAACATCAATGAATGTGAACGAAATATTCATGGCAATAGCTAAAAAGTTGCCAAAGAATGAACCACA
GAATCCAGGAGCAAATTCTGCCAGAGGAAGAGGAGTAGATCTTACTGAACCCACACAGCCAACCAGGAGTCAGTGTTGTA
GTAAC

Alignment

ORF - retro_ogar_2175 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.8 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAGRGGTARPNGPAAGNKICQFKLVLLGESAVGKSSLVLRFVKGQFHEYQESTIGAAFLTQTVCLDDTTV
          MA.RG.T.RPNGP..GNKICQFKLVLLGESAVGKSSLVLRFVKGQFHE.QESTIGAAFLT.TVCLDDTTV
Retrocopy MANRGAT-RPNGPNTGNKICQFKLVLLGESAVGKSSLVLRFVKGQFHEFQESTIGAAFLTRTVCLDDTTV

Parental  KFEIWDTAGQERYHSLAPMYYRGAQAAIVVYDITNTDTFARAKNWVKELQRQASPNIVIALAGNKADLAS
          KFEI.DTAGQE.YHS.APMYYRGAQAAIVV.DITN...FARAKNWVKELQRQASPN.V.AL.GNKADLA.
Retrocopy KFEI*DTAGQE*YHS*APMYYRGAQAAIVVGDITNEESFARAKNWVKELQRQASPNTVTALSGNKADLAN

Parental  KRAVEFQEAQAYADDNSLLFMETSAKTAMNVNEIFMAIAKKLPKNEPQNAAGAPGRNRGVDLQENNPASR
          KRAV..QEAQ.YADDNSLLFMETSAKT.MNVNEIFMAIAKKLPKNEPQN......R.RGVDL.E.....R
Retrocopy KRAVDCQEAQSYADDNSLLFMETSAKTSMNVNEIFMAIAKKLPKNEPQNPGANSARGRGVDLTEPTQPTR

Parental  SQCCSN
          SQCCSN
Retrocopy SQCCSN

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_2175 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
Ailuropoda melanoleuca	ENSAMEG00000006003	1 retrocopy	retro_amel_543,
Callithrix jacchus	ENSCJAG00000000472	2 retrocopies	retro_cjac_189, retro_cjac_1948,
Macropus eugenii	ENSMEUG00000005614	1 retrocopy	retro_meug_2118,
Monodelphis domestica	ENSMODG00000014792	1 retrocopy	retro_mdom_1399,
Otolemur garnettii	ENSOGAG00000009456	2 retrocopies	retro_ogar_2175 , retro_ogar_985,
Otolemur garnettii	ENSOGAG00000015779	1 retrocopy	retro_ogar_2851,
Pongo abelii	ENSPPYG00000008398	1 retrocopy	retro_pabe_2664,