RetrogeneDB ID: retro_ogar_2441

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873623.1:2508001..2508461(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RAB13
• Ensembl ID: ENSOGAG00000016969
• Aliases: None
• Description: RAB13, member RAS oncogene family [Source:HGNC Symbol;Acc:9762]

Sequence

>retro_ogar_2441
CACATCTCCACCATCGGAACTGATTTCAAGATCCCCACTGTGGATGTAGAGAGGAAGAAGATCAAGCTGCAAATGTGGGA
CACGGCTGGGCAAGAGTCATTCAAGACCATAACTACTGCCTGTGACCGTGGAGTCATGGACATTATCCTAGTATATAACG
TCACCGATGAGAAGTCCTTTGAGAATATTCAAAACTGAATGAAAAGCAGCATCAAAGAGAATGCCTCAGCTCCGGTGGAG
CACCTCTTGCTGGACAACAAAGCGACATGGAGACCAAGAGGAAGGAGCAGGCTTGAGAGCACAGAATTGGATTTTTTAGA
TGAGTGCTAAACCCGGTATGAGTGTGGATGAGGCTTTTAGTTCCCTGGGCCGGGACATCTTGCTGAAGTCAGGAAGCTGG
AGATTAGGAAATGGCAACAAACCTCCCAGCATTGATCTGAAAACCTGTGACAAGAAGAGC

Alignment

ORF - retro_ogar_2441 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.33 %
• Parental protein coverage: 79.6 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  YISTIGIDFKIRTVNIEGKKIKLQVWDTAGQERFKTITTAYYRGAMGIILVYDITDEKSFENIQNWMKS-
          .ISTIG.DFKI.TV..E.KKIKLQ.WDTAGQE.FKTITTA..RG.M.IILVY..TDEKSFENIQN.MKS.
Retrocopy HISTIGTDFKIPTVDVERKKIKLQMWDTAGQESFKTITTACDRGVMDIILVYNVTDEKSFENIQN*MKSS

Parental  IKEHASAGVERLLLGNKC-DMEAKRRVQKEQADKLAQEHGIRFFE-TSAKSSVNVAEAFSSLARDILLKS
          IKE.ASA.VE.LLL.NK..DME.K....KEQ....A.EH.I.FF...SAK....V.EAFSSL.RDILLKS
Retrocopy IKENASAPVEHLLLDNKA<DMETK---RKEQ----A*EHRIGFFR<MSAKPGMSVDEAFSSLGRDILLKS

Parental  GSRRRGNDNKPPSTDLKPCDKNT
          GS.R.GN.NKPPS.DLK.CDK..
Retrocopy GSWRLGNGNKPPSIDLKTCDKKS

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_2441 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 8 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000017389	1 retrocopy	retro_cfam_1756,
Homo sapiens	ENSG00000143545	1 retrocopy	retro_hsap_1122,
Loxodonta africana	ENSLAFG00000032079	1 retrocopy	retro_lafr_45,
Macaca mulatta	ENSMMUG00000017586	1 retrocopy	retro_mmul_324,
Otolemur garnettii	ENSOGAG00000010405	1 retrocopy	retro_ogar_2033,
Otolemur garnettii	ENSOGAG00000013894	1 retrocopy	retro_ogar_2356,
Otolemur garnettii	ENSOGAG00000016969	1 retrocopy	retro_ogar_2441 ,
Pan troglodytes	ENSPTRG00000001370	1 retrocopy	retro_ptro_681,