RetrogeneDB ID: retro_ogar_3287

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873767.1:676872..677535(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOGAG00000029338
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: TRAPPC13
• Ensembl ID: ENSOGAG00000010787
• Aliases: None
• Description: trafficking protein particle complex 13 [Source:HGNC Symbol;Acc:25828]

Sequence

>retro_ogar_3287
GACTTATTTCTTGAAGTCCTAATTCAGAATATTTCATCTTCAACTGTGTTTATACAAAAGGTTTCCTTAGAGTTGTCTGA
AATGTTCACTGGAGTAGAATTAAATACCATCAAGCAGGATGGAGAAGATGAGTGTACATTTGGAACAAGGACATTTTTGC
AGTCAACAGAAGGACGCCAATACTTATACCATCTTCAGCTCAAGCAAGAGTTTTCCAAGAAAGCTGGTACTATTAGGGGA
CTAACAGAAATTGGAAAATTGGATATAGTGTGGAAAAGAAACCTAGGTGAAATGGCAATGCTACAGACAATCCAACTGGA
AAGAGAGACTACAGGTTATGGAAACATGAGGCTGTCTTTGGAGATGATCCCAGATACTGTAATTCTAGAAGAGCCATTTC
AAATTACCTGCAAGATAACAAACTGCAGTGATAGAAAAATGAAATTGGTTTTGAAAATGTATGATACAGATTCTATTCGT
TGGTGTGGAACTTCAGGAAGGTATCTTGGAAAGCTTTCTCCAAATTCATCTCTATGTTTTACCTTAACACTACTATGCTT
AAAACTTGGCCTGCGAAGTGTCTCTGGTATACAGATAACAGACAGATTATTAAAGAAAAAGTATGAATTTAGTGATATTG
CAAATGTCTGTGTAATACCTTCC

Alignment

ORF - retro_ogar_3287 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.81 %
• Parental protein coverage: 55.09 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EVFLEAQIQNITTSPMFMEKVSLEPSIMYNVTELNSVSQAGECVSTFGSRAYLQPMDTRQYLYCLKPKKE
          ..FLE..IQNI..S..F..KVSLE.S.M....ELN...Q.GE...TFG.R..LQ....RQYLY.L..K.E
Retrocopy DLFLEVLIQNISSSTVFIQKVSLELSEMFTGVELNTIKQDGEDECTFGTRTFLQSTEGRQYLYHLQLKQE

Parental  FAEKAGIIKGVTVIGKLDIVWKTNLGERGRLQTSQLQRMAPGYGDVRLSLEAIPDTVNLEEPFHITCKIT
          F..KAG.I.G.T.IGKLDIVWK.NLGE...LQT.QL.R...GYG..RLSLE.IPDTV.LEEPF.ITCKIT
Retrocopy FSKKAGTIRGLTEIGKLDIVWKRNLGEMAMLQTIQLERETTGYGNMRLSLEMIPDTVILEEPFQITCKIT

Parental  NCSSERTMDLVLEMCNTNSIHWCGISGRQLGKLNPSSSLCLALTLLSSVQGLQSISGLRLTDTFLKRTYE
          NC.S.R.M.LVL.M..T.SI.WCG.SGR.LGKL.P.SSLC..LTLL....GL.S.SG...TD..LK..YE
Retrocopy NC-SDRKMKLVLKMYDTDSIRWCGTSGRYLGKLSPNSSLCFTLTLLCLKLGLRSVSGIQITDRLLKKKYE

Parental  YDDIAQVCVVSS
          ..DIA.VCV..S
Retrocopy FSDIANVCVIPS

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_3287 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 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000006026	1 retrocopy	retro_chof_1834,
Otolemur garnettii	ENSOGAG00000010787	1 retrocopy	retro_ogar_3287 ,
Procavia capensis	ENSPCAG00000005623	1 retrocopy	retro_pcap_370,
Tarsius syrichta	ENSTSYG00000004582	1 retrocopy	retro_tsyr_18,