RetrogeneDB ID: retro_ogar_2798

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873665.1:2204986..2205623(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: STARD4
• Ensembl ID: ENSOGAG00000007595
• Aliases: None
• Description: StAR-related lipid transfer (START) domain containing 4 [Source:HGNC Symbol;Acc:18058]

Sequence

>retro_ogar_2798
CAGAAAGAAAAAATGGAAGCCCTGCTTGATGTTACTTCTTTTGCAACTAAACTTAAAAACACTCTCATAAAGTACCATAG
TACTGAAGATGATAAGTGGCGAGTTGCCAAGAAAACATAAGATGTAACAGTTTGGAGAAAACCTTCAGAATTATTTAATG
GCTATCTCTACAAAGCTCAAGGTGTCATAGATGACATTTTCAGTAGTACCATAGACCATATAGGCCCAGGGCCTTGTCAT
TTGGATTGGGACTACTTAATGAATTCATTGGATATTTTGGAGCACTTTGAAGAGAATTACTGTGTGATGCATTATACTAC
TGCTGGTCAGTTTTGGAATATAATTTCCCCAAGAGAGTTTTTTGATTTCTCCTATACTGTGAGCTATCAAGAAGGGCTTT
TATCCTGTGGGATAAGTATTGACTGGAGTGAAAAGAGACCAGAATTTGTTAGAGGATATAACCATCCCTGTGGTTGGTTT
TGTGTTCCACTCAAAGACAATCCAAGCCAGAGTCTTTTGACCGGCTACATTCAGACAGACCTGCATGGGATGATTCCTCA
GTCTGCGGTAGACACAGCCATGGCAAGCACTTTAACCAACTTCTACGGCGACTTAACGAAAGGCTTTACAGAAGACA

Alignment

ORF - retro_ogar_2798 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.02 %
• Parental protein coverage: 93.81 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  RKEKMEALPDVTSFGTKLKNTLIQYHSTEDDKWRVAKKTKDVTVWRKPSELFNGYLYKAQGVIDDVFSST
          .KEKMEAL.DVTSF.TKLKNTLI.YHSTEDDKWRVAKKT.DVTVWRKPSELFNGYLYKAQGVIDD.FSST
Retrocopy QKEKMEALLDVTSFATKLKNTLIKYHSTEDDKWRVAKKT*DVTVWRKPSELFNGYLYKAQGVIDDIFSST

Parental  IDHIRPGPCRLDWDSLMTSLDILEHFEENCCVMRYTTAGQLWNIISPREFVDFSYTVSYQEGLLSCGISL
          IDHI.PGPC.LDWD.LM.SLDILEHFEEN.CVM.YTTAGQ.WNIISPREF.DFSYTVSYQEGLLSCGIS.
Retrocopy IDHIGPGPCHLDWDYLMNSLDILEHFEENYCVMHYTTAGQFWNIISPREFFDFSYTVSYQEGLLSCGISI

Parental  DWSEKRPEFVRGYNHPCGWFCVPLKDNPSQSLLTGYIQTDLRGMIPQSAVDTAMASTLTNFYGDL-RKAL
          DWSEKRPEFVRGYNHPCGWFCVPLKDNPSQSLLTGYIQTDL.GMIPQSAVDTAMASTLTNFYGDL.RKAL
Retrocopy DWSEKRPEFVRGYNHPCGWFCVPLKDNPSQSLLTGYIQTDLHGMIPQSAVDTAMASTLTNFYGDL>RKAL

Parental  QKT
          QKT
Retrocopy QKT

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_2798 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 2 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000030762	1 retrocopy	retro_cfam_902,
Otolemur garnettii	ENSOGAG00000007595	2 retrocopies	retro_ogar_2798 , retro_ogar_929,