RetrogeneDB ID: retro_ogar_2863

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873673.1:158229..159016(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: KITLG
• Ensembl ID: ENSOGAG00000009638
• Aliases: None
• Description: KIT ligand [Source:HGNC Symbol;Acc:6343]

Sequence

>retro_ogar_2863
ACACAAACTTGGATTATCACTTGCATTTATCTTTGACTACTTCTATTTAATCCTCTCGTCAAGATCAAAGGGATCTGCAG
GAATCGTGTGACTAATGATGTAAAATACATCACAAAATTGGTGGCAAATCTTTCAAAAGACTACATGATTACCCTCAAAT
ATGTTCCTGGGATGGATATTTTGCCGAGTCATTGTTGGATAAGGAGATGGTAGTACAATTATTAGACAGTTTGATGATCT
TCTGGACAAGTTTTCAAATATTTCTGAAGGCTTGAGTAATTATCCTATCATAGACAAGCTTGTAAACATAGTGGATGACC
TTGTAGAGGATGAGAAAGAAAACTCATCTCAGAATATAAAAAAAATCATCTACAAGTCCAGAACCTAGGCTCTTTCCTCC
TGAAGAATTCTTTAGAATTTTTAATAGACCCACTGATGCCTTCAAGGACTTTATGGTGGCATATGAAACCAGTGATTGTG
TGATTTCTTAAATATTAAGTCCTGCAAAAGATTTCAGATTCAGTGTCACAAAACCATTTATGATATCTCCATTTCCACCA
GTTCCCTTAGGAATGACAGCAGTAGCAGTAATAGGAAGGCCCTCAGTTCCACTGGAGACTTGAGCCTACAATGGGTGGCT
GCAGGGTTGCCAGCATTCTTTTCTATTCTAATTGGCTTTGCTTTTAGAGCTTTATACTGGAAGAAGAAACACCCAAATCT
TTCAAGGGCAGTCAAAAATATACAAATTACTGTAAAGGACAGAGATAAGTATATGACAAGAAAGAGA

Alignment

ORF - retro_ogar_2863 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.9 %
• Parental protein coverage: 96.69 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  TQTWIITCIYLQLLLFNPLVKTKGICGNRVTNNVKDVTKLVANLPKDYMITLKYVPGMDVLPSHCWI-SE
          TQTWIITCIYL.LLLFNPLVK.KGIC.NRVTN.VK..TKLVANL.KDYMITLKYVPGMD.LPSHCWI..E
Retrocopy TQTWIITCIYL*LLLFNPLVKIKGICRNRVTNDVKYITKLVANLSKDYMITLKYVPGMDILPSHCWI<KE

Parental  MVVQLSDSL-TDLLDKFSNISEGLSNYSIIDKLVSIVDDLVECVKENSSKN-VKKSSKSPEPRLFTPEEF
          MVVQL.DSL..DLLDKFSNISEGLSNY.IIDKLV.IVDDLVE..KENSS.N....SS.SPEPRLF.PEEF
Retrocopy MVVQLLDSL<DDLLDKFSNISEGLSNYPIIDKLVNIVDDLVEDEKENSSQN>XXXSSTSPEPRLFPPEEF

Parental  FRIFNRSIDAFKDFMVASETSDCVISSTLSPEKDSRVSVTKPFMLPP-VAASSLRNDSSSSNRKALNSTG
          FRIFNR..DAFKDFMVA.ETSDCVIS..LSP.KD.R.SVTKPFM..P....SSLRNDSSSSNRKAL.STG
Retrocopy FRIFNRPTDAFKDFMVAYETSDCVIS*ILSPAKDFRFSVTKPFMISP<ISTSSLRNDSSSSNRKALSSTG

Parental  DSSLQWAATALPAFFSLLIGFAFGALYWKKKQPNLSRAVETIQINEEDNEISMLQEK
          D.SLQW.A..LPAFFS.LIGFAF.ALYWKKK.PNLSRAV..IQI...D....M....
Retrocopy DLSLQWVAAGLPAFFSILIGFAFRALYWKKKHPNLSRAVKNIQITVKDRDKYMTRKR

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_2863 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 3 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000019661	2 retrocopies	retro_cjac_3502, retro_cjac_3860,
Oryctolagus cuniculus	ENSOCUG00000017687	1 retrocopy	retro_ocun_560,
Otolemur garnettii	ENSOGAG00000009638	1 retrocopy	retro_ogar_2863 ,