RetrogeneDB ID: retro_ogar_3157

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873731.1:446053..446749(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CAB39L
• Ensembl ID: ENSOGAG00000016755
• Aliases: None
• Description: calcium binding protein 39-like [Source:HGNC Symbol;Acc:20290]

Sequence

>retro_ogar_3157
AGAATAGCCCAAGAACTCTATAACAGCGGGCTGCTGGTGATGCTGATAGCTGACTCACAGCTGGTAGACTTTGAGGGAAT
AAAAGATGTGACCCAGATATTTAACAACATTCTGAGAAGATGGACAGGCACTCGGGGTCCCGCTGTGGAGTCATCAGCAC
TCACCCCCACATCCTGTTCTTGCTCCTCAGGGGATATGAAGCCCCACAGCCTTGCATTGTGGGGTTATACTGGGAGAGTG
CATTCGACATGAACCTTTTGCCAAAATCATCCTCTCTTCTAATCAAGTTAGTGATTTCTTTAGGTATGGGGAGATGTCAA
CCTTTGATATTGCTTCAGATGCCTTTGCTACTTTTAAGGATTTTCTAACAAGACATAAAGTGTTGATGGCAGACTTCTTA
GAAAAAATTATGACACTATCTTTGAAGACTATGAAAGATTGCTTCAGTCTGAGAACTATGTGACGAAGAGACAATCTTTA
AAGTTGCTAGGTGAACTGATCCTGGACAGCTACCATGTTGCCGTCATGGCCAAGTACATCAGCAAGCCGGAGAACCTGAA
GCTGACGATGAATCTCCTTTAGGATAAGAATCCCACCATCCAGTTTGAAGCCTTTCACGTTTTTAAAATGTTTGTGGCAA
GTGCTCACAAGACCCCACCTGCTGTGGAGATTCTGTTAAAAAATCAGCCCAAACTC

Alignment

ORF - retro_ogar_3157 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.48 %
• Parental protein coverage: 69.85 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  QLAQELYSSGLLVTLIADLQLIDFEGKKDVTQIFNNILRRQIGARSPTVE-YISAHPHILFMLLK-GYEA
          ..AQELY.SGLLV.LIAD.QL.DFEG.KDVTQIFNNILRR..G.R.P.VE..IS.HPHILF.LL..G...
Retrocopy RIAQELYNSGLLVMLIADSQLVDFEGIKDVTQIFNNILRRWTGTRGPAVE<VISTHPHILFLLLR<GI*S

Parental  PQIALRCGIMLRECIRHEPLAKIILFSNQFRDFFKYVEMSTFDIASDAFATFKDLLTRHKVLVADFLEQ-
          P..AL.CG..L.ECIRHEP.AKIIL.SNQ..DFF.Y.EMSTFDIASDAFATFKD.LTRHKVL.ADFLE..
Retrocopy PT-ALHCGVILGECIRHEPFAKIILSSNQVSDFFRYGEMSTFDIASDAFATFKDFLTRHKVLMADFLEK<

Parental  NYDAIFEDYEKLLQSENYVTKRQSLKLLGELILDRHNFAVMTKYISKPENLKLMMNLLRDKSPNIQFEAF
          NYD.IFEDYE.LLQSENYVTKRQSLKLLGELILD....AVM.KYISKPENLKL.MNLL.DK.P.IQFEAF
Retrocopy NYDTIFEDYERLLQSENYVTKRQSLKLLGELILDSYHVAVMAKYISKPENLKLTMNLL*DKNPTIQFEAF

Parental  HVFKVFVASPHKTPPIVEILLKNQPKL
          HVFK.FVAS.HKTPP.VEILLKNQPKL
Retrocopy HVFKMFVASAHKTPPAVEILLKNQPKL

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_3157 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
Choloepus hoffmanni	ENSCHOG00000001915	1 retrocopy	retro_chof_1402,
Otolemur garnettii	ENSOGAG00000002000	1 retrocopy	retro_ogar_1455,
Otolemur garnettii	ENSOGAG00000016755	2 retrocopies	retro_ogar_2297, retro_ogar_3157 ,