RetrogeneDB ID: retro_ogar_1358

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873543.1:20616941..20617669(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CCNDBP1
• Ensembl ID: ENSOGAG00000011162
• Aliases: None
• Description: cyclin D-type binding-protein 1 [Source:HGNC Symbol;Acc:1587]

Sequence

>retro_ogar_1358
GAAACCCAGAGGTTCCGTGAACAAGTCCATGCTGCTATCAAGGCAATAATTGCAGAATACTATTCACTTCCTAATGATCC
AGGGGTCACTGTGAGAAAGCTAGTATGAGGCACCACTTTGGACATCGTGGATGGCATGGCTCAGCTTGTGGAAGCATTTT
CCATTACTCCGGCTCAGAGCACTGACAACAAAGACCTTATTTCCTGCAACAGTGTCTGGGTTGCATGCCAGCAGGTGCCT
CGGATACCAAGAAATAACAAAGCTGCAGCCCTTGTAATGCTGACAAATTGTGGATCTTGTGAAGTATGCACGTGAAGAAA
TGAGCAGGCTGTGGAAGAATGTGACCCTTACTGCAGCCTCTCAAATGACAGTGAAGAGGACACCTCTCAGAACCATAATG
ATGAGGATGATGTGTTGGGGTTTCCAACCAATCAGGACTTACACTGGTCAGAGGAAGACCAAGAGCTCATAATCCCATGC
CTTGTACTCTGAGGGCATCCAAAGCCTGCCTGAAGAAAATCCTGATCTTAGTGGCAGAGAATGGGAAGAAAGATCAGGTG
GCCCAGGTGGATGACATTGTGAATATTTCCGATGAAATCAGCCCCAGTATGGATGATTTGGCTCTGAGCATATATCCACC
TATGTGCTACCTAACTGTATGAATTAATTCTGTATTTTCAAATTCTGTGAAACTTGTATATATTTTAAAGAAGGCACTTG
AAATTACA

Alignment

ORF - retro_ogar_1358 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.02 %
• Parental protein coverage: 68.16 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  ETQRFCEKVHAAIKAIIAVYYSLPKDQGITLRKLVRGTTLEIVDGMAQLVEALSITPAQSPENKDFISCN
          ETQRF.E.VHAAIKAIIA.YYSLP.D.G.T.RKLV.GTTL.IVDGMAQLVEA.SITPAQS..NKD.ISCN
Retrocopy ETQRFREQVHAAIKAIIAEYYSLPNDPGVTVRKLV*GTTLDIVDGMAQLVEAFSITPAQSTDNKDLISCN

Parental  SVWVACQQVPRIPRDNKAAALLTLTKN-VDFVKDAHEEM-EKAVEECDPYCGLLNDSE-DTSDHHNDEDD
          SVWVACQQVPRIPR.NKAAA.L....N.VD.VK.A.EEM.E.AVEECDPYC.L.NDSE.DTS..HNDEDD
Retrocopy SVWVACQQVPRIPRNNKAAA-LVMLTN>VDLVKYAREEM<EQAVEECDPYCSLSNDSEEDTSQNHNDEDD

Parental  VLGSPTNQDLYWSEEDQELIIPCLAL-VRASKACLKKIRILVAENGKKDQVAQLDDIVDISDEISPSVDD
          VLG.PTNQDL.WSEEDQELIIPCL.L..RASKACLKKI.ILVAENGKKDQVAQ.DDIV.ISDEISPS.DD
Retrocopy VLGFPTNQDLHWSEEDQELIIPCLVL<LRASKACLKKILILVAENGKKDQVAQVDDIVNISDEISPSMDD

Parental  LALSIYPPVCHPTVRINSAKLVSVLKKALEITKASHVT
          LALSIYPP.C..TV.INS....SV.K......KA...T
Retrocopy LALSIYPPMCYLTV*INSVFSNSV-KLVYILKKALEIT

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_1358 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	ENSCHOG00000012594	2 retrocopies	retro_chof_1251, retro_chof_1832,
Loxodonta africana	ENSLAFG00000004497	1 retrocopy	retro_lafr_680,
Otolemur garnettii	ENSOGAG00000011162	1 retrocopy	retro_ogar_1358 ,