RetrogeneDB ID: retro_ogar_1770

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873564.1:10223667..10224284(-)
• Located in intron of: ENSOGAG00000009098

Retrocopy information

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

Parental gene information

• Parental gene symbol: CCNB2
• Ensembl ID: ENSOGAG00000012885
• Aliases: None
• Description: cyclin B2 [Source:HGNC Symbol;Acc:1580]

Sequence

>retro_ogar_1770
GCCCAAGTAGCTAAGAAAACTCAGAACACCAAAGTACCAGTTCAGCCCAGCAAAACAACAAATGTCACAAATAGCTGAAG
CCTACTGCCTCTGCAAAACCAGTGCAGAGGGAAATGTTAGCCCCAGAGCATCCTTCCACACCTGAGGATGTCTCCATGAA
GAAAGAGAACCTCTGCCAAGCTTTTTCTGATGCCTTGCTCTGCAAAGTCAAAGACATTGACAGTGAGGATTGTGAGAACC
GTCAGCTCTGAAGTGACTATGTTAAGGATATTTGCCAGTGTCTCAGGCAGCCTGAGGTTTTACAGTCTATAAACCCACAT
TTCTTAGATGGAAGAGATATAAACCGATGTCTGCGTGCCATCCTGGTGGACCAGTTATTACAAGCCCCAAGCCCACTCCA
AGTTTAGGTTTCTGCAGGAGACTCTGTACATGTGTGTTGCTATGTGGATCGATTTTTACAGGTTCAGCCAGTCTCACATA
AAAAGCTTCAACTGGTTGGGATTACTGCTCTGCTCTTGGCTTCCAAGTATAAGATGTTTTCTCCAAATATTGAAGACTTC
ATTTACATCATAGGCTATACTTATACCAGTTCCCAAATCCCAGTGATGGAAACTCTT

Alignment

ORF - retro_ogar_1770 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.33 %
• Parental protein coverage: 51.76 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  AQVAKKAQNTKVPVQPTKTTNG-NKQLKPTASVKPVQMEMLTPKRPSSTPEDVSMKEENLCQAFSDALLC
          AQVAKK.QNTKVPVQP.KTTN...K.LKPTAS.KPVQ.EML.P..PS.TPEDVSMK.ENLCQAFSDALLC
Retrocopy AQVAKKTQNTKVPVQPSKTTNV<HK*LKPTASAKPVQREMLAPEHPS-TPEDVSMKKENLCQAFSDALLC

Parental  KIEDIDSEDWENPQLCSDYVKDIYQYLRQLEVLQSINPHFLDGRDINGRMRAILVDWLVQVHSKFRL---
          K..DIDSED.EN.QL.SDYVKDI.Q.LRQ.EVLQSINPHFLDGRDIN...RAILVD.L.Q..S.......
Retrocopy KVKDIDSEDCENRQL*SDYVKDICQCLRQPEVLQSINPHFLDGRDINRCLRAILVDQLLQAPSPLQV*VS

Parental  LQETLYMCVAIMDRFLQVQPVSRKKLQLVGITALLLASKYEEMFSPNIEDFVYITDNAYTSSQIREMETL
          .......C....DRFLQVQPVS.KKLQLVGITALLLASKY..MFSPNIEDF.YI....YTSSQI..METL
Retrocopy AGDSVHVC-CYVDRFLQVQPVSHKKLQLVGITALLLASKY-KMFSPNIEDFIYIIGYTYTSSQIPVMETL

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_1770 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 11 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000005269	1 retrocopy	retro_btau_1584,
Homo sapiens	ENSG00000157456	1 retrocopy	retro_hsap_3816,
Nomascus leucogenys	ENSNLEG00000011543	1 retrocopy	retro_nleu_212,
Otolemur garnettii	ENSOGAG00000005208	1 retrocopy	retro_ogar_977,
Otolemur garnettii	ENSOGAG00000006217	2 retrocopies	retro_ogar_3309, retro_ogar_930,
Otolemur garnettii	ENSOGAG00000012885	2 retrocopies	retro_ogar_1770 , retro_ogar_2766,
Otolemur garnettii	ENSOGAG00000034667	1 retrocopy	retro_ogar_1793,
Pongo abelii	ENSPPYG00000006517	2 retrocopies	retro_pabe_3073, retro_pabe_3074,
Pan troglodytes	ENSPTRG00000007123	1 retrocopy	retro_ptro_2597,
Ictidomys tridecemlineatus	ENSSTOG00000001275	1 retrocopy	retro_itri_229,
Tarsius syrichta	ENSTSYG00000013818	1 retrocopy	retro_tsyr_1402,