RetrogeneDB ID: retro_ogar_1804

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873566.1:8653611..8654133(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: YY1
• Ensembl ID: ENSOGAG00000006955
• Aliases: None
• Description: YY1 transcription factor [Source:HGNC Symbol;Acc:12856]

Sequence

>retro_ogar_1804
ATTGATTATGAGACAGTGTTTAAAAAACAGATCATTGGAGAGAACTCGGCTCCTGGATTCAGAGTATATGACAGGAAAGA
AAGAGGAGTACCTGGCATTGACCTCTCACACTCCAAACAACGGGCAGAATTTACTAGGATGAAGCCAAGAAAAGTTAAAG
ACTAATCTCCAAGAACAATAGGTTGCCCTCATAAAGATTGCAGAAAGATGTTCAGGAATTACTCTGCCATGAGAAAACAT
CTGCAGACTCACGGTCCCAGAGTCTAGTCTGTGTAGAATGTGGCAAATTTTGTTGGGAGCTCAAAATTAAAACACCACCA
ACTGGTTCCTACTGGAGTTTCCCATTCAGTGCATAAAGGCTGCAGAAAATACTTTTCACTGGACTTCAATTTGCACACAC
ATGTGCAAATCCATACTGGAGACAGGCCCTATGTGTGCCCCTTCTATGGTTGTAATAAGTTTGCTCAAGTAGCTAACCTG
AAATCTCACATCTTAACACATGCTAAGGCCAAAAACAAGCAG

Alignment

ORF - retro_ogar_1804 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.41 %
• Parental protein coverage: 96.83 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  IDHETVVEEQIIGENSPPDYSEYMTGKKLPPGGIPGIDLSDPKQLAEFARMKPRKIKEDDAPRTIACPHK
          ID.ETV...QIIGENS.P....Y.......PG....IDLS..KQ.AEF.RMKPRK.K.D..PRTI.CPHK
Retrocopy IDYETVFKKQIIGENSAPGFRVYDRKERGVPG----IDLSHSKQRAEFTRMKPRKVK-D*SPRTIGCPHK

Parental  GCTKMFRDNSAMRKHLHTHGPRV-HVCAECGKAFVESSKLK-RHQLVHTGEKPFQCTFEGCGKRFSLDFN
          .C.KMFR..SAMRKHL.THGPRV..VC.ECGK.F....K.K..HQLV.TG.........GC.K.FSLDFN
Retrocopy DCRKMFRNYSAMRKHLQTHGPRV<LVCVECGK-FCWELKIK>HHQLVPTGVS--HSVHKGCRKYFSLDFN

Parental  LRTHVRIHTGDRPYVCPFDGCNKKFAQSTNLKSHILTHAKAKNNQ
          L.THV.IHTGDRPYVCPF.GCN.KFAQ..NLKSHILTHAKAKN.Q
Retrocopy LHTHVQIHTGDRPYVCPFYGCN-KFAQVANLKSHILTHAKAKNKQ

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_1804 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.

---

Parental genes homology:

Parental genes homology involve 10 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000011146	1 retrocopy	retro_amel_2,
Callithrix jacchus	ENSCJAG00000016853	2 retrocopies	retro_cjac_1931, retro_cjac_4045,
Equus caballus	ENSECAG00000005805	1 retrocopy	retro_ecab_97,
Homo sapiens	ENSG00000100811	2 retrocopies	retro_hsap_106, retro_hsap_97,
Gorilla gorilla	ENSGGOG00000026332	2 retrocopies	retro_ggor_190, retro_ggor_2,
Mus musculus	ENSMUSG00000021264	1 retrocopy	retro_mmus_190,
Nomascus leucogenys	ENSNLEG00000000999	3 retrocopies	retro_nleu_1092, retro_nleu_116, retro_nleu_2225,
Otolemur garnettii	ENSOGAG00000006955	4 retrocopies	retro_ogar_1231, retro_ogar_1804 , retro_ogar_1857, retro_ogar_289,
Pongo abelii	ENSPPYG00000025949	3 retrocopies	retro_pabe_145, retro_pabe_3616, retro_pabe_534,
Pan troglodytes	ENSPTRG00000006717	3 retrocopies	retro_ptro_3093, retro_ptro_45, retro_ptro_494,