RetrogeneDB ID: retro_ogar_2405

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873620.1:239294..239828(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RAB11B
• Ensembl ID: ENSOGAG00000003227
• Aliases: None
• Description: RAB11B, member RAS oncogene family [Source:HGNC Symbol;Acc:9761]

Sequence

>retro_ogar_2405
CTGTGGCGTTTCACGCGCAAGGAGACCAACCTGGAGAGCGAAAGAGCCATCAGGCGGAGCTCGCCGCCCGCAGCGCCCGG
AGGACAGCAGGACCACCAAGGCGCGGATCCCGGACGCAGCCGGCAAGCGGTGGCCGCGCCATCACCTCCGCTTACTGCCG
CGGCGCGGTGGGTGAGCTGCAGGTGTATGACACCGCCCAACACCTGACCCGTGAGAACGCCGAGCGCCGGCTGGGGAAGC
GGCGGGACCGTGCCGAAGGCAACGTCGTCATCACGTAGGTGGGCACGACTCACCCGCGCCACCTGCGAGCTGTGACCACT
GACGAGGCCCACGCCATTGCAGAAAAGAACAGCTTGTCCTTCACTGAGACCTCAGCCTTGGATTCCACCAACATAAAAGA
AGCATTCAAAGACTTCCTCCGAAGAGATCTTCCAAATTGTGTCCCCAAAGCAGATTGCCCACCGTGCAGCCCACGAGGAG
TACCCTGGCAACAACGTGGCGGACATCTGTGCGCCGCCTACCACCGACAGACAA

Alignment

ORF - retro_ogar_2405 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.04 %
• Parental protein coverage: 81.82 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  LSRFTRNEFNLESKSTIG-VEFATRSIQ-VDGKTIKAQIWDTAGQERY-RAITSAYYRGAVGALLVYDIA
          L.RFTR.E.NLES...I...E.A.RS....D..T.KA.I.D.AG..R..RAITSAY.RGAVG.L.VYD.A
Retrocopy LWRFTRKETNLESERAIR<AELAARSAR<EDSRTTKARIPDAAG-KRW>RAITSAYCRGAVGELQVYDTA

Parental  KHLTYENVERWLKELRDHADSNIVIMLVGNKSDLRHLRAVPTDEARAFAEKNNLSFIETSALDSTNVEEA
          .HLT.EN.ER.L...RD.A..N.VI..VG.....RHLRAV.TDEA.A.AEKN.LSF.ETSALDSTN..EA
Retrocopy QHLTRENAERRLGKRRDRAEGNVVIT*VGTTHP-RHLRAVTTDEAHAIAEKNSLSFTETSALDSTNIKEA

Parental  FKNIL-TEIYRIVSQKQIADRAAHDESPGNNVVDISVPPTTDGQ
          FK..L..EI..IVS.KQIA.RAAH.E.PGNNV.DI..PPTTD.Q
Retrocopy FKDFL>EEIFQIVSPKQIAHRAAHEEYPGNNVADICAPPTTDRQ

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_2405 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 9 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000013525	1 retrocopy	retro_chof_1582,
Callithrix jacchus	ENSCJAG00000010778	2 retrocopies	retro_cjac_3866, retro_cjac_3917,
Erinaceus europaeus	ENSEEUG00000009165	2 retrocopies	retro_eeur_284, retro_eeur_565,
Mus musculus	ENSMUSG00000077450	1 retrocopy	retro_mmus_1846,
Otolemur garnettii	ENSOGAG00000003227	1 retrocopy	retro_ogar_2405 ,
Otolemur garnettii	ENSOGAG00000012973	1 retrocopy	retro_ogar_710,
Petromyzon marinus	ENSPMAG00000009335	1 retrocopy	retro_pmar_25,
Pteropus vampyrus	ENSPVAG00000009645	1 retrocopy	retro_pvam_64,
Tupaia belangeri	ENSTBEG00000000667	1 retrocopy	retro_tbel_4634,