RetrogeneDB ID: retro_ogar_2220

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873603.1:2051977..2052721(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RBBP7
• Ensembl ID: ENSOGAG00000014995
• Aliases: None
• Description: retinoblastoma binding protein 7 [Source:HGNC Symbol;Acc:9890]

Sequence

>retro_ogar_2220
GGCTGCAGGAAACATAGAGGCCGTGAGTGCAGAGGCAGCAGCTGCAGGCTCCCAGCCCTGCCTGTGTACAACCCTGGGAT
CACCCCTGAAACTTGCTTGCCCACCCTGGCTGATTAGGAATCAGCCTTTAACAATGCTGTAAAGAATGTGTAATCAACAA
GGAATACAAAATATGGAGAAAGAATACCGTTTTTATGATTTGGGGATGACCCCGGGTCTGGAGTGGCCCTGCCTAACTGC
ACAGTGGCTTCCAGAGGTGACCAGACCAGAAGGGAAGATTTCAGTATTCATGGGCTCATCCTGGGGACACACACATCAAG
ATCAACAAAACCACTTGTGAAGTGGAGTGAGGCTCCCTCATGATGATGCTCAATTTGATGCATCATGACACTATGACAGT
GAAAAAGGAGAATTAGCAGGTTTTGGCTCTGTTACTGGGAAAATTGAAAGAGAAATTAAATCAACCAAGAAGGAGAAGTA
AATAGGTCCCATTATATGCACCAGATCACTTGCATCATTGCAACAAAGGCTCCATCCAGTGATGTTCTTGTTTGACCATA
CCAAACATCCTTCTGGAGACCCGGCCCTTCTGGAGAGTGCAACCCAGACTTACGTCTCCATGGACCTCAGAAGGAAGGCC
ATGGGCTTTCTTGGCAGACAAATCTCAGTGGGCACTTACTTAGTGCTTCAGATGATCATACCATCAGCCTGTGGGACATC
CATGCAGTTTCAAAGGAAGGACGT

Alignment

ORF - retro_ogar_2220 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.38 %
• Parental protein coverage: 53.76 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  GAAAFPGGGWRERACGFLLHVVSSPSVGRAALLSTGLHLRTVFEDTVE-ERVINEEYKIW-KKNTPFLYD
          G.....G...R...C......V..P.......L.T.......F...V..E.VIN.EYKIW..K...F.YD
Retrocopy GCRKHRGRECRGSSCRLPALPVYNPGITPETCLPTLAD*ESAFNNAVK<ECVINKEYKIW<EKEYRF-YD

Parental  LVMTHALQWPSLTVQWLPEVTKPEGK-DYALHWLVLGTHTS-DEQNHLVVARVHIPNDDAQFDAS-HCDS
          L.MT..L.WP.LT.QWLPEVT.PEGK.D...H.L.LGTHTS.D.QNHL....V..P.DDAQFDAS.H.DS
Retrocopy LGMTPGLEWPCLTAQWLPEVTRPEGK<DFSIHGLILGTHTS>DQQNHL*-SGVRLPHDDAQFDAS*HYDS

Parental  DKGEFGGFGSVTGKIECEIK-INHEGEVNRARYMPQNPHIIATKTPSSDVLVFDYTKHPAKPDPSGECNP
          .KGE..GFGSVTGKIE.EIK.IN.EGEVNR..YM.Q...IIATK.PSSDVLV..Y......P.PSGECNP
Retrocopy EKGELAGFGSVTGKIEREIK<INQEGEVNRSHYMHQITCIIATKAPSSDVLV*PYQTSFWRPGPSGECNP

Parental  DLRLRGHQKEGYGLSWNSNLSGHLLSASDDHTVCLWDINAGPKEGK
          DLRL.G.QKEG.GLSW..NLSGHLLSASDDHT..LWDI.A..KEG.
Retrocopy DLRLHGPQKEGHGLSWQTNLSGHLLSASDDHTISLWDIHAVSKEGR

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_2220 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 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000002820	1 retrocopy	retro_btau_1579,
Mus musculus	ENSMUSG00000031353	1 retrocopy	retro_mmus_3529,
Oryctolagus cuniculus	ENSOCUG00000000683	1 retrocopy	retro_ocun_1939,
Otolemur garnettii	ENSOGAG00000011632	2 retrocopies	retro_ogar_3079, retro_ogar_3297,
Otolemur garnettii	ENSOGAG00000014995	1 retrocopy	retro_ogar_2220 ,
Petromyzon marinus	ENSPMAG00000007189	1 retrocopy	retro_pmar_26,
Pan troglodytes	ENSPTRG00000021702	5 retrocopies	retro_ptro_1802, retro_ptro_1909, retro_ptro_2226, retro_ptro_2987, retro_ptro_896,
Rattus norvegicus	ENSRNOG00000005157	1 retrocopy	retro_rnor_1182,
Sorex araneus	ENSSARG00000008079	3 retrocopies	retro_sara_308, retro_sara_571, retro_sara_602,
Tupaia belangeri	ENSTBEG00000010151	2 retrocopies	retro_tbel_3031, retro_tbel_4341,
Tarsius syrichta	ENSTSYG00000002385	4 retrocopies	retro_tsyr_1608, retro_tsyr_1838, retro_tsyr_1957, retro_tsyr_427,