RetrogeneDB ID: retro_ogar_5

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873604.1:7374861..7376742(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOGAG00000006953
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: TKT
• Ensembl ID: ENSOGAG00000016911
• Aliases: None
• Description: transketolase [Source:HGNC Symbol;Acc:11834]

Sequence

>retro_ogar_5
GCCATGGCAGACGACGCCAAGCCCGATGCAAAGACTCTGCAGGCGCTCCGGGACGCTGCCAACCGCCTGCGGATCCACTC
TATTAGAGCCACGTGTGCCTCCAGCTCCGGCCACCCCACGTCGTGCTGCAGCGCTGCGGAGATCATGTCTGTCCTCTTCT
TCCACACCATGCGGTATAAGCGGACGGACCCGCAGCACCCGGACAACGACCGCTTCGTCCTCTCCAAGGGCCACGCTGCC
CCAGTCCTCTATGCCGCTTGGGCAGAGGTGGGCGACATCAGTGAATCCGACTTGCTGAACTTGAGGAAAATCCACTGCGA
CTTGGAGGGACACCCCACCCCGCGACTGCCATTTGTCGATGTGGCAACGGGATCCCTGGGGCAGGGATTAGGCGCAGCCT
GTGGAATGGCGTACACCGGCAAGTACTTCGACAAGGCTAGCTACCGCGTGTTCTGCCTCATGGGGGACGGCGAGTCCTCG
GAAGGCTCCGTCTGGGAGGCTTTGGCCTTTGCTTCCCACTACAGTTTGGACAATCTTGTGGCAGTCTTCGACGTGAACCG
CTTGGGACAGAGTGGCACCGCGCCCCTTGAGCACTGCACGGACATCTATCAGAATCGCTGTGAAGCCTTTGGCTGGAACA
CTTACATAGTGGATGGCCACGATGTGGAGGCTTTGTGCCAAGCCTTTTCGCAGGCAGCCCAAGTGAAGAACAAGCCCACT
GCTATAGTTGCCAAGACCTTCAAGGGTCGAGGTATTCCAAACATTGAAGATGCAGAAAATTGGCACGGAAAACCAGTGCC
GAAAGAAAGAGCAGAGGCAATTATCAAATTAATTCAAAGTCAGATACAGACCCAGGGGAATCCCATATCGAAACCCCCTG
TGGAAGATTCACCTCAAATCAGCATCACAAATATACAAATGACCTCTCCACCTGCTTACAAAATGGGCGACAAGATAGCT
ACTCAGAAAGCCTATGGTTTGGCTCTGGCTAAACTGGGCCATGAAAACAAAAGAGTTATTGTTCTGGATAGTGACACAAA
GAACCCCACCTTTTCTGAGATATTCAAGAAAGAACACCCTGAACGTTTCATAGAGTGTTTTATTCCTGAGCAAAACATGG
TGAGTGTGGCACTGGGCTGTGCTACACGTGGTCGAACCATTGTTTTTGCTAATACTTTCTCCGCCTTTTTCACTCGAGCA
TTTGATCAGATCCGAATGGGAGCCATCTCTCAAACCAATATTAACCTCATTGGTTCTCATTGTGGCGTATCCATAGGTGA
AGATGGGCCCTCCCAGATGGCCCTGGAGGATCTAGCCATGTTCCGAAGCATTCCCAATTGCACTGTTTTCTATCCCAGTG
ATGCCCTCTCCACAGAGCATGCTGTTTATCTAGCTGCTAACACCAAAGGAATGTGCTTCATACGGACCAGCCAACCAGAA
ACTGAAGTTATTTATACGGCACAAGAAAAGTTTGAGATTGGACAGGCCAAAGTGGTCCTTCACAGTGACAATGACAAGGT
CACAGTTATTGGAGCTGGAATTACTCTACATGAAGCCTTAGCAGCAGCTGACAATCTTTCTCAACAAGGTATTGCTATCC
GTGTCATCGACCCATTTACTATTAAACCTCTGGATGCTGCTACCATTATCTCCAGTGCAAAAGCCACAGGTGGTCGGGTT
ATCACAGTGGAGGATCACCACAAAGAAGGTGGCCTTGGAGAAGCTGTATGTGCAGCCGTCTCCAGGGAGCCTGACATCCT
TGTTCATCAGCTGGCAGTGTCAGGCCTGCCTCAAAGTGGGAAGCCTGGTGAATTGCTGGATATGTTTGGAATCAGTGCTG
GACACATTGTATCAGCTGTAAGAAATATTTTAATGAACTAA

Alignment

ORF - retro_ogar_5 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.9 %
• Parental protein coverage: 98.72 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KPDQQKLQALKDTANRLRISSIQATTAAGSGHPTSCCSAAEIMAVLFFHTMRYKSQDPRNPHNDRFVLSK
          KPD...LQAL.D.ANRLRI.SI.AT.A..SGHPTSCCSAAEIM.VLFFHTMRYK..DP..P.NDRFVLSK
Retrocopy KPDAKTLQALRDAANRLRIHSIRATCASSSGHPTSCCSAAEIMSVLFFHTMRYKRTDPQHPDNDRFVLSK

Parental  GHAAPILYAVWAEAGFLPEAELLNLRKISSDLDGHPVPKQAFTDVATGSLGQGLGAACGMAYTCKYFDKA
          GHAAP.LYA.WAE.G...E..LLNLRKI..DL.GHP.P...F.DVATGSLGQGLGAACGMAYT.KYFDKA
Retrocopy GHAAPVLYAAWAEVGDISESDLLNLRKIHCDLEGHPTPRLPFVDVATGSLGQGLGAACGMAYTGKYFDKA

Parental  SYRVYCMLGDGELSEGSVWEAMAFAGIYKLDNLVAILDINRLGQSDPAPLQHQLDVYQKRCEAFGWHAII
          SYRV.C..GDGE.SEGSVWEA.AFA..Y.LDNLVA..D.NRLGQS..APL.H..D.YQ.RCEAFGW...I
Retrocopy SYRVFCLMGDGESSEGSVWEALAFASHYSLDNLVAVFDVNRLGQSGTAPLEHCTDIYQNRCEAFGWNTYI

Parental  VDGHSVEELCKAFGQA---KHQPTAIIAKTFKGRGITGVEDKESWHGKPLPKNMADQTIQEIYSQIQSKK
          VDGH.VE.LC.AF.QA...K..PTAI.AKTFKGRGI...ED.E.WHGKP.PK..A...I..I.SQIQ...
Retrocopy VDGHDVEALCQAFSQAAQVKNKPTAIVAKTFKGRGIPNIEDAENWHGKPVPKERAEAIIKLIQSQIQTQG

Parental  KILATPPQEDAPSVDITNIRMPTPPSYKVGDKIATRKAYGQALAKLGHASDRIIALDGDTKNSTFSEIFK
          .....PP.ED.P...ITNI.M..PP.YK.GDKIAT.KAYG.ALAKLGH...R.I.LD.DTKN.TFSEIFK
Retrocopy NPISKPPVEDSPQISITNIQMTSPPAYKMGDKIATQKAYGLALAKLGHENKRVIVLDSDTKNPTFSEIFK

Parental  KEHPDRFIECYIAEQNMVSIAVGCATRNRTVPFCSTFAAFFTRAFDQIRMAAISESNINLCGSHCGVSIG
          KEHP.RFIEC.I.EQNMVS.A.GCATR.RT..F..TF.AFFTRAFDQIRM.AIS..NINL.GSHCGVSIG
Retrocopy KEHPERFIECFIPEQNMVSVALGCATRGRTIVFANTFSAFFTRAFDQIRMGAISQTNINLIGSHCGVSIG

Parental  EDGPSQMALEDLAMFRAVPMSTVFYPSDGVATEKAVELAANTKGICFIRTSRPENAIIYNNNEDFQVGQA
          EDGPSQMALEDLAMFR..P..TVFYPSD...TE.AV.LAANTKG.CFIRTS.PE...IY...E.F..GQA
Retrocopy EDGPSQMALEDLAMFRSIPNCTVFYPSDALSTEHAVYLAANTKGMCFIRTSQPETEVIYTAQEKFEIGQA

Parental  KVVLKSKDDQVTVIGAGVTLHEALAAAELLKKEKINIRVLDPFTIKPLDRKLILDSARATKGRILTVEDH
          KVVL.S..D.VTVIGAG.TLHEALAAA..L....I.IRV.DPFTIKPLD...I..SA.AT.GR..TVEDH
Retrocopy KVVLHSDNDKVTVIGAGITLHEALAAADNLSQQGIAIRVIDPFTIKPLDAATIISSAKATGGRVITVEDH

Parental  YNEGGIGEAVCTAVVGEPGITVTRLAVTQVPRSGKPAELLKMFGIDKDAIVQAVRGLV
          ..EGG.GEAVC.AV..EP.I.V..LAV...P.SGKP.ELL.MFGI....IV.AVR...
Retrocopy HKEGGLGEAVCAAVSREPDILVHQLAVSGLPQSGKPGELLDMFGISAGHIVSAVRNIL

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_5 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 19 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000003758	1 retrocopy	retro_btau_176,
Callithrix jacchus	ENSCJAG00000007253	1 retrocopy	retro_cjac_2128,
Cavia porcellus	ENSCPOG00000000072	1 retrocopy	retro_cpor_45,
Dipodomys ordii	ENSDORG00000001392	1 retrocopy	retro_dord_329,
Homo sapiens	ENSG00000163931	1 retrocopy	retro_hsap_47,
Macropus eugenii	ENSMEUG00000005312	3 retrocopies	retro_meug_1397, retro_meug_160, retro_meug_796,
Myotis lucifugus	ENSMLUG00000000943	1 retrocopy	retro_mluc_67,
Macaca mulatta	ENSMMUG00000014433	1 retrocopy	retro_mmul_74,
Mus musculus	ENSMUSG00000021957	1 retrocopy	retro_mmus_220,
Oryctolagus cuniculus	ENSOCUG00000015904	2 retrocopies	retro_ocun_319, retro_ocun_62,
Otolemur garnettii	ENSOGAG00000016911	1 retrocopy	retro_ogar_5 ,
Ochotona princeps	ENSOPRG00000009891	1 retrocopy	retro_opri_10,
Pan troglodytes	ENSPTRG00000015024	1 retrocopy	retro_ptro_126,
Pteropus vampyrus	ENSPVAG00000016283	1 retrocopy	retro_pvam_352,
Rattus norvegicus	ENSRNOG00000016064	1 retrocopy	retro_rnor_146,
Sarcophilus harrisii	ENSSHAG00000017349	1 retrocopy	retro_shar_827,
Sus scrofa	ENSSSCG00000021408	1 retrocopy	retro_sscr_996,
Tupaia belangeri	ENSTBEG00000012114	1 retrocopy	retro_tbel_3510,
Takifugu rubripes	ENSTRUG00000003009	1 retrocopy	retro_trub_23,