RetrogeneDB ID: retro_meug_1397

Retrocopy location

• Organism: Wallaby (Macropus eugenii)
• Coordinates: Scaffold39002:11192..12668(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TKT
• Ensembl ID: ENSMEUG00000005312
• Aliases: None
• Description: transketolase [Source:HGNC Symbol;Acc:11834]

Sequence

>retro_meug_1397
AAATAAGCTTTTAGAGATGTGGTTACTGGCTCCCTAGGTCAGGGGCTTGGAGCAGTGTGTGGAATGGACTACAATAGGTG
CATACTTCTACAAAGCCAGTTACCATGTATATTGTTTGCTTAGGTAATGGGGAGGTTTCTGAAGGCTCCATGTGACAGGC
CATGGTCTTTGCAGGATTCTACATGTTGGACATGGTTGCCATCTTTGATTTTAGGCTGGGCCAAAGACCCAGTCCTACTG
TGGCACAACTTGGAAATGCACCAGAAGTGATGTGAATCCTTTGGTTGGAATGTCACGGTTGTGAATGGACACAGAGTGGA
AGAACTCTGAAATGTCTTCAACAAGGGCAAGGATAAGCCACTGGCTGTCATTGCAAAGGCATATAAAGACAGAGGAATCT
CAGGTGTAGAAGATAAGGAAGCTTGGCATGGGAAGCTCCTTCTCCAAAACATGGAAGAACAGTTCATCAAGGAAATATAC
AGTCAAATCCAAAGCAAGAAGAAGATTCTAGCTACCCTTCCCAAAGAAGATGCCCCCACAGTGAACATTACCAAAATCTG
GGTGCCATCTCCCTCAAATTTCACACTTTTTAGAGAAAAACTAGACACCAGAAAAGCCTATGGCATGATGCTGGTCAAAC
TTGGGCATGCCACTGACCATGTGATTGCCGTGGATGAGGACATCAAGAATTCTACTTTCTCAGAACTCTTTAAGAAGGAG
TGTCCCAATCACTTCATTGAATGTTTCTTTGCAGAACAGAACATGGTGATCATCACCGTGGGATGTACCACATGGGGCAG
GACCATACCTGTTGCTTTCTTCAGGAGGGCCTTCAACTAGATCCATATGGCAGCCATTTATGATAGCAACATCAACCTGT
GTGGTTCGCACTGTGGGCTGTCTATCAGTGAAGATGGTCCTCCTCAGATGGCCCTTGAAGATCTTGCCATGTTCTGGAAC
ATTCCCAATGGGACAGTCTTTTACCTGAGTGATGCTGTGGCTACTGAGAAAATGGTTGAGTTAGCTGCTAACACAAAAGG
CACCAGTTTCATAAGAACTAGCTACTCGGACAATGCAATCATTTATAAAAACAATAAACACTTCCAGATTGATCAGGTTA
AGATGGTCCTGAAGAGCAAGGATAACAAGGTGATTGGAGCTGAAATGACCCTCCATGAAGCTCTGGCAGCTGCAGAGCTG
CTAAGGAAAGAAAATATCAACATTTGGATGCTTGATTCTTTTACAATTAAGCCCCGGGATAAGAAACTTGTCCTTGACAG
TGCCCCAGTCACTCATGACTAAATTCTGGCTATGAAAGACCATTACCATGAGAGTGCCATAGGAGATATTGTAGCTGCCA
CCTTAATGGGTGAACCTGGCATCACCATCACTCTCTTGATGGTCTCTAAAGTCCCTAGAAGCAGGAAGCTGGCAGAGCTG
CTGAAGACATATGGCATTGACAAAGGTGCCATTATT

Alignment

ORF - retro_meug_1397 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.41 %
• Parental protein coverage: 86.46 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  KQAFKDVATGSLGQGLGAPCGISYT-GKYFDKARYRVYCL-LGYGEVSEGSMWEAMVFSGFYKLDNLVAI
          K.AF.DV.TGSLGQGLGA.CG..Y..G.YF.KA.Y.VYCL.LG.GEVSEGSM..AMVF.GFY.LD..VAI
Retrocopy K*AFRDVVTGSLGQGLGAVCGMDYN>GAYFYKASYHVYCL>LGNGEVSEGSM*QAMVFAGFYMLD-MVAI

Parental  FDINQLGQSDPGP-LQHHMEVYLKRCDSFRWNIMVVDGHSVEELCKVFNQGKGKPLAVIAKTHKNRGISS
          FD...LGQ..P.P.L.H..E...K.C.SF.WN..VV.GH.VEEL..VFN.GK.KPLAVIAK..K.RGIS.
Retrocopy FDF-RLGQR-PSP>LWHNLEMHQK*CESFGWNVTVVNGHRVEEL*NVFNKGKDKPLAVIAKAYKDRGISG

Parental  VEDREAWHGKPFPKNIAEQVIEEIYS-IQSKKKILATLPKEDAPTVNIANIWMPSPPNFKL-GDKLATCK
          VED.EAWHGK....N..EQ.I.EIYS.IQSKKKILATLPKEDAPTVNI..IW.PSP.NF.L...KL.T.K
Retrocopy VEDKEAWHGKLLLQNMEEQFIKEIYSQIQSKKKILATLPKEDAPTVNITKIWVPSPSNFTLFREKLDTRK

Parental  AYGMSLAKLGHASDCVIALNGDTKNSTFSEFFKKEYPNHFIECFIAEQNMVSTAVGCATWNKTVPFSTFA
          AYGM.L.KLGHA.D.VIA...D.KNSTFSE.FKKE.PNHFIECF.AEQNMV...VGC.TW..T.P.....
Retrocopy AYGMMLVKLGHATDHVIAVDEDIKNSTFSELFKKECPNHFIECFFAEQNMVIITVGCTTWGRTIP----V

Parental  AFFTRAFDQIPLAVISESKINLCGSHCRVSIGEDGLSQMVLEDLAMFWSIPNGTGFYLSDAVAIEKANEL
          AFF.RAF..I..A.I..S.INLCGSHC..SI.EDG..QM.LEDLAMFW.IPNGT.FYLSDAVA.EK..EL
Retrocopy AFFRRAFN*IHMAAIYDSNINLCGSHCGLSISEDGPPQMALEDLAMFWNIPNGTVFYLSDAVATEKMVEL

Parental  AANTKDICFIRNSCPDNAVIYNNNYNFQIGQAKVVLKSKDDQVTLIGSGVTLHEAFAPAEQLKKEKINIR
          AANTK...FIR.S..DNA.IY.NN..FQI.Q.K.VLKSKD..V..IG...TLHEA.A.AE.L.KE.INI.
Retrocopy AANTKGTSFIRTSYSDNAIIYKNNKHFQIDQVKMVLKSKDNKV--IGAEMTLHEALAAAELLRKENINIW

Parental  VLHLFTIKPLDKKLVLDSVWATHGSILTMEDHYYEXXXXXXXXXATLGKPGITITCLMVGSIPKSRKLEE
          .L..FTIKP.DKKLVLDS...TH..IL.M.DHY.E............G.PGITIT.LMV...P.SRKL.E
Retrocopy MLDSFTIKPRDKKLVLDSAPVTHD*ILAMKDHYHESAIGDIVAATLMGEPGITITLLMVSKVPRSRKLAE

Parental  LLMIFLINKDAII
          LL....I.K.AII
Retrocopy LLKTYGIDKGAII

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Macropus eugenii was not studied using RNA-Seq expression data.

ChIP-Seq

Macropus eugenii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_meug_1397 retrocopy.

TSS

Macropus eugenii was not studied using FANTOM5 data.

Lab

retro_meug_1397 was not experimentally validated.

Homology

Retrocopy orthology:

Macropus eugenii 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,