RetrogeneDB ID: retro_rnor_146

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 16:24833388..24835272(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSRNOG00000014185
• Aliases: Tktl2, RGD1304767
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: Tkt
• Ensembl ID: ENSRNOG00000016064
• Aliases: None
• Description: transketolase [Source:RefSeq peptide;Acc:NP_072114]

Sequence

>retro_rnor_146
ATGGCCTTGGCTAGAGATGCCAAGCTGGAGTCAGACATCTTTCAGGCGCTTCAGGATGTGGCCAATCGCCTGCGAATCCA
CTCAATCAGGGCCACGTGTGCCTCCAGCTCCGGACATCCCACATCGTGCTGTAGTGCGGCCGAGATCATGGCTGTGCTCT
TCTTCCATACCATGAGGTACAAACAGGCAGACCCAGAACACCCGGACAACGACCGCTTCGTCCTCTCCAAGGGCCACGCG
GCGCCCATCCTCTATGCGGTTTGGGTGGAGGTGGGCCGTATCTGTGAATCGGACTTGCTGAACTTGCGAAAAATTCACTG
CGACCTGGAGGGTCATCCCACCCCTCGGCTATCGTTTGTGGATGTTGCAACAGGGTCCCTTGGGCAAGGACTGGGTGCTG
CCTGCGGAATGGCTTACACCGGCAAGTACTTTGACAAGGCCAGCTACCGCGTGTTCTGCCTCATGGGGGATGGTGAGTCC
TCTGAAGGTTCTGTCTGGGAGGCCTTGGCCTTCGCTTCCCACTACAAGTTGGACAATCTCCTGGCAATCTTTGACGTGAA
CCGCCTGGGGCAAAGCGGCACAGCACCCCTAGAGCACTGTACCGACATCTACGAGACGCGCTGCCAAGCGTTTGGGTGGA
ATACTTACGTGGTGGATGGTCACGATGTTGAAGCTCTCTGCCAGGCCTTTTGGAAAGCAGCTCAAGTCAAGAACAAACCT
ACGGCCCTGATTGCCAAGACCTTCAAGGGCAGAGGTATTCCAAATGTCGAGGATGCGGAAAATTGGCATGGAAAGCCTAT
GCCGAAAGACAGAGTTGATGGAATTGTCAAACTAATTGAAAGTCAGATACAGACAAACCGAAATCTCACCCCGAAGCCCC
CTGTTGAAGACTCACCCCGGATCAGCATATCCAATACGAAAATGACCTCTCTGCCTGCTTACAAACTGGGAGACATGATA
GCTACCCGAGAAGCCTACGGCGTGGCTCTGGCTAAATTGGGCCACTCTAACCAAAGAGTTATTGTTTTAGATGGCGACAC
GAAAAACTCTACCTTTTCGGAGGTATTCAAGAAAGAGCACCCTGAGCGTTTCATAGAGTGCTTCATTGCTGAGCAAAACA
TGGTAAGTGTGGCACTGGGGTGTGCCACACGAGGGCGAACTATTGCTTTCGTTAGTACCTTCGCTGCCTTCCTGACCCGA
GCCTTTGATCAGATCCGAATGGGAGCCATCTCTCAAACCAACGTCAACTTCGTTGGTTCCCACTGCGGGGTGTCTATTGG
AGAAGATGGACCTTCCCAGATGGCCCTGGAGGATCTAGCCATGTTCAGAAGCATCCCCAACTGCACTATTTTCTATCCAA
GCGATGCTGTCTCTACAGAACACGCCATTTATCTGGCAGCCAACACCAAGGGGATGTGCTTCATTCGTACCACCCGGCCC
AAATTAGCGGTTATTTATACATCCGAAGAAAATTTTGTGATTGGACAGGCCAAGGTGATCCGCCACAGTGCAGACGACAA
GGTGACAGTTGTTGGAGCAGGGGTTACTCTGCATGAAGCCTTAGAGGCTGCTGACGAGCTTTCTCAACAAGGGATTTCTA
TCCGTGTCATTGACCCGTTCACTATCAAACCTCTGGATGCTTCCACCATTATCCAAAGTGCCAAAGCCACAGGTGGCCAG
ATCATCACCGTGGAAGATCACTACCGAGAAGGTGGCATTGGGGAGGCTGTGTGTGCGGCCATCTCTAGAGAGCCTGACAT
CGTCGTTCATCAACTTGCAGTAACAGAAGTGCCTCGAAGCGGGAAACCTAGTGAACTACTGGATATGTTTGGAATCAGTG
CCAGACACATTATAGCAGCTGTGAAAGATACCGTAATGAAATGA

Alignment

ORF - retro_rnor_146 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.39 %
• Parental protein coverage: 94.2 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KPDQQKLQALKDTANRLRISSIQATTAAGSGHPTSCCSAAEIMAVLFFHTMRYKALDPRNPHNDRFVLSK
          K......QAL.D.ANRLRI.SI.AT.A..SGHPTSCCSAAEIMAVLFFHTMRYK..DP..P.NDRFVLSK
Retrocopy KLESDIFQALQDVANRLRIHSIRATCASSSGHPTSCCSAAEIMAVLFFHTMRYKQADPEHPDNDRFVLSK

Parental  GHAAPILYAVWAEAGFLPEAELLNLRKISSDLDGHPVPKQAFTDVATGSLGQGLGAACGMAYTGKYFDKA
          GHAAPILYAVW.E.G...E..LLNLRKI..DL.GHP.P...F.DVATGSLGQGLGAACGMAYTGKYFDKA
Retrocopy GHAAPILYAVWVEVGRICESDLLNLRKIHCDLEGHPTPRLSFVDVATGSLGQGLGAACGMAYTGKYFDKA

Parental  SYRVYCMLGDGEVSEGSVWEAMAFAGIYKLDNLVAIFDINRLGQSDPAPLQHQVDVYQKRCEAFGWHAII
          SYRV.C..GDGE.SEGSVWEA.AFA..YKLDNL.AIFD.NRLGQS..APL.H..D.Y..RC.AFGW....
Retrocopy SYRVFCLMGDGESSEGSVWEALAFASHYKLDNLLAIFDVNRLGQSGTAPLEHCTDIYETRCQAFGWNTYV

Parental  VDGHSVEELCKAF---GQAKHQPTAIIAKTFKGRGITGIEDKEAWHGKPLPKNMAEQIIQEIYSQVQSKK
          VDGH.VE.LC.AF....Q.K..PTA.IAKTFKGRGI...ED.E.WHGKP.PK.....I...I.SQ.Q...
Retrocopy VDGHDVEALCQAFWKAAQVKNKPTALIAKTFKGRGIPNVEDAENWHGKPMPKDRVDGIVKLIESQIQTNR

Parental  KILATPPQEDAPSVDIANIRMPTPPNYKVGDKIATRKAYGLALAKLGHASDRIIALDGDTKNSTFSELFK
          .....PP.ED.P...I.N..M...P.YK.GD.IATR.AYG.ALAKLGH...R.I.LDGDTKNSTFSE.FK
Retrocopy NLTPKPPVEDSPRISISNTKMTSLPAYKLGDMIATREAYGVALAKLGHSNQRVIVLDGDTKNSTFSEVFK

Parental  KEHPDRFIECYIAEQNMVSIAVGCATRDRTVPFCSTFAAFFTRAFDQIRMAAISESNINLCGSHCGVSIG
          KEHP.RFIEC.IAEQNMVS.A.GCATR.RT..F.STFAAF.TRAFDQIRM.AIS..N.N..GSHCGVSIG
Retrocopy KEHPERFIECFIAEQNMVSVALGCATRGRTIAFVSTFAAFLTRAFDQIRMGAISQTNVNFVGSHCGVSIG

Parental  EDGPSQMALEDLAMFRSVPMSTVFYPSDGVATEKAVELAANTKGICFIRTSRPENAIIYSNNEDFQVGQA
          EDGPSQMALEDLAMFRS.P..T.FYPSD.V.TE.A..LAANTKG.CFIRT.RP..A.IY...E.F..GQA
Retrocopy EDGPSQMALEDLAMFRSIPNCTIFYPSDAVSTEHAIYLAANTKGMCFIRTTRPKLAVIYTSEENFVIGQA

Parental  KVVLKSKDDQVTVIGAGVTLHEALAAAEMLKKEKIGVRVLDPFTIKPLDKKLILDCARATKGRILTVEDH
          KV...S.DD.VTV.GAGVTLHEAL.AA..L....I..RV.DPFTIKPLD...I...A.AT.G.I.TVEDH
Retrocopy KVIRHSADDKVTVVGAGVTLHEALEAADELSQQGISIRVIDPFTIKPLDASTIIQSAKATGGQIITVEDH

Parental  YYEGGIGEAVSAAVVGEPGVTVTRLAVSQVPRSGKPAELLKMFGIDKDAIVQAVKGLVTK
          Y.EGGIGEAV.AA...EP...V..LAV..VPRSGKP.ELL.MFGI....I..AVK..V.K
Retrocopy YREGGIGEAVCAAISREPDIVVHQLAVTEVPRSGKPSELLDMFGISARHIIAAVKDTVMK

Legend:

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

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP017611_brain	0.00 RPM	126.54 RPM
SRP017611_kidney	0.00 RPM	265.03 RPM
SRP017611_liver	0.00 RPM	187.26 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_146 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_146 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_146 has 0 orthologous retrocopies within eutheria group .

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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,