RetrogeneDB ID: retro_btau_176

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 6:2146518..2148399(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSBTAG00000008947
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: TKT
• Ensembl ID: ENSBTAG00000003758
• Aliases: None
• Description: transketolase [Source:RefSeq peptide;Acc:NP_001003906]

Sequence

>retro_btau_176
ATGGCGGACAGCGCGACACTGGACGCGACCACAGTGCAAGTGCTGCAGGACCTGGCCAACCGCCTGCGCGTCCATTCCAT
CAGGGCTACATGTGCCTCTGGCTCCGGCCACCCCACGTCGTGCTGCAGTGCGGCAGAGATCGTGTCGGTGCTTTTCTTCC
ACACGATGAGGTACAGACAGACTGAGCCCGCGCACCCCGACAACGACAGATTCGTCCTTTCCAAGGGTCATGCCGCTCCA
CTGCTCTATGCTGCCTGGGTGGAGGCAGGCAGCATCAGTGAACCTGACCTGCTGAACTTGAGGACAATTCATTGCGACCT
TGAGGGACACCCCACCCCCAGGCTGTCGTTTGTGGATGTGGCGACAGGATCGCTCGGGCAAGGTTTGGGGGCTGCATGTG
GAATGGCTTATACTGGCAAGTACTTGGACAAAGCCAGCTACCGGGTATTCTGCCTCCTGGGCGACGGTGAGTCCTCAGAA
GGCTCCGTCTGGGAAGCTTTGGCTTTTGCTTCCCACTACGGTTTGGACAATCTCGTAGCAGTGTTCGACGTGAACCGCTT
GGGGCAAAGTGGCGTTGCGCCCCTGAAGCACTGCACAGACATCTATCGGAATCGCTGCGAGGCCTTTGGGTGGAATACTT
ACTTAGTAGATGGCCATGATGTGGAGGCGTTGTGCCAGGCTTTTTCTCAAGCTGCTCAAGGGAAGAACAAGCCCACTGCC
ATAATTGCAAAGACCTACAAGGGCCGGGGTATTCCAAATGTTGAGGATGCAGAAAATTGGCATGGAAAGCCACTGCCAAA
AGAAAGAGCAGATGAAATCATTAGACTAATTAAAAGTCAGATAAAGACCAACAGGAATCTCCTACCAAAACCTCCTGTTG
AAGGCTCACCTCCAGTCAGCATCACAAATATAAAAATGACCTGTTTGCCTGATTATAAAGTTGGTGACAAGGTAGCTACT
CAGAAAGCATATGGTTTGGCTCTGGCTAAACTCGGCCTTGCAAATGAAAGAGTTGTTGTCCTGGATGGTGACCCAAAGAA
CTCCACCTTTTTTGAAATATTCAAGAAAGAACATCCTGAGCGTTTTATTGAGTGTTTTGCTGCGGAACAAAACATGGTGA
GTGTGGCACTGGGCTGTGCCACACGTGGTCGAACCATTACTTTTGTTACTACTTTAGGTGCCTTTTTGACTAGAGCATTT
GATCAGATCCGGATGGGAGCCATATCTCAAAGTAATATAAATCTTATTGGTTCTCACTGTGGGGTGTCTGTTGGTGAAGA
TGGCCCTTCCCAGATGGCTTTGGAAGATCTAGCCATGTTCCGGAGCATTCCCAATTGCACTGTTTTCCTCCCAAGTGATG
CTGTCTCGACAGAGCATGCTGTTTATCTGGCTGCCAATAGCGAAGGAATGTGCTTCATTCGGACCAACCGATCAGAAACT
GCAGTTATTTATACCCCACAAGAACATTTTGAGATTGGAAGGGCCAAGGTCATCCGCCACAGTAATAATGACAAAGTCAC
AGTAATTGGAGCTGGAGTTACTCTGCATGAAGCCTTAGCAGCTGCTGATGCTCTTTCTCAGCAAGATATTTCTATCTGTG
TTATTGACCCATTTACCATTAAACCCCTGGATGCTGCCACCATCATCTCCTGTGCAAAAGCTACTGATGGCCGGGTTGTC
ACAGTGGAAGATCATTACCAGGAAGGTGGCATTGGCGAAGCCGTGTGTGCAGCAGTGTCTGGGGAGCCTGCCATCCATGT
TCATCAGCTATCGGTGTCAGGAGTGTCTGAAAGAAACAGGAAACCTAGTGAATTACTGAGTATATTTGGTGTCAGTGCAA
GACACATCATAGCAGCTGTGAAATATACTTTAATGAACTAA

Alignment

ORF - retro_btau_176 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.75 %
• Parental protein coverage: 97.91 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  DQQKLQALKDTANRLRISSIQATTAAGSGHPTSCCSAAEIMAVLFFHTMRYKALDPRNPHNDRFVLSKGH
          D....Q.L.D.ANRLR..SI.AT.A.GSGHPTSCCSAAEI..VLFFHTMRY....P..P.NDRFVLSKGH
Retrocopy DATTVQVLQDLANRLRVHSIRATCASGSGHPTSCCSAAEIVSVLFFHTMRYRQTEPAHPDNDRFVLSKGH

Parental  AAPILYAVWAEAGFLPESELLNLRKISSDLDGHPVPKQAFTDVATGSLGQGLGAACGMAYTGKYFDKASY
          AAP.LYA.W.EAG...E..LLNLR.I..DL.GHP.P...F.DVATGSLGQGLGAACGMAYTGKY.DKASY
Retrocopy AAPLLYAAWVEAGSISEPDLLNLRTIHCDLEGHPTPRLSFVDVATGSLGQGLGAACGMAYTGKYLDKASY

Parental  RVYCMLGDGELSEGSVWEAMAFASIYKLDNLVAILDINRLGQSDPAPLQHQMDIYQKRCEAFGWNAVIVD
          RV.C.LGDGE.SEGSVWEA.AFAS.Y.LDNLVA..D.NRLGQS..APL.H..DIY..RCEAFGWN...VD
Retrocopy RVFCLLGDGESSEGSVWEALAFASHYGLDNLVAVFDVNRLGQSGVAPLKHCTDIYRNRCEAFGWNTYLVD

Parental  GHSVEELCKAFGQV---KNQPTAIIAKTFKGRGITGIEDKESWHGKPLPKNMADQIIQEISGQIQSKKKI
          GH.VE.LC.AF.Q....KN.PTAIIAKT.KGRGI...ED.E.WHGKPLPK..AD.II..I..QI......
Retrocopy GHDVEALCQAFSQAAQGKNKPTAIIAKTYKGRGIPNVEDAENWHGKPLPKERADEIIRLIKSQIKTNRNL

Parental  LATPPEEDAPSVDITNIRMPTPPNYKVGDKIATRKAYGQALAKLGHASNRIIALDGDTKNSTFSELFKKE
          L..PP.E..P.V.ITNI.M...P.YKVGDK.AT.KAYG.ALAKLG.A..R...LDGD.KNSTF.E.FKKE
Retrocopy LPKPPVEGSPPVSITNIKMTCLPDYKVGDKVATQKAYGLALAKLGLANERVVVLDGDPKNSTFFEIFKKE

Parental  HPDRFIECYIAEQNMVSIAVGCATRDRTVPFCSTFAAFFTRAFDQIRMAAISESNINLCGSHCGVSIGED
          HP.RFIEC..AEQNMVS.A.GCATR.RT..F..T..AF.TRAFDQIRM.AIS.SNINL.GSHCGVS.GED
Retrocopy HPERFIECFAAEQNMVSVALGCATRGRTITFVTTLGAFLTRAFDQIRMGAISQSNINLIGSHCGVSVGED

Parental  GPSQMALEDLAMFRSIPTSTVFYPSDGVATEKAVELAANTKGICFIRTSRPENAIIYNNNEDFQIGQAKV
          GPSQMALEDLAMFRSIP..TVF.PSD.V.TE.AV.LAAN..G.CFIRT.R.E.A.IY...E.F.IG.AKV
Retrocopy GPSQMALEDLAMFRSIPNCTVFLPSDAVSTEHAVYLAANSEGMCFIRTNRSETAVIYTPQEHFEIGRAKV

Parental  VLKNKDDQVTVIGAGVTLHEALAAADLLKREKINIRVLDPFTIKPLDKKLILDSARATKGRILTVEDHYY
          ......D.VTVIGAGVTLHEALAAAD.L....I.I.V.DPFTIKPLD...I...A.AT.GR..TVEDHY.
Retrocopy IRHSNNDKVTVIGAGVTLHEALAAADALSQQDISICVIDPFTIKPLDAATIISCAKATDGRVVTVEDHYQ

Parental  EGGIGEAVASAVVGEPGVTVTRLAVSQV-PRSGKPAELLKMFGIDRDAIAQAVR
          EGGIGEAV..AV.GEP...V..L.VS.V..R..KP.ELL..FG.....I..AV.
Retrocopy EGGIGEAVCAAVSGEPAIHVHQLSVSGVSERNRKPSELLSIFGVSARHIIAAVK

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
ERP005899_liver	0.36 RPM	16.73 RPM
ERP005899_muscle	0.05 RPM	358.97 RPM
SRP017611_brain	0.46 RPM	110.77 RPM
SRP017611_kidney	0.30 RPM	143.97 RPM
SRP017611_liver	0.08 RPM	34.36 RPM
SRP030211_testis	67.46 RPM	49.24 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

5 EST(s) were mapped to retro_btau_176 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
BM481098	2147374	2147788	100	414	0	414
DT836569	2146496	2147358	100	862	0	862
DY110973	2146515	2146833	100	318	0	318
DY161828	2146515	2146781	99.3	264	2	262
EV610427	2146498	2147159	99.9	659	1	657

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_176 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_176 has 6 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_47
Pan troglodytes	retro_ptro_126
Macaca mulatta	retro_mmul_74
Mus musculus	retro_mmus_220
Oryctolagus cuniculus	retro_ocun_62
Equus caballus	retro_ecab_6

---

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,