RetrogeneDB ID: retro_sscr_996

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 8:55592169..55593995(-)
• Located in intron of: ENSSSCG00000008891

Retrocopy information

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

Parental gene information

• Parental gene symbol: TKT
• Ensembl ID: ENSSSCG00000021408
• Aliases: None
• Description: Sus scrofa transketolase (TKT), mRNA. [Source:RefSeq mRNA;Acc:NM_001112681]

Sequence

>retro_sscr_996
GACACAGCCACTGCACAGGTGCTGCAGGACGTGGCCAACCGCCTGCACATCCATTGCATCAGAGCCATATGTGCCTCTGG
CTCTGGCCACCCCACTTAGTGCTGCAGTGCTGCTGAGATCATGTCGGTGCTATATTTTCACACCATGAAGTACAGACAGA
TGGAGCCAAGACACCCGGACAACGACAGGTTCATCCTCTCCAAGGGCCATGCGGCCCCACTCCTCTACGCCGCCTGGGTA
GAGGCGGGAGGCATTAGTGAGCCTGACCTGCTGAATCTGCGGACCATTAACTGCGACTTAGAGGGACATCCCACCCCCAG
ACTGTCATTCGTGGATGTGGCAACCGGGTCGCTGGGCCAAGGACTGGGGGCCGCGTGCGGAATGGCTTTTACTGGCAAGT
ACTTGGACAGGGCCAGCTACTGGGTGTTCTGCCTCTTGGGCGATGGCGAGTCCTCAGAAGGCTCTGTCTGGGAAGCTCTG
GCCTTTGCATCCCACTACAATTTGGGCAATCTGGTGGCAGTCTTTGACGTGAACCGCTTGGGGCAGAGTGGCATGGCGCC
CCTTGCGCACTGCATGGATACCTATCAGAGTCGCTGTGAAGACTTTGGGTGGAATACTTACCTAGTGGACGGCCACGACT
TGGAGGCCTTGTGCCTTGCGTTTTGCCAGGCAGCTCAAGTGAAGACAAAGCCCACTGCCATAATTGCGAAGACGTTCAAG
GGCCGGGGGATTCCAGACGTTGAGGATGCAGAAAATTGGCATGGAAAGCCAATGCCTACAGAAAGAGCAGATGAGGTCAT
CAGACTAATTGAGAGTCAGATACAGACTAACAAGAATCCGATACCCAACCCACCTGCTGAAGGCTCCACTCAGATCAGCA
TCATCACGAATATAAAAATGACCTGTCCGCCTGGTTATAAAGTTGGCAACAAGATAGCTACTCAGCAAGCTTATAGTTTG
GCTCTAATTAAACTGGGCCGTGCAAACGAAAGAGTTGTTGTCCTGGATGGTGATCCAAAGAACTCCACCTTTTCTGAGAT
ATTCAAGAAGGAACACCCTGAGCATTTCACTGCAGAACAGAACATGGTCAGTGTGGCACTGGCTTTGCTGCCCGGGGTCG
AACTATTGCTTTTGTTAGTACCTTAGCTGCCTTTCTCACAAGAGCCTTTGATCAGATCCGGATGGGAGCCATATCTCAAA
CCAATATCAATCTTATTGCTTCCCACTGTGGGGTGTCAGTGGGTGAATTTGGACCCCCCAAGCTGACCCTGGAAGATCTA
GCTATGTTCCGAAGCGTTCCCAATTGCACGGTTTTCTACCCACGTGATGCCGTCTCCACGGAGCATGCTGTCTACCTGGC
TGCCAGTTCCAAAGGAATGTGCTTCATTCGCACCAGAGGACCAGAAACTGCAGTTATTTACACCCCCCAAGAAAATTTCG
AGATTGGACAGGCCAAGGTTATCCGAAGCAGTGTTAATGACAAAGTCACAGTTATTAGAGCTGGCATTACCCTGCATGAA
GCCTTAGCAGCTGCAGATGCCCTTTTCCAACAAGGTATTTCTGTCCGAATCATTGACCCGTTTACCATTAAACCCCTGGA
CACTGCCACCATTATCTCCAGCGCAAAAGCCACAGGTGGCCGGATAATCACAGTGGAGGATCACTACCAGGAAGGTGGTC
TTGGAGAAGCTGTGTGTGCAGCCGTCTCTGGGGAGCCGGACATCCACATACATCAGCTGGCAGTGTCTGGAATGCCTCAA
AGTGGAAAACCTAGTGAATTGCTGGATGTGTTTGGGATCAGTGCTAGACACATCTAATCGGCTGTG

Alignment

ORF - retro_sscr_996 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.5 %
• Parental protein coverage: 97.75 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  DQQKLQALKDTANRLRISSIQATTAAGSGHPTSCCSAAEIMAVLFFHTMRYKAQDPRNPHNDRFVLSKGH
          D....Q.L.D.ANRL.I..I.A..A.GSGHPT.CCSAAEIM.VL.FHTM.Y....PR.P.NDRF.LSKGH
Retrocopy DTATAQVLQDVANRLHIHCIRAICASGSGHPT*CCSAAEIMSVLYFHTMKYRQMEPRHPDNDRFILSKGH

Parental  AAPILYSVWAEAGFLPEAELLNLRKISSDLDGHPVPKQAFTDVATGSLGQGLGAACGMAYTGKYFDKASY
          AAP.LY..W.EAG...E..LLNLR.I..DL.GHP.P...F.DVATGSLGQGLGAACGMA.TGKY.D.ASY
Retrocopy AAPLLYAAWVEAGGISEPDLLNLRTINCDLEGHPTPRLSFVDVATGSLGQGLGAACGMAFTGKYLDRASY

Parental  RVYCLLGDGELSEGAVWEAMAFAGIYKLDNLVAILDINRLGQSDPAPLQHQMDVYQKRCEAFGWHAIIVD
          .V.CLLGDGE.SEG.VWEA.AFA..Y.L.NLVA..D.NRLGQS..APL.H.MD.YQ.RCE.FGW....VD
Retrocopy WVFCLLGDGESSEGSVWEALAFASHYNLGNLVAVFDVNRLGQSGMAPLAHCMDTYQSRCEDFGWNTYLVD

Parental  GHSVEELCKAF---GQVKNQPTAIIAKTFKGRGITGVEDKESWHGKPLPQNMADQVIQEIYSQIQNKKKI
          GH..E.LC.AF....QVK..PTAIIAKTFKGRGI..VED.E.WHGKP.P...AD.VI..I.SQIQ..K..
Retrocopy GHDLEALCLAFCQAAQVKTKPTAIIAKTFKGRGIPDVEDAENWHGKPMPTERADEVIRLIESQIQTNKNP

Parental  LATPPQEDAPSVD-ITNIRMPTPPSYKVGDKIATRKAYGQALAKLGHASDRIIALDGDTKNSTFSELFKK
          ...PP.E.......ITNI.M..PP.YKVG.KIAT..AY..AL.KLG.A..R...LDGD.KNSTFSE.FKK
Retrocopy IPNPPAEGSTQISIITNIKMTCPPGYKVGNKIATQQAYSLALIKLGRANERVVVLDGDPKNSTFSEIFKK

Parental  EHPDRFIECYIAEQNMVSIAV-GCATRNRTVPFCSTFAAFFTRAFDQIRMAAISESNINLCGSHCGVSIG
          EHP..F.....AEQNMVS.A..G.A.R.RT..F.ST.AAF.TRAFDQIRM.AIS..NINL..SHCGVS.G
Retrocopy EHPEHF----TAEQNMVSVAL<GFAARGRTIAFVSTLAAFLTRAFDQIRMGAISQTNINLIASHCGVSVG

Parental  EDGPSQMALEDLAMFRSVPMSTVFYPSDGVATEKAVELAANTKGICFIRTSRPENAIIYNNNEDFQIGQA
          E.GP....LEDLAMFRSVP..TVFYP.D.V.TE.AV.LAA..KG.CFIRT..PE.A.IY...E.F.IGQA
Retrocopy EFGPPKLTLEDLAMFRSVPNCTVFYPRDAVSTEHAVYLAASSKGMCFIRTRGPETAVIYTPQENFEIGQA

Parental  KVVLKSKDDQVTVIGAGVTLHEALAAADLLKKEKINIRVLDPFTVKPLDRKLILDSARATKGRILTVEDH
          KV...S..D.VTVI.AG.TLHEALAAAD.L....I..R..DPFT.KPLD...I..SA.AT.GRI.TVEDH
Retrocopy KVIRSSVNDKVTVIRAGITLHEALAAADALFQQGISVRIIDPFTIKPLDTATIISSAKATGGRIITVEDH

Parental  YYEGGLGEAVAAAVVGEPDVTVTRLAVSQVPRSGKPAELLKMFGIDKDAIARAV
          Y.EGGLGEAV.AAV.GEPD.....LAVS..P.SGKP.ELL..FGI....I..AV
Retrocopy YQEGGLGEAVCAAVSGEPDIHIHQLAVSGMPQSGKPSELLDVFGISARHI*SAV

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
SRP014902_placenta	2.65 RPM	216.75 RPM
SRP014902_testis	0.14 RPM	204.39 RPM
SRP018288_heart	0.00 RPM	15.11 RPM
SRP018288_kidney	0.00 RPM	202.03 RPM
SRP018288_liver	0.00 RPM	104.42 RPM
SRP018288_lung	0.10 RPM	266.58 RPM
SRP018856_adipose	0.37 RPM	487.43 RPM
SRP035408_brain	0.03 RPM	204.00 RPM
SRP035408_liver	0.00 RPM	124.64 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_996 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_996 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_996 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,