RetrogeneDB ID: retro_cjac_2128

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 3:28244111..28245605(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000012463
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: TKT
• Ensembl ID: ENSCJAG00000007253
• Aliases: None
• Description: None

Sequence

>retro_cjac_2128
CCACGACTGCCATTTGTTGACGTGGCAACAGGGTCCCTAGGGCAGGGAGTCGGTGTTGCATGTGGAATGGCTTATACTGG
CAAGTACCTTGACAAGGCCAGCTACCGGGTATTCTGCCTTATGGGAGCTGGTGAAGCCTCAGAAGGCTCTGTGTGGGAGG
CTTTTGCCTTTGCCTCCCACTACAACTTGGACAATCTCGTGGTGGTCTTCGAAGTGAACCGCTTGGGACAAAGTGGCCCT
GCACCCCTTGAGCACTGCACAGACATCTATCAGAATCGCTGTGAAGCCTTTGGATGGAATACTTACTTAGTGGATGGCCA
TGATGTGGAGGCCTTATGCCAAGCATTTTGGCAAGCAAGTCAAGTGAAGAACAAGCCTACTGCTATAGTTGCCAAGACCT
TCAAAGGTCGGGGTATTCCAAATATTGAGGATACAGAAAATTGGCATGGAAAGCCAGTGCCAAAAGAAAGAGCAGATGCA
ATTATCAAATTAATTGAGAGTCAGATACAGACCAATGAGAATCTCATACCAAAATCCCCTGTGGAAGACTCACCTCAAAT
CAGCATCACAGATATAAAAATGACCACCCCACCTGCTTACAAAATTGGTGACAAGATAGCTACTCAGGGAACATTTGGTT
TGGCTCTGGCTAAACTGGGCCGTGCAAATGAAAGAGTTATTGTTCTGAGTGGTGACACGGTGAACTCCACCTTTTCTGAG
ACATTCAAGAAACAACACCCTGAGCGTTTCATAGAGTGTGTTATTGCAGAGCAAAACATGGTAAGTGTGGCACTAGGCTG
TGCCACACGTGGTCGAACCATTGCTTTTGCTAGTGCGTTTGCTGCCTTTTTTACTAGAGCATTTGATCAGCTCCGAATGG
GAGCCAATTCTCAAGCCAATATCAACCTTACTGGTTCCCACTGTGTGATATCTGCTGGAGAAGACGGACCCTCCTGGATA
GCCCTGGAGGATCTAGCCGTGTTCCGAAGCATTCCCAGTTGCACTGTTTTCTATCCAAGTGATGCCATCTTGACAGAGCA
TGCTGTTTATCTAGCTGCCAATACCAAGGGAATATGCTTCATTCGAACCAGCCAACCAGAAACTGCAGTTATTTATACTC
CACAAGGAAATTTTGAGATTGGCTGGGCCAAGGTGGCCTGCCACAGTGTCGATGATAAAATCACAGTTATTGGAGCTGGA
GTTACTCTCCATGAAGCCTTAGCAGCTGCTGACCATCTTTCTCAACAAGGTATTTCTGTCCGTGTCATCGACCCTTTTAC
AATTAAACCCCTGGATGCCGCCACCATCATCTCCAATGCAAAAGCCACAGGCGGCCGAGTTATCACAGTGGAGGATCACT
GCAGGGAAGGTGGCATTGGAGAAGCTGTTTGTGCAGCTGTCTCCGGGGAGCCTGATATCCTTGTTCATCAGCTGGCAGTG
TCAGGAGTGCCTCAAAGTGAGAAAACGAGTGAATTCCTGGCTATGTCTGGAATC

Alignment

ORF - retro_cjac_2128 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.06 %
• Parental protein coverage: 83.33 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  PKQAFTDVATGSLGQGLGAACGMAYTGKYFDKASYRVYCLLGDGELSEGSVWEAMAFASIYKLDNLVAIL
          P...F.DVATGSLGQG.G.ACGMAYTGKY.DKASYRV.CL.G.GE.SEGSVWEA.AFAS.Y.LDNLV...
Retrocopy PRLPFVDVATGSLGQGVGVACGMAYTGKYLDKASYRVFCLMGAGEASEGSVWEAFAFASHYNLDNLVVVF

Parental  DINRLGQSDPAPLQHQMDIYQKRCEAFGWHAIIVDGHSVEELCKAFGQA---KHQPTAIIAKTFKGRGIS
          ..NRLGQS.PAPL.H..DIYQ.RCEAFGW....VDGH.VE.LC.AF.QA...K..PTAI.AKTFKGRGI.
Retrocopy EVNRLGQSGPAPLEHCTDIYQNRCEAFGWNTYLVDGHDVEALCQAFWQASQVKNKPTAIVAKTFKGRGIP

Parental  GVEDKESWHGKPLPKNMADQIIQEIYSQIQSKKKILATPPQEDAPSVDIANIHMPSPPSYKVGDKIATRK
          ..ED.E.WHGKP.PK..AD.II..I.SQIQ.........P.ED.P...I..I.M..PP.YK.GDKIAT..
Retrocopy NIEDTENWHGKPVPKERADAIIKLIESQIQTNENLIPKSPVEDSPQISITDIKMTTPPAYKIGDKIATQG

Parental  AYGQALAKLGHASDRIIALDGDTKNSTFSELFKKEHPDRFIECYIAEQNMVSIAVGCATRSRTVPFCSTF
          ..G.ALAKLG.A..R.I.L.GDT.NSTFSE.FKK.HP.RFIEC.IAEQNMVS.A.GCATR.RT..F.S.F
Retrocopy TFGLALAKLGRANERVIVLSGDTVNSTFSETFKKQHPERFIECVIAEQNMVSVALGCATRGRTIAFASAF

Parental  AAFFTRAFDQIRMAAISESNINLCGSHCGVSIGEDGPSQMALEDLAMFRSVPMSTVFYPSDGVATEKAVE
          AAFFTRAFDQ.RM.A.S..NINL.GSHC..S.GEDGPS..ALEDLA.FRS.P..TVFYPSD...TE.AV.
Retrocopy AAFFTRAFDQLRMGANSQANINLTGSHCVISAGEDGPSWIALEDLAVFRSIPSCTVFYPSDAILTEHAVY

Parental  LAANTKGICFIRTSRPENAIIYNNNEDFQVGQAKVVLKSKDDQVTVIGAGVTLHESLAAAELLKKEKINI
          LAANTKGICFIRTS.PE.A.IY.....F..G.AKV...S.DD..TVIGAGVTLHE.LAAA..L....I..
Retrocopy LAANTKGICFIRTSQPETAVIYTPQGNFEIGWAKVACHSVDDKITVIGAGVTLHEALAAADHLSQQGISV

Parental  RVLDPFTIKPLDRKLILDSARATKGRILTVEDHYYEGGIGEAVSTAVVGEPGITVTRLAVHRVPRSGKPA
          RV.DPFTIKPLD...I...A.AT.GR..TVEDH..EGGIGEAV..AV.GEP.I.V..LAV..VP.S.K..
Retrocopy RVIDPFTIKPLDAATIISNAKATGGRVITVEDHCREGGIGEAVCAAVSGEPDILVHQLAVSGVPQSEKTS

Parental  ELLKMFGI
          E.L.M.GI
Retrocopy EFLAMSGI

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
SRP051959_colon	0.00 RPM	65.94 RPM
SRP051959_heart	0.00 RPM	22.56 RPM
SRP051959_kidney	0.00 RPM	55.71 RPM
SRP051959_liver	0.00 RPM	103.86 RPM
SRP051959_lung	0.00 RPM	27.36 RPM
SRP051959_lymph_node	0.00 RPM	23.63 RPM
SRP051959_skeletal_muscle	0.00 RPM	4.96 RPM
SRP051959_spleen	0.02 RPM	31.01 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2128 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2128 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2128 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,