RetrogeneDB ID: retro_cpor_45

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_1:54874857..54876741(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCPOG00000019878
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: TKT
• Ensembl ID: ENSCPOG00000000072
• Aliases: None
• Description: None

Sequence

>retro_cpor_45
ATGGCCGCAGCTAACGACTCTCAGCCTCATGCGGAGACCGTGCAGGTGCTGCGGGACACGGCCAATCGCCTGCGAATCCA
TTCCATCAGGGCTACTAGCACCTGCGGCTCTGGCCATCCTACGTCGTGCTGCAGTGCAGCTGAGATCATGTCCGTGCTCT
TCTTCCACGCCATGAGGTATAAACAGAGCGACCCGGAGCACCCTGACAACGACAGACTAGTGCTGTCCAAGGGCCACGCC
CCGCCAGTGCTCTACGCCACATGGGCCGAAGTGTGCGACATCTGTCCCTGTGACTTAATGAGCCTGAGGAGGTTTCACTG
CAAACTAGAAGGATACCCCACCCCGCGACTGTCGTTTGTGGATGCGGCCATGGGGTTCCTTGGGCAAGGCCTGGGAGCTG
CGTGCGGAATGGCCTACACCGGCAAGTACTTCGACAAGGCCAGCTACCGGGTGTTCTGCCTCATGGGAGATGGCGAAGCC
GCAGAAGGCTCTGTCTGGGAGGCTTTGGCTTTTGCTGCCCACTATGGTTTGGACAATCTCGTGGCAATCTTTGATGTGAA
CCGCTTGGGACAGAGTGGCACTGCGCCCCTTGAGCACCGCACAGACATTTATAAGAATCGCTGTGAAGCTTTTGGGTGGA
ATGCTTACATTGTGGATGGTCATGATGTGGAGGCTTTGTGCCAAGCATTTTGGCAAGCAGCTCATGTGAAGAATAAACCC
ACCGCTATAATTGCTAAGACCTTCAAGGGTCGGGGTATTCCAAACATTGAGGATGCAGACTATTGGCATGGAAAGCCAAT
GCCAAAGGAGAGAGCAGATGCAATTATCAAATTAATTGAGAGTCAGATACAGACTAACAGAAATCTCACACCGAAACCCC
CTATTGAAGATTCACCTCAGATCAACATCTCTCATATAAAAATGACCTCTCTGCCTGCCTACAAAGTTGGTGAGAAGATA
GCTACTACGGAAGCATATGGAATAGCTCTGGCTAAATTGGGCCACGCATGTGAAAGAGTTATTGCTCTGGATGGGGACAC
GAAGAACACCACCTTTTCTGAGATATTTAAGAAAGATCACCCTGAGCGTTTCATCGAGTGTTTTATTGCTGAGCAAAATA
TGGTAAGTGTGGCCCTGGGCTGTGCCACACGGGACAGAACCATTGTTTTTGTTAGTACGTTTGCTGCCTTTTTGACCCGA
GCATTTGGTCAGATCCGAATGGGAGCCATCTCTCAAACCAGTATCAACCTTGTTGGTTCTCACTGTGGGGTGTCTGTTGG
TGAAGATGGACCTGCTCAGATGGCCCTGGAGGATCTAGCCATGTTCCGAAGCACTCCCAATTGCACGATTTTCTGTCCAA
GTGATGCAGTCTCAACAGAGCATGCTGTTTGTCTGGCTGCCAATACTAAGGGCATGTGCTTCATTCGTATCAGCCAGCTG
GAAACTGCAGTTATTTACCCTCCAGAAGAAAATTTTGAGATTGGACAGGCCAAAGTGGTTCACTACAGCGTCGATGACAA
GGTCACAGTTATTGGAGCTGGAGTTACTCTACATGAAGCCTTAGCAGCTGCTGCTGATCTTTCTCAACAAGGTATTTCTA
TTCGTGTCATTGACCCATTTACTATTAAACCTCTGGATGCTGCCACTATCATTTCCAATGCCAGAACCACTGGTGGCCGG
ATTATCACAGTGGAAGATCACTACAGAGAAGGTGGCATTGGAGAAGCTGTGTGTGCGGCTGTCTCCAGAGAGCCTGACAT
CTCTGTTCATCAGTTGGCGGTCACAGAAGTACCTCGGAGGGGAAACCCTGGTGAACTGCTGGATATGTTTGGAATCAGTG
CCAAACACATCATAAAAGCTGTGAAATCTACTTTAATGAACTAA

Alignment

ORF - retro_cpor_45 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.0 %
• Parental protein coverage: 99.5 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  IRLSSLPGRSHPTSCCSAAEIMAVLFFHTMRYKALDPRNPHNDRFILSKGHAAPILYAVWAEAGFLPEAE
          IR..S..G..HPTSCCSAAEIM.VLFFH.MRYK..DP..P.NDR..LSKGHA.P.LYA.WAE........
Retrocopy IRATSTCGSGHPTSCCSAAEIMSVLFFHAMRYKQSDPEHPDNDRLVLSKGHAPPVLYATWAEVCDICPCD

Parental  LLNLRKISSDLDGHPVPKQAFTDVATGSLGQGLGAACGMAYTGKYFDKASYRVYCMLGDGELSEGSVWEA
          L..LR.....L.G.P.P...F.D.A.G.LGQGLGAACGMAYTGKYFDKASYRV.C..GDGE..EGSVWEA
Retrocopy LMSLRRFHCKLEGYPTPRLSFVDAAMGFLGQGLGAACGMAYTGKYFDKASYRVFCLMGDGEAAEGSVWEA

Parental  MAFAGIYKLDNLVAILDINRLGQSDPAPLQHQLDIYQKRCEAFGWHAIIVDGHSVEELCKAFGQARH---
          .AFA..Y.LDNLVAI.D.NRLGQS..APL.H..DIY..RCEAFGW.A.IVDGH.VE.LC.AF.QA.H...
Retrocopy LAFAAHYGLDNLVAIFDVNRLGQSGTAPLEHRTDIYKNRCEAFGWNAYIVDGHDVEALCQAFWQAAHVKN

Parental  QPTAVIAKTFKGRGITGIEDKELWHGKPLPKNMAEEIIQEIYSQIQSKKKIMATPPQEDAPSVDIANIRM
          .PTA.IAKTFKGRGI..IED...WHGKP.PK..A..II..I.SQIQ........PP.ED.P...I..I.M
Retrocopy KPTAIIAKTFKGRGIPNIEDADYWHGKPMPKERADAIIKLIESQIQTNRNLTPKPPIEDSPQINISHIKM

Parental  PSPPNYKVGDKIATRKAYGQALAKLGHSSDRIIALDGDTKNSTFSEIFKKEHPDRFIECYIAEQNMVSIA
          .S.P.YKVG.KIAT..AYG.ALAKLGH...R.IALDGDTKN.TFSEIFKK.HP.RFIEC.IAEQNMVS.A
Retrocopy TSLPAYKVGEKIATTEAYGIALAKLGHACERVIALDGDTKNTTFSEIFKKDHPERFIECFIAEQNMVSVA

Parental  VGCATRNRTVPFCSTFAAFFTRAFDQIRMAAISESNINLCGSHCGVSIGEDGPSQMALEDLAMFRAVPMS
          .GCATR.RT..F.STFAAF.TRAF.QIRM.AIS...INL.GSHCGVS.GEDGP.QMALEDLAMFR..P..
Retrocopy LGCATRDRTIVFVSTFAAFLTRAFGQIRMGAISQTSINLVGSHCGVSVGEDGPAQMALEDLAMFRSTPNC

Parental  TVFYPSDGVATEKAVELAANTKGICFIRTSRPENAIIYSNSEDFQVGQAKVVLKNKDDQVTVIGAGVTLH
          T.F.PSD.V.TE.AV.LAANTKG.CFIR.S..E.A.IY...E.F..GQAKVV....DD.VTVIGAGVTLH
Retrocopy TIFCPSDAVSTEHAVCLAANTKGMCFIRISQLETAVIYPPEENFEIGQAKVVHYSVDDKVTVIGAGVTLH

Parental  EALAAAELLKKDKINIRVLDLFTVKPLDTKLILDSARVTKGRILTVEDHYYEGGIGEAVSAAVVGEPGVT
          EALAAA..L....I.IRV.D.FT.KPLD...I...AR.T.GRI.TVEDHY.EGGIGEAV.AAV..EP...
Retrocopy EALAAAADLSQQGISIRVIDPFTIKPLDAATIISNARTTGGRIITVEDHYREGGIGEAVCAAVSREPDIS

Parental  VTRLAVSQVPRSGKPAELLKMFGIDKDAIAQAVRGLI
          V..LAV..VPR.G.P.ELL.MFGI....I..AV....
Retrocopy VHQLAVTEVPRRGNPGELLDMFGISAKHIIKAVKSTL

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	156.50 RPM
SRP017611_kidney	0.00 RPM	217.75 RPM
SRP017611_liver	0.00 RPM	158.52 RPM
SRP040447_lung	0.00 RPM	263.61 RPM
SRP040447_skeletal_muscle	0.00 RPM	25.75 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_45 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_45 was not experimentally validated.

Homology

Retrocopy orthology:

Cavia porcellus 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,