RetrogeneDB ID: retro_opri_10

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_9763:43835..45719(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOPRG00000017002
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: TKT
• Ensembl ID: ENSOPRG00000009891
• Aliases: None
• Description: transketolase [Source:HGNC Symbol;Acc:11834]

Sequence

>retro_opri_10
GCGATGGCCACTGCCTGCGACGCAGTGCCCAACCCGGCGACCGTGCAGGGGCTGCGGGATGTGGCCAACCGCCTGCGCGT
CCTCGCCATCAGGGCCACGTGTGCCTGCAGCTCGGGCCACCCCACGTCCTGCTGCAGTGCCGCGGAGATCATGGCCGTCC
TCTTCTTCCACACAATGCGGTACAAACAGACGGAGCCCGAGCACCCCGACAACGACCGATTCGTCCTCTCCAAGGGCCAC
GCCGCCCCGGTCCTCTACGCCGCCTGGATGGAGGCTGGCCATGTCAGCGAGGCAGACCTGCTGAACCTGAGGAAAGTGCA
CTGCGACCTGGAGGGGCATCCCACCCCTCGGCTGTCGTTCGTGGACGTGGCCACGGGCTCCCTGGGGCAAGGGCTGGGCG
CTGCGTGCGGAATGGCCTACACCGGCAAGTACTTGGACAAGGCCAGCTACCGCGTGTTCTGCCTCATGGGGGACGGGGAG
TCCTCCGAGGGCTCGGTCTGGGAGGCCCTGGCGTTCGCCTCCCACTACCGTCTGGACAATCTCGTGGCGGTCTTCGACGT
GAACCGCTTGGGGCAAAGCGGCAGCACACCCTTGGGGCACTGCACCGACGTGTACCAGGAGCGCTGTGAAGCCTTTGGGT
GGAATACCTGCTTGGTGGACGGCCACGATGTGGAGGCCTTGTGTCGGGCATTTTGGCAAGCAACCCAGGTACAGAACAAG
CCCACGGCTATCATCGCCAAGACCTTCAAGGGTCGAGGCATCCCGAACATTGAAGACGCAGAAAACTGGCACGGAAAGCC
AGTGCCAAGAGAGAGAGCGGATGCCATTGTCAAGTTGATCGAGAGTCAGATCCAGACCCACAGCAGTCTCATACCCAAAG
CCCCCGTGGAAGACTCCCCTCCGGTCAACATCACGAATATAAAGATGACCTCCCCACCTGCTTACAAAGTCGGCCACGTG
ATGGCCACTCGAAAAGCATGTGGCTTGGCTCTAGCCAAACTGGGTCACGCCCACGAAAGGGTGATCGTCCTGGACGGTGA
CACGAAGAACTCCACCTTCTCCGAGATCTTCAAGAAAGAGCACCCGGAGCGTTTCATCGAATGCTTTATCGCGGAGCAGA
ACATGGTGAGCGTGGCCCTGGGGTGCGCCGCACGTGGTCGGACCGTAGCCTTTGCCAGCACCTTCGCTGCCTTTTTAACT
CGAGCTTTCGATCAGCTCCGAATGGGAGCCATCTCTGAAAGCAACATCAACCTCGTTGGTTCCCACTGCGGCGTGTCCGT
AGGTGAGGACGGCCCTTCCCAGATGGCCCTGGAGGATCTGGCCATGTTCCGAAGCATTCCCGGCTGCACTGTTTTCTACC
CGAGCGACGCGGTCTCCACGGAGCACGCTGTGCGTCTCGCCGCCAACACCAAAGGTATGTGCTTCATCCGCACCAGCAGA
CCAGAAACTGCAGTTCTCTATACTCCGCAAGAAAATTTTGCGGTTGGACAGGCCAAGGTATTGCGCCACAGCGTTGAGGA
CGAGGCCACGGTCATCGGAGCTGGGGTCACTCTGCACGAAGCCTTAGCTGCCGCCGGGGATCTTTCTCAAGAAGGTATTT
CCATTCGGGTCATTGACCTGTTCACCGTGAAGCCCCTGGACGCAGGCACCATCGTCTCCAACGCGAGAGCCACGGGAGGT
CGGCTGCTCACCGTGGAGGACCACTACCCAGAAGGCGGCATCGGAGAAGCGGTGTGCGCAGCCGTCGCCCAGCAGCCGGG
CATCCGTGTCCGGCAGCTGGCAGTGTCCCACGTGCCCCGGAGTGGGAAACCCAGCGAACTGCTGGACATGTTCGGGATTA
GTGCCAGACACATTGCCGAGGCTGTAAAGTGCATGTTGAAGTAG

Alignment

ORF - retro_opri_10 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.2 %
• Parental protein coverage: 98.07 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  PDQQKLQALKDTANRLRISSIQATTAAGSGHPTSCCSAAEIMAVLFFHTMRYKAQDPRNPHNDRFVLSKG
          P.....Q.L.D.ANRLR...I.AT.A..SGHPTSCCSAAEIMAVLFFHTMRYK...P..P.NDRFVLSKG
Retrocopy PNPATVQGLRDVANRLRVLAIRATCACSSGHPTSCCSAAEIMAVLFFHTMRYKQTEPEHPDNDRFVLSKG

Parental  HAAPILYAVWAEAGYLPEAELLNLRKISSDLDGHPVPKQAFTDVATGSLGQGLGAACGMAYTGKYFDKAS
          HAAP.LYA.W.EAG...EA.LLNLRK...DL.GHP.P...F.DVATGSLGQGLGAACGMAYTGKY.DKAS
Retrocopy HAAPVLYAAWMEAGHVSEADLLNLRKVHCDLEGHPTPRLSFVDVATGSLGQGLGAACGMAYTGKYLDKAS

Parental  YRVYCLLGDGELSEGSVWEAMAFASFYKLDNLVAILDVNRLGQSDPTPLQHQVDVYQKRCEAFGWHAIIV
          YRV.CL.GDGE.SEGSVWEA.AFAS.Y.LDNLVA..DVNRLGQS..TPL.H..DVYQ.RCEAFGW....V
Retrocopy YRVFCLMGDGESSEGSVWEALAFASHYRLDNLVAVFDVNRLGQSGSTPLGHCTDVYQERCEAFGWNTCLV

Parental  DGHSVEELCKAFGQA---KHQPTAIIAKTFKGRGITGIEDKESWHGKPLPKNMADQVIQEIHNQIQSKKK
          DGH.VE.LC.AF.QA......PTAIIAKTFKGRGI..IED.E.WHGKP.P...AD.....I..QIQ....
Retrocopy DGHDVEALCRAFWQATQVQNKPTAIIAKTFKGRGIPNIEDAENWHGKPVPRERADAIVKLIESQIQTHSS

Parental  ILATPPQEDAPSVDISNIRMPSPPNYKVGDKIATRKAYGQALAKLGHGSDRIIALDGDTKNSTFSELFKK
          .....P.ED.P.V.I.NI.M.SPP.YKVG...ATRKA.G.ALAKLGH...R.I.LDGDTKNSTFSE.FKK
Retrocopy LIPKAPVEDSPPVNITNIKMTSPPAYKVGHVMATRKACGLALAKLGHAHERVIVLDGDTKNSTFSEIFKK

Parental  EHPDRFIECYIAEQNMVSVAVGCATRNRTVPFCSTFAAFLTRSFDQIRMAAISESNINLCGSHCGVSIGE
          EHP.RFIEC.IAEQNMVSVA.GCA.R.RTV.F.STFAAFLTR.FDQ.RM.AISESNINL.GSHCGVS.GE
Retrocopy EHPERFIECFIAEQNMVSVALGCAARGRTVAFASTFAAFLTRAFDQLRMGAISESNINLVGSHCGVSVGE

Parental  DGPSQMALEDLAMFRSLPMSTVFYPSDAVATEKAVELAANTKGICFIRTSRPENTIIYNNNEDFQIGQAK
          DGPSQMALEDLAMFRS.P..TVFYPSDAV.TE.AV.LAANTKG.CFIRTSRPE....Y...E.F..GQAK
Retrocopy DGPSQMALEDLAMFRSIPGCTVFYPSDAVSTEHAVRLAANTKGMCFIRTSRPETAVLYTPQENFAVGQAK

Parental  VVQKNKDDQVTVIGAGVTLHEALAAAELLKKERINIRIVDPFTIKPLDKKLILESARATKGRILTVEDHY
          V......D..TVIGAGVTLHEALAAA..L..E.I.IR..D.FT.KPLD...I...ARAT.GR.LTVEDHY
Retrocopy VLRHSVEDEATVIGAGVTLHEALAAAGDLSQEGISIRVIDLFTVKPLDAGTIVSNARATGGRLLTVEDHY

Parental  YEGGIGEAVSTAVVGEPGITVTRLAVAQVPRSGKPAELLKMFGIDKDAIAQAVR
          .EGGIGEAV..AV...PGI.V..LAV..VPRSGKP.ELL.MFGI....IA.AV.
Retrocopy PEGGIGEAVCAAVAQQPGIRVRQLAVSHVPRSGKPSELLDMFGISARHIAEAVK

Legend:

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

Expression

RNA-Seq

Ochotona princeps was not studied using RNA-Seq expression data.

ChIP-Seq

Ochotona princeps was not studied using ChIP-Seq data.

EST

Ochotona princeps was not studied using EST data.

TSS

Ochotona princeps was not studied using FANTOM5 data.

Lab

retro_opri_10 was not experimentally validated.

Homology

Retrocopy orthology:

Ochotona princeps 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,