RetrogeneDB ID:

retro_tbel_3510

Retrocopy
location
Organism:Treeshrew (Tupaia belangeri)
Coordinates:scaffold_143147:10390..11510(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSTBEG00000008226
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:TKT
Ensembl ID:ENSTBEG00000012114
Aliases:None
Description:transketolase [Source:HGNC Symbol;Acc:11834]


Retrocopy-Parental alignment summary:






>retro_tbel_3510
ATGGCGGCCTACCCCAAGCCCGACGCGGGGACCCTGCAGGCCCTGCGGGAACTCGGCCAACCGCCTGCGGGTCCAGTCCA
TCCGGGCCACGTGCGCCTGCAGCTCCGGCCACCCCACGTCGTGCTGCAGCGCTGCGGAGATCGTGTCGGTCCTCTTCTTC
CGCACCATGAGGTACAAGCCGGCCCACCCCAGACACCCGGACAACGACCGCTTTGTCCTCTCCAAGGGCCATGCAGCCCC
GGTCCTCTACGCCGCTTGGGCCGAGCTGGGCGACATCAGCCAGTCCGACTTGCTGAGCTTGAGGAAAATCCACTGCAACC
TGGAGGGACATCCCACTCCTCGACTGTCGTTTGTGGACGTGGCCACAGGGTCGCTTGGGCAAGGGTTAGGCGCCGCGTGT
GGGATGGCCTACACTGGCAAGTACTTCGACAGGGCCAGCTACCGGGTGTTCTGCCTCGTGGGAGACGGCGAGTCCTCAGA
GGGCTCGGTCTGGGGAGGCTTTAGCCTTTGCATCCCACTATGGTTTGGACAATCTTGTGGCAGTATTTGATGTAAATCGT
CTGGGGACAGAGTGGCTCCACGCCCCTTGAGCACTGCACAGACGTTTACCAGAGTCGTTGTGAAGCCTTTGGGTGGGAAT
ACTTACCTAGTGGATGGCCACGATGTGGAGGCGTTGTGCCAGGTGTTTTGGCAAGCAGCTCAAGTGAAGAACAAGCCCAC
GGCTGTGATTGCCAAGACCTTTAAGGGCCGGGGTATTCCAAACATCGAGGATGCAGAGAATTGGCATGGGAAGCCAATGC
CGAAAGAAAGAGCAGATGCAATTATCAAATTAATTGAGAGTCAAATACAGACCAACAGGAATCTTATACCACAAGTCCCT
GTTGAAGACTCCCCCCAAATCAACATCACCAATATAAAAATGACCTCTCTACCTGCTTATAAAGTTGGAGACAAGATAGC
TACTGAGAAAGCATGTGGTTTGTCTCTGGCTAAACTAGGCCACACACATGAGAGAGTTATTGTTCTGGACGGTGACTCAA
AGAATTCCACCTTGTCTGAGCTATTCAGGAAAGACCATCCCGAGCGGTTCATAGAGTGTTTTATTGCTGAGCAAAACATG

ORF - retro_tbel_3510 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 63.03 %
Parental protein coverage: 65.0 %
Number of stop codons detected: 0
Number of frameshifts detected: 4


Retrocopy - Parental Gene Alignment:

ParentalMEGYHKPDQQKLQALKD-TANRLRISXXXXXXXXXXXHPTSCCSAAEIMAVLFFHTMRYKPQDPRNPHND
M..Y.KPD...LQAL....ANRLR.............HPTSCCSAAEI..VLFF.TMRYKP..PR.P.ND
RetrocopyMAAYPKPDAGTLQALRE>SANRLRVQSIRATCACSSGHPTSCCSAAEIVSVLFFRTMRYKPAHPRHPDND
ParentalRFVLSKGHAAPILYAVWAEAGFLPEAELLNLRKISSDLDGHPVPKQAFTDVATGSLGQGLGAACGMAYTG
RFVLSKGHAAP.LYA.WAE.G......LL.LRKI...L.GHP.P...F.DVATGSLGQGLGAACGMAYTG
RetrocopyRFVLSKGHAAPVLYAAWAELGDISQSDLLSLRKIHCNLEGHPTPRLSFVDVATGSLGQGLGAACGMAYTG
ParentalKYFDKASYRVYCMLGDGELSEGSVW-EAMAFAGFYKLDNLVAILDINRL-GQSDPAPLQHQVDVYQKRCE
KYFD.ASYRV.C..GDGE.SEGSVW.EA.AFA..Y.LDNLVA..D.NRL.GQS...PL.H..DVYQ.RCE
RetrocopyKYFDRASYRVFCLVGDGESSEGSVW>EALAFASHYGLDNLVAVFDVNRL>GQSGSTPLEHCTDVYQSRCE
ParentalAFGW-HSVIVDGHSVEELCKAFGQA---KHQPTAIIAKTFKGRGISGVEDKESWHGKPLPKNMADQVIQE
AFGW.....VDGH.VE.LC..F.QA...K..PTA.IAKTFKGRGI...ED.E.WHGKP.PK..AD..I..
RetrocopyAFGW>NTYLVDGHDVEALCQVFWQAAQVKNKPTAVIAKTFKGRGIPNIEDAENWHGKPMPKERADAIIKL
ParentalIYSQIQSKKKIMATPPQEDAPSVDISNIRMPTPPSYKVGDKIATRKAYGQALAKLGHSSDRIIALDGDTK
I.SQIQ.........P.ED.P...I.NI.M...P.YKVGDKIAT.KA.G..LAKLGH...R.I.LDGD.K
RetrocopyIESQIQTNRNLIPQVPVEDSPQINITNIKMTSLPAYKVGDKIATEKACGLSLAKLGHTHERVIVLDGDSK
ParentalNSTFSEL---KEPDR-IECY-AEQNM
NST.SEL.....P.R.IEC..AEQNM
RetrocopyNSTLSELFRKDHPERFIECFIAEQNM

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






RNA-Seq - click to see more details

Tupaia belangeri was not studied using RNA-Seq expression data.

ChIP-Seq - click to see more details

Tupaia belangeri was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_tbel_3510 retrocopy.

TSS - click to see more details

Tupaia belangeri was not studied using FANTOM5 data.

Lab - click to see more details

retro_tbel_3510 was not experimentally validated.

Retrocopy orthology:
Tupaia belangeri 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.
Parental genes homology:
Parental genes homology involve 19 parental genes, and 22 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000037581 retrocopy
retro_btau_176,
Callithrix jacchus ENSCJAG000000072531 retrocopy
retro_cjac_2128,
Cavia porcellus ENSCPOG000000000721 retrocopy
retro_cpor_45,
Dipodomys ordii ENSDORG000000013921 retrocopy
retro_dord_329,
Homo sapiens ENSG000001639311 retrocopy
retro_hsap_47,
Macropus eugenii ENSMEUG000000053123 retrocopies
retro_meug_1397, retro_meug_160, retro_meug_796,
Myotis lucifugus ENSMLUG000000009431 retrocopy
retro_mluc_67,
Macaca mulatta ENSMMUG000000144331 retrocopy
retro_mmul_74,
Mus musculus ENSMUSG000000219571 retrocopy
retro_mmus_220,
Oryctolagus cuniculus ENSOCUG000000159042 retrocopies
retro_ocun_319, retro_ocun_62,
Otolemur garnettii ENSOGAG000000169111 retrocopy
retro_ogar_5,
Ochotona princeps ENSOPRG000000098911 retrocopy
retro_opri_10,
Pan troglodytes ENSPTRG000000150241 retrocopy
retro_ptro_126,
Pteropus vampyrus ENSPVAG000000162831 retrocopy
retro_pvam_352,
Rattus norvegicus ENSRNOG000000160641 retrocopy
retro_rnor_146,
Sarcophilus harrisii ENSSHAG000000173491 retrocopy
retro_shar_827,
Sus scrofa ENSSSCG000000214081 retrocopy
retro_sscr_996,
Tupaia belangeri ENSTBEG00000012114 1 retrocopy
retro_tbel_3510 ,
Takifugu rubripes ENSTRUG000000030091 retrocopy
retro_trub_23,


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