RetrogeneDB ID: retro_tbel_3175

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_132949:9993..11361(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HK1
• Ensembl ID: ENSTBEG00000016359
• Aliases: None
• Description: hexokinase 1 [Source:HGNC Symbol;Acc:4922]

Sequence

>retro_tbel_3175
AATAAGGAAGGCCTCCACAACGACAAAGAAATCCTGAACCACCTGGGAGTAGAGCCATCAGGTGACGACTGTATCTCAGT
CTAGCATGTGTACACCCTCGTCTCCTTTCACTCGGCCAACCTCATGGCTACCAGCTGGGTGCCATCTGGAACAGCCCACG
TGATAACAAGGGCATGCCCAGGCTGTGGACCACAGTTGGTGTCCACATGTCTCTTTACAAGATGCACCCACAGTATGTCC
AGCATTTTCACAGAACTCTGACCGCTTGGTGCCAGACTCGACCTCTGATTCCTCTTGGAGAGTGGCAGTAGCAAGGGGGC
CACCATGGTGACCGCAGTGACCTGCCGCCTGACTGAGCCGCACCAGTATATTGAGGAGACCCTGGCCCACTTCTTCCTCA
CCAAGGACGTGCTGCTGAGGAGAAGAGGGGCTGAGATGGAGCCGGGGCAGAGAGAGCAGACGCACAACAATGCTGTAAAG
ATGCTGCCCTTCTTCATCCAGAGCACCCTAGGTGGGACAGAGCATGGTGATTTTTGGCCCTGGATCCCAGAGGAACGAAT
TTCTGTGGTCTACTGGTGAAAATATATAGCAAAAAGAGAGAACGGTGGAAATGCACAACATGATCTACACTGTCCCCATT
GAGATCATGCAGGGCACCAGCAAAGAGCTGTCTGACCACATCGTCTACTGCATCTCTGACTTTCTGAACTACATGGGGAT
AAAAGGCCCCAGGATATCTCTGAGCTTCATGTTCTCATTTCTCTACAGGCAGATGAGTCTGGATGTGGGAATCTTGATCA
CCTGGACCAAGGATTTTAAGGCAACTGACCGTGTGGAGCACAATGCAGTCACCTTACTAGGGGGTGCCATAAAAAGGAGA
GAGGAATTTGACATGGATGTGGTGACTATGGTCAACGACATGGTGGGCACCATGATGGTCTGTGCTTATGGGAACCCATA
CGTGAGGTTGGACTCATTGTAGAAATGGGCAGCAATGCTTGCTACATGGAGGAAATGAAGAAAGTGGAGATACTGAAAGG
GACCGAGGGTCAAATGTGCATCAACATGCAGTGTGAACCTTTGGGGACAACGAGTGTCTGGATGACATCAGAACAACTTC
AACAGATTGGTGGATGGATATTCTCTAAATGCAGGAAGGCGAAGGCTTGAGAAGATGATCAGTGGTATGTACTTGGAGGT
AATTACCCGCAACATCTTGATCAACGTCACCAAGAAGGGATTCTTCTTTTGAGGGCAAATCTCAGAGCCGTTGAAGACCT
AGGGCATCTTTGAGACCAAGTGTCTCTCTTGGATGGAAAGGGAGCAATTAGTGCTTCTCCAGGTCCAGCCATCCTCCAGC
AGCTGGGT

Alignment

ORF - retro_tbel_3175 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.98 %
• Parental protein coverage: 50.33 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 9

Retrocopy - Parental Gene Alignment:

Parental  NKEGLHNAKEILTRLGVEPSDDDCISVQHVCTIVSFRSANLVATT-KGAILKRLADNY-MPWLLTTIVVD
          NKEGLHN.KEIL..LGVEPS.DDCISV.HV.T.VSF.SANL.AT...GAI.....DN..MP.L.TT..V.
Retrocopy NKEGLHNDKEILNHLGVEPSGDDCISV*HVYTLVSFHSANLMATS<LGAIWNSPRDNKGMPRLWTTVGVH

Parental  GSLYKMHPQYARRFHKTLR-RLVPDS-DVRFLLSESGSGKGAAMVTAVAYRLAEQHRQIEETLAHFRLTK
          .SLYKMHPQY...FH.TL..RLVPDS.D..FLL.ESGS.KGA.MVTAV..RL.E.H..IEETLAHF.LTK
Retrocopy MSLYKMHPQYVQHFHRTLT<RLVPDS<DL*FLL-ESGSSKGATMVTAVTCRLTEPHQYIEETLAHFFLTK

Parental  DMLLEVKRRMRTEMELGLRKQTHDDAVVKMLPSFVRSTPDGTEHGDF-LALDLGGTNFRVLLVKIRSGKK
          D.LL...RR...EME.G.R.QTH..AV.KMLP.F..ST..GTEHGDF.LALD..GTNF..LLVKI.S.K.
Retrocopy DVLL---RRRGAEMEPGQREQTHNNAV-KMLPFFIQSTLGGTEHGDF<LALDPRGTNFCGLLVKIYSKKR

Parental  -RTVEMHNKIYAIPVEIMQGTGEELFDHIVSCISDFLDYMGIKGPRMPLGFTFSFPCKQTNLDVGILITW
          .RTVEMHN.IY..P.EIMQGT..EL.DHIV.CISDFL.YMGIKGPR..L.F.FSF...Q..LDVGILITW
Retrocopy <RTVEMHNMIYTVPIEIMQGTSKELSDHIVYCISDFLNYMGIKGPRISLSFMFSFLYRQMSLDVGILITW

Parental  TKGFKATDCVGHDVVTLLRDAIKRREEFDLDVVAVVNDTVGTMMTCAYE-EPTCEVGLIVGTGSNACYME
          TK.FKATD.V.H..VTLL..AIKRREEFD.DVV..VND.VGTMM.CAY..EP..EVGLIV..GSNACYME
Retrocopy TKDFKATDRVEHNAVTLLGGAIKRREEFDMDVVTMVNDMVGTMMVCAYG<EPIREVGLIVEMGSNACYME

Parental  EMKNVEMLEGTEGRMCINMEWG-AFGDNGCLDDIRT-EYDRLVDEYSLNAGKQRYEKMISGMYLGEIVRN
          EMK.VE.L.GTEG.MCINM.....FGDN.CLDDIRT....RLVD.YSLNAG..R.EKMISGMYL..I.RN
Retrocopy EMKKVEILKGTEGQMCINMQCE<TFGDNECLDDIRT<NFNRLVDGYSLNAGRRRLEKMISGMYLEVITRN

Parental  ILIDFTKKGFLFRGQISEPLKTRGIFETKFLSQIESDRLALLQVR-AILQQLG
          ILI..TKKGF.F.GQISEPLKT.GIFETK.LS..E...L.LLQV..AILQQLG
Retrocopy ILINVTKKGFFF*GQISEPLKT*GIFETKCLSWMEREQLVLLQVQ<AILQQLG

Legend:

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

Expression

RNA-Seq

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

ChIP-Seq

Tupaia belangeri was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_tbel_3175 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_3175 was not experimentally validated.

Homology

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.

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Oryctolagus cuniculus	ENSOCUG00000006697	1 retrocopy	retro_ocun_966,
Tupaia belangeri	ENSTBEG00000016359	1 retrocopy	retro_tbel_3175 ,