RetrogeneDB ID: retro_tbel_2368

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_109594:40309..42001(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SMEK1
• Ensembl ID: ENSTBEG00000008535
• Aliases: None
• Description: SMEK homolog 1, suppressor of mek1 (Dictyostelium) [Source:HGNC Symbol;Acc:20219]

Sequence

>retro_tbel_2368
CAAGGAAAGGAGTCTTCACTGGACATCACTGAGGACCTAGATGCATCTGAAGAGTCTTTTGATGATTTGTCATCACCAGA
TATAGAATTGCCATCTTGTGAATTAAGTTGCCTGGGGGAAATTGCAGAACTTGTGACATCAACTTTACTTTCCCCCCTTT
CCCATGAAAAACTTGCTCTAGCACTGGAAAAAGAAGGTTATATTAAAAAACTTTTACAGCTTTTTCATATGTGTGAGGAT
TTGGACTTTGTGGAAGGACTGCACCACTTGCATGAAATTATCAAAGGCATCTTCCTCTTAAAACAGACTTCTCTTTTTGA
AATTATGTTTTCTGAGGAATGTATAATGGACGTCATCGGATGTTTAGAATATGATCCTGCTTTATCGCAACCACAGAAAC
ACAGAGAATTTCTAACACAAACAGCCAAATTTAAAGAAGCAATTCCCATATCAGATCCTAAGCTGAAACAAAAAATTCAT
CAGACCTTCAGAATTCAGTATATACAAGATACAATTCTACCTTCTCCATCTATCCTCGAAGAAGAAATGTTACCAACACT
TCACTCCTTTATCTTGTTCAATAAGATAGAAATTGTTGATATGTTACAGGAAGATAAACAGTTTATGACAGATTTGTTTG
CACAACTAACAGATGAAGCAACAGATGTGGGAAAAAGACAGGAATTGGTTAACTTTTTAAAAGAATTTTGTGTTTTTTCC
TTAACACTACAATCTCATGACACAGATGCTTTTTTCAAGACTTTGTCAAACATGGGCATATTACCAACTTTAGAATTCAT
CCTCAATATGAATGATATACAGGTGCGAAATGCTGCTACTGACATAGTCTCATACTTGGTTGATTATAATCCCTCCATGG
TAGGAGAGTTTGTCCTGCAGAAGGCACAACAGAATGATGGTAACATTTTGTTCATCAGACTCATTATAGAGCATATGATA
TGTGATACAGATCCTGAACTTGGAGGAGCAGTCAAACGTATGGACCTGCTTCAAACTTTACTTGACCCAGAGAACGTGCT
AGCCACTGCTAGTGAAACAGAAAAATCTGAATTTCTGGGTTTCTTCTATGCGCACTGTATGCATCTTCTCACTGCTCCCT
TACTAGCAAATACGACAGAAGACAAGCCTAATAAAGATGATTTTCAAACTGCCCAGTTATTGGCACTTATATTGGAATTG
TTAACATTTTGTGTGGAGCGCCATACCTACCACATAAAGAACTACATCATTGATAAGGATATCCTTCGGCGAGTGCTAGT
TCTTATGGCCTCAAAGCATGCTTTTTTGGCATTATGTGCCCTTCGTTTTAAGAGAAAGATTATTGGATTAAAAGATGAGT
TTTACAATTGCTACATAATGGAAAGTTTTTTGTTTGAACCAGTAGTCAAAGCATTTCTCAACAATGGATCTCGCTACAAT
CTGATGAACTCTGCCATAATAGAAATGTTTGAATTTATCAGAGTGGAAGATATAAAATCATTAACCATTCATGTAGTTGA
AAATTACTGGAAAGCACTGGAAGATGTAGATTATGTACAGACATTTAAAGGATTAAAACTGAAATTTGAACAGCAAAGAG
ATAATCAGTATAGTCCCAACCTTGGCAATATGCATTCCAGTATGAGAGAACATGACTATCAAAGAAATAGCAGAACATTA
GAAGATGAAAAG

Alignment

ORF - retro_tbel_2368 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.51 %
• Parental protein coverage: 64.69 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  QGKDPSVDITQDLVDESEEERFDDMSSPGLELPSCELSRLEEIAELVASSLPSPLRREKLALALENEGYI
          QGK..S.DIT.DL.....EE.FDD.SSP..ELPSCELS.L.EIAELV.S.L.SPL..EKLALALE.EGYI
Retrocopy QGKESSLDITEDL--DASEESFDDLSSPDIELPSCELSCLGEIAELVTSTLLSPLSHEKLALALEKEGYI

Parental  KKLLELFHVCEDLENIEGLHHLYEIIKGIFLLNRTALFEVMFSEECIMDVIGCLEYDPALSQPRKHREFL
          KKLL.LFH.CEDL...EGLHHL.EIIKGIFLL..T.LFE.MFSEECIMDVIGCLEYDPALSQP.KHREFL
Retrocopy KKLLQLFHMCEDLDFVEGLHHLHEIIKGIFLLKQTSLFEIMFSEECIMDVIGCLEYDPALSQPQKHREFL

Parental  TKTAKFKEVIPISDPELKQKIHQTYRVQYIQDMVLPTPSVFEENMLSTLHSFIFFNKVEIVGMLQEDEKF
          T.TAKFKE.IPISDP.LKQKIHQT.R.QYIQD..LP.PS..EE.ML.TLHSFI.FNK.EIV.MLQED..F
Retrocopy TQTAKFKEAIPISDPKLKQKIHQTFRIQYIQDTILPSPSILEEEMLPTLHSFILFNKIEIVDMLQEDKQF

Parental  LTDLFAQLTDEATDEEKRQELVNFLKEFCAFSQTLQPQNRDAFFKTLSNMGILPAXXXXXGMDDTQVRSA
          .TDLFAQLTDEATD..KRQELVNFLKEFC.FS.TLQ....DAFFKTLSNMGILP.......M.D.QVR.A
Retrocopy MTDLFAQLTDEATDVGKRQELVNFLKEFCVFSLTLQSHDTDAFFKTLSNMGILPTLEFILNMNDIQVRNA

Parental  ATDIFSYLVEYNPSMVREFVMQEAQQNDDXXXLINLIIEHMICDTDPELGGAVQLMGLLRTLVDPENMLA
          ATDI.SYLV.YNPSMV.EFV.Q.AQQND.....I.LIIEHMICDTDPELGGAV..M.LL.TL.DPEN.LA
Retrocopy ATDIVSYLVDYNPSMVGEFVLQKAQQNDGNILFIRLIIEHMICDTDPELGGAVKRMDLLQTLLDPENVLA

Parental  TANKTEKTEFLGFFYKHCMHVLTAPLLANTTEDKPSKDDFQTAQLLALVLELLTFCVEHHTYHIKNYIIN
          TA..TEK.EFLGFFY.HCMH.LTAPLLANTTEDKP.KDDFQTAQLLAL.LELLTFCVE.HTYHIKNYII.
Retrocopy TASETEKSEFLGFFYAHCMHLLTAPLLANTTEDKPNKDDFQTAQLLALILELLTFCVERHTYHIKNYIID

Parental  KDILRRVLVLMASKHALLALCALRFKRKIIGLKDEFYNRYIMKSFLFEPVVKAFLNNGSRYNLMNSAIIE
          KDILRRVLVLMASKHA.LALCALRFKRKIIGLKDEFYN.YIM.SFLFEPVVKAFLNNGSRYNLMNSAIIE
Retrocopy KDILRRVLVLMASKHAFLALCALRFKRKIIGLKDEFYNCYIMESFLFEPVVKAFLNNGSRYNLMNSAIIE

Parental  MFEFIRVEDIKSLTAHVIENYWKALEDVDYVQTFKGLKLRFEQQRERQDNPKLDSMRSILRNHRYRRDAR
          MFEFIRVEDIKSLT.HV.ENYWKALEDVDYVQTFKGLKL.FEQQR..Q..P.L..M.S..R.H.Y.R..R
Retrocopy MFEFIRVEDIKSLTIHVVENYWKALEDVDYVQTFKGLKLKFEQQRDNQYSPNLGNMHSSMREHDYQRNSR

Parental  TLEDEE
          TLEDE.
Retrocopy TLEDEK

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_2368 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_2368 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 8 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Dipodomys ordii	ENSDORG00000012467	1 retrocopy	retro_dord_714,
Erinaceus europaeus	ENSEEUG00000006324	1 retrocopy	retro_eeur_316,
Pan troglodytes	ENSPTRG00000006638	1 retrocopy	retro_ptro_124,
Pteropus vampyrus	ENSPVAG00000015294	1 retrocopy	retro_pvam_1091,
Tupaia belangeri	ENSTBEG00000008535	1 retrocopy	retro_tbel_2368 ,
Tarsius syrichta	ENSTSYG00000010333	1 retrocopy	retro_tsyr_863,
Tursiops truncatus	ENSTTRG00000013598	1 retrocopy	retro_ttru_1398,
Vicugna pacos	ENSVPAG00000002765	1 retrocopy	retro_vpac_536,