Status
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Gene information
General information
TC013944 Gene

The sequence from the iB fragment is matched against the genes from the official gene set. The matche(s) is/are visualizied in a genome browser.

NC_007420.3: 2664919..2676443
Sequence information
Transcripts / Proteins (1) Get mRNA sequence
Get CDS sequence
Get protein sequence
Ortholog information (from OrthoDB)

The information about the homolog genes in Drosophila is provided by OrthoDB http://www.orthodb.org/. The homologs are sorted according to their similarity score. For an orthology statement additional analysis are required.
The data basis for the orthologs is OrthoDB v9 containing OGS3 for Tribolium castaneum and 2015_04 (r6.07) for Drosophila melanogaster.

Closest fly homologs
    		TC013944
    Gene ontology

    GO terms for Tribolium

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    There are no GO terms for Tribolium at the moment. You can help the community by providing some GO terms for this gene.


    GO terms for the homologous Drosophila genes

    Assign a GO term to this Tribolium gene by filling in the fields. Repeat to add several GO terms. Search AmiGO for the correct GO ID. Use only the most specific term - use "graph views" to browse related terms ("child terms" are more specific; the more general "parent" terms will be automatically linked). Only information based on Tribolium data should be entered - do not define terms just based on Drosophila knowledge. We will review this information and submit the annotation to the Gene Ontology consortium.


    Gene
    {{ goGene }}
    The Tribolium gene the GO term is assigned to.
    GO ID *
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    The ID of the GO term you assign to the gene. Please enter only the ID of the GO term with proceeding 'GO:'. This information is mandatory.
    Evidence
    {{ blurEvidenceResult }}
    The evidence code describes with which method the function or location, expressed by the GO term, was show for this gene. Please refer to this page for a definition of the evidence code and a decision tree.
    Reference *
    {{ blurReferenceResult }}
    The reference where the function or location is described for the gene. Please enter a PubMed ID. This information is mandatory.
    Quotation
    If you paste here the relevant section of the reference it is for us a great help to review your annotation. The quotation may be also be displayed to the users of iBeetle-Base.
    Name
    You may enter your name. The contact information can help us to clarify any questions. If you agree, we may show your name on this page to honor your contribution.
    Email
    We will use your email address only for possible questions regarding this annotation. We will never show your address or give it away.
    Publish name
    If you have entered your name and agree by marking the checkbox. we might show your name on this page to honor your contribution.
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    * : mandatory fields
    For help on how to submit larger datasets or non experimental data please contact us.
    iBeetle screen iB_05528

    Attention! iBeetle is a first pass screen. Hence, the documented phenotypes need to be confirmed by independent experiments using non-overlapping dsRNA fragments! Phenotypes with a penetrance > 50% are frequently reproduced. See Schmitt-Engel et al. 2015 for details on reproducibility.

    iB sequence
    Phenotype after pupal injection
    Usually 10 injected animals

    Pupal injection procedure

    Day 0: 10 female pupae of the pBA19 strain (muscle enhancer trap line) were injected with dsRNA.

    3 days post injection (dpi): Hatch control: Pupal and adult lethality as well as metamorphosis defects (molting, eclosion) were documented. For mating, 4 males of the black strain were added.

    9 dpi: First egg-lay was collected and incubated for cuticle analysis. Adult lethality and egg production (reduced/ no egg-lay) was documented.

    11 dpi: Second egg-lay was collected and incubated for embryonic muscle analysis. Adult lethality and egg production (reduced/ no egg-lay) were documented.

    Note: The adult morphology was not analyzed systematically at 3/9/11 dpi. Only obvious phenotypes, visible without magnification, have been annotated.

    13 dpi: Egg productivity and Ovary analysis
    The percentage of hatched larvae was documented and not hatched larvae/ eggs were embedded for cuticle analysis (15 dpi). In case of a reduction of egg production, 4 injected females were dissected to analyze the gross morphology of the ovaries.

    14 dpi: Analysis of embryonic musculature and early embryonic development
    Offspring of the injected females (hatched and not hatched larvae/ eggs) were analysed for embryonic lethality and muscle defects.

    15 dpi: Analysis of larval instar 1 cuticle
    Offspring of injected females were analysed and cuticle phenotypes were annotated.

    22 dpi: Stink gland analysis
    Documentation of defects in abdominal and thoracic stink glands (colour, size, content) of the injected femals.

    Terms used in the pupal injection procedure

    larval pantagmatic defects
    At least two tagmata (head, thorax, abdomen or terminus) show similar/ comparable defects.
    empty eggs
    Just empty shells are visible, no cuticle has been developed.
    strong defects
    L1 cuticle larvae which show severe defects. These strong defects are subdivided into three categories
    strongly fragmented (cuticle crumbs)
    No segments or appendages are identifiable, only residues of cuticle and bristles can be identified.
    cuticle remnants (with unidentifiable segments)
    Segments or parts of appendages are recognizable, but identity is not clear.
    cuticle remnants (with some identifiable segments)
    At least one segment or appendage is clearly regonizable.
    number of eggs on slide
    affected embryos usually (not always) do not hatch. Only the not hatched were used for cuticle analysis.
    For the embryonic muscle analysis the hatched as well as the not hatched were analysed.
    total number of affected eggs/embryos/larvae
    Summary of all different phenotypes/ phenotypic series which were annotated.
    inside-out
    The L1 larva shows a partial or complete inversion., e.g. bristles, appendages or parts of the abdominal segments are inverted into the interior of the cuticle.
    starved
    Dissected females show a strong resorption of fatbody predominately in the abdomen and the oogenesis is blocked. These are considered as eventually lethal phenotypes and the blocked oogenesis probably a secondary defect due to starvation.
    eclosion not fulfilled
    The emergence of the adult from the pupa stage is interrupted. This phenotype shows pupal as well as adult features.
    Please see the help page for more information
    Metamorphosis and survival

    Lethality 11 days after pupal injection: 50.0% (includes death as pupa, adult)

    eclosion not fulfilled (with pupal and adult features) - Number of animals showing the phenotype: 3 (3 dpi)
    Days post injection

    adult lethality - Number of animals showing the phenotype: 2 (9 dpi)
    Days post injection

    Analysis of embryonic musculature and early development
    number of eggs/embryos/larvae on slide: > 50 embryo/egg with muscle fluorescence/pattern, but not hatched (pot. late embryonic lethality) - Penetrance (percentage of animals/eggs on slide): 30% - 50%

    embryo/egg with embryonic tissue, no cuticle, no fluorescence - Penetrance (percentage of animals/eggs on slide): less than 30%

    larval musculature fluorescence decreased - Penetrance (percentage of animals/eggs on slide): less than 30%

    larval musculature potentially degenerated - Penetrance (percentage of animals/eggs on slide): 30% - 50%

    larval musculature pattern irregular - Penetrance (percentage of animals/eggs on slide): less than 30%

    larval musculature potentially thinner - Penetrance (percentage of animals/eggs on slide): less than 30%

    larval musculature partially not present - Penetrance (percentage of animals/eggs on slide): less than 30%
    larval musculature partially ectopicallypresent - Penetrance (percentage of animals/eggs on slide): less than 30%
    affected eggs/embryos/larvae total percentage of affected eggs/embryos/larvae on slide - Penetrance (percentage of animals/eggs on slide): more than 80%
    Analysis of larval stage 1 cuticle
    number of eggs/embryos/larvae on slide: > 50
     egg without cuticle embryo/egg without visible larval cuticle in cuticle preparation - Penetrance (percentage of animals/eggs on slide): less than 30%
    head bristle pattern irregular - Penetrance (percentage of animals/eggs on slide): 30% - 50%

    dorsal ridge row need term irregular - Penetrance (percentage of animals/eggs on slide): 30% - 50%
    Comment: dorsal ridge row bristles can be either partially missing or be of irregular size (bristles replaced by setae or vice versa)
    gena triplet seta irregular - Penetrance (percentage of animals/eggs on slide): less than 30%
    Comment: irregular number of gena triplet bristles. sometimes one or more are missing or duplicated.
    affected eggs/embryos/larvae total percentage of affected eggs/embryos/larvae on slide - Penetrance (percentage of animals/eggs on slide): 50% - 80%
    Phenotype after larval injection
    Usually 10 injected animals

    Larval injection procedure

    Day 0: 10 female L5-6 larvae of the D17Xhom strain (females express RFP in the eyes and in the CNS; pupae express GFP in the thorax) were injected with dsRNA.

    11 days post injection (dpi): Pupal morphology Documentation of larval/ pupal death and defects of metamorphosis (eclosion, delayed development). Screening for alterations of pupal head and appendages, pupal thorax, pupal thoracic musculature, pupal legs, pupal wings, pupal abdomen and pupal genital lobes.

    16 dpi: Adult morphology Documentation of larval/ pupal and adult death and defects of metamorphosis (eclosion, delayed development). Screening for alterations of adult head and appendages, adult thorax, adult elytra and hindwings, adult legs and cuticle properties. For mating 4 males of the black strain were added.

    19 dpi: Sieving and egg-lay Documentation of adult lethality and enduring metamorphosis defects.

    22 dpi: Ovary analysis (Fertility) In case of a reduction of egg production 4 females were dissected and the gross morphology of the ovaries were analysed.

    41 dpi: Fertility and stink gland analysis Documentation of defects in abdominal and thoracic stink glands development (colour, size, content) of the injected females. Check for fertility of injected larvae (no or decreased offspring).

    Terms used in the larval injection procedure

    pupal/ adult pantagmatic defects
    At least two tagmata (head, thorax, abdomen or terminus) show similar/ comparable defects.
    pupal molt not fulfilled
    The hatching from the larva to the pupa is interrupted. Either it dies as prepupa or the phenotype shows larval as well as pupal features.
    eclosion not fulfilled
    The emergence of the adult from the pupa stage is interrupted. This phenotype shows pupal as well as adult features.
    starved
    Dissected females show a strong resorption of fatbody predominately in the abdomen and the oogenesis is blocked. These are considered as eventually lethal phenotypes and the blocked oogenesis probably a secondary defect due to starvation.
    Metamorphosis and survival

    Lethalities 11 days after larval injection: -1.0% (includes death as larva, prepupa, pupa)
    Lethalities 22 days after larval injection: -1.0% (includes death as larva, prepupa, pupa, adult)

    RNAi sequence
    Primers
    Left: Right:
    Protein sequence
    • >TC013944 RA
      MSDEGKESH KSLPLDLAR TQITTVRTV EGKAPLLMT 
NQGLRGVRV LTQGTPPNS GQASSNAQT IITTNIVPT 
VFKPDAART QIASILTTS QPQSSAANI TIQRPTQIT 
LSTTPVVPC GTNYHVPRG PAVVANLAA PRSNVASVR 
APMVVTAQT GGQAHAFVR PPRTPSPAQ GTAWLTNTS 
NGSQIKGAT TVLSSPVRG ASVTGKPQL VSRSQAGLQ 
NVSTIRPGT TILHSAITI GHSFKPGQN ASGIQGLGN 
TVTIAQVLP SRTQAVVYS ANTSGQFTA TPRLTVSSS 
AQNQRQSTA ARPMVTTAR LTIPVNVTQ TGARLVAPQ 
ATVLTSGAR ITAVSQAST VIGTTPNRI VTTQPNVTI 
GRLSVAASP AQVSNSNII GQTRTLNLL AVANPSQPR 
SVHTQQATK VITQPAQGA IHFTPISAP VKTTQTVVT 
AANRTVNVP AAIVSQRQP AVVSSQTIP IANVYSQQG 
DNQQGQTPA SVFIPLSSV PRRTSPSPT SAPQTSINT 
TTSSVTTYS LAASSYFYD GRSFGQQPT SFTALPQST 
QQIRPTSLN TQVHGIVTN QQMRFNPVM VVDQNRTQQ 
FPTQSAAEL NSEQSQTVP TKMTSSPRP SILRKRDHE 
GSPLKAAKN LTPVLTNLT QQPLPSISP PSRPDSRGN 
GHSSGGSTT ISATSSPGL AEVNEDSMP HAPMNKEEE 
NVKPPMEMS PRKKPRKQQ LTGSNDIDE HNDDMQFIT 
DSSLKKEQE DSDGNQSDE PRDGAPEAG QVTTVRKPA 
SASLLNSYR QTWKATHNH YLRYSDVRP KDERRPTIM 
DLANQYRVQ EKVNGWKIY HLSTQMEDL AEQEQQVYN 
QLNELLKNT ESQEELDFE KDINRINEL IKGNLQRIK 
IINDGMIEA KTQIMKIFD HKGHVTDII NRCASKRNF 
KKRDKS
    CDS sequence
    • >TC013944 RA
      atgagtgac gagggcaag gagtcccac aagtccttg 
cctctggat ttggccagg acccaaata accaccgtt 
cggacagtg gaagggaaa gcccccttg ttgatgacg 
aatcaaggc ttgcgtgga gtgcgtgtc ctgactcag 
ggaacgcca ccaaactcg ggccaggct tcttccaac 
gcccaaaca ataatcaca actaatatt gtccccacc 
gtgtttaag ccagatgct gcaaggact caaattgcg 
agtattttg acgacgagt cagccgcaa tcgagtgct 
gctaacatc actattcaa agacccacc caaatcacc 
ctttcgaca actccggtg gtaccatgt ggtactaat 
taccatgtc ccacggggg cccgcagtc gtggcgaat 
ttggcggcc cctcgcagc aacgtggcg tcggtgcgc 
gcccccatg gtggtcacg gcgcaaaca ggcggccag 
gcgcacgca tttgtgagg ccccctcgt actccgagc 
cccgctcag ggcacggca tggctcacc aacacgtcg 
aacgggtct cagattaag ggggcaacg actgtgttg 
agttcacca gtgcggggt gcaagtgtc accgggaag 
ccccaactt gtctctcgg tcacaagcc gggcttcaa 
aacgtgtca acaattcgt ccaggaacg acaattttg 
cattcagct atcacgatt ggacactcg ttcaagcct 
ggacaaaac gcgtccggg attcaggga ttaggcaat 
actgtgact atagcacag gtacttccg tcgaggacc 
caggctgtg gtttatagt gctaatact agtggccag 
tttacggca acacccaga cttacagtg tcgagttcg 
gcgcaaaat caaagacag agcactgcg gctagacct 
atggtaacg acggcacgt ttgacgatt cctgttaat 
gttacgcaa actggggcg cggttggtg gccccccaa 
gcgactgtt ttgacttct ggggctagg atcactgct 
gtgtctcaa gcctcgaca gtgatcggt actacaccg 
aatagaatt gtgacaacg cagcctaat gttacgata 
gggcgattg tctgtggct gcaagtccg gcacaagtc 
tcaaactcc aatattatc ggccagacc cggacactt 
aatcttctt gctgtagct aatccttcg cagcctaga 
agtgtgcat acgcagcaa gctactaag gttataacg 
caacctgct caaggtgcc attcatttt actccaata 
tcagcccct gtgaagacg acgcaaact gtcgtcacg 
gcggctaat cgaactgtt aatgttcca gctgcaata 
gttagtcag aggcaacca gcggttgtt tcttcgcaa 
actatacca atagctaat gtgtattct caacaaggc 
gataatcaa caaggacaa actccagcc agtgttttt 
attccgttg tcgtctgtg cctaggaga acctctcca 
agtcctaca agtgcaccc caaaccagc atcaacaca 
acaactagc agcgtaaca acatattcg ctcgccgca 
agttcgtat ttttacgat ggccgttct ttcggccaa 
caaccgaca tctttcacc gctcttcca caatccact 
caacaaata cggccaacg tctctaaac acacaagtc 
cacggtatt gtgaccaat caacaaatg cgctttaac 
ccagtcatg gtagtcgac cagaaccgt actcaacaa 
ttccccacc caatcggcg gcggagcta aattcggaa 
caatcccaa accgttcca accaaaatg acatcgtca 
ccacgtccc agcattcta cgaaagcga gaccacgag 
gggtcgccc ctcaaagcg gccaaaaat ctaactccg 
gtcctgact aatctcacc caacagccg ctaccgtcg 
atttcacca ccttcgagg ccggattca cgaggaaat 
ggacacagt tctggcgga agtacgact atttctgca 
acgtccagt cccggattg gccgaagtg aacgaggat 
agcatgccc cacgccccc atgaataag gaggaggag 
aacgtgaag ccgcccatg gagatgagc ccaaggaaa 
aaacccaga aagcagcaa ttgactggg agcaatgat 
attgatgag cataacgat gacatgcag tttataact 
gacagttcg ctgaagaag gagcaggag gactccgat 
gggaatcaa agtgatgag ccgagagat ggcgctccg 
gaggctggg caagtgact acggttcgg aaaccggcc 
tctgcgagt ctgttgaat agttatcga cagacttgg 
aaggctaca cacaaccac tatttaagg tattcagat 
gtgaggcct aaagacgag cggaggcct accatcatg 
gacttggcc aatcaatac agagtgcaa gaaaaagtg 
aacggatgg aagatttat catctttcg actcaaatg 
gaggatttg gccgagcaa gagcaacaa gtctacaac 
cagttgaat gagctgctt aaaaacacc gaatctcaa 
gaggagcta gattttgag aaggatata aaccgaatc 
aacgaactc atcaagggt aatttacag agaattaaa 
attatcaac gatggaatg attgaggcg aagacccaa 
attatgaag atcttcgac cataagggc catgtgacc 
gatataatc aatagatgt gccagtaaa cgtaacttc 
aagaaacga gataaatcg taa
    mRNA sequence
    • >TC013944 RA
      gagcaatgg cgtcagttc ggaatttgc gttttgtgg 
tgttgttgt agtctatta ttgtagatt ttttaagtg 
caaacctta gtcttaagt ttaaccaaa aaaccatgt 
tattttgtt ccgaaaaat tgccaaaaa gctgccaag 
gtttcattt ttacacttt gcaaaacct cctaattac 
cctctgttc agttttaat gcagatgcg tttaacgta 
acaaataaa gttttttat gggtaaatt taaaacctg 
cgaaatatg agtgacgag ggcaaggag tcccacaag 
tccttgcct ctggatttg gccaggacc caaataacc 
accgttcgg acagtggaa gggaaagcc cccttgttg 
atgacgaat caaggcttg cgtggagtg cgtgtcctg 
actcaggga acgccacca aactcgggc caggcttct 
tccaacgcc caaacaata atcacaact aatattgtc 
cccaccgtg tttaagcca gatgctgca aggactcaa 
attgcgagt attttgacg acgagtcag ccgcaatcg 
agtgctgct aacatcact attcaaaga cccacccaa 
atcaccctt tcgacaact ccggtggta ccatgtggt 
actaattac catgtccca cgggggccc gcagtcgtg 
gcgaatttg gcggcccct cgcagcaac gtggcgtcg 
gtgcgcgcc cccatggtg gtcacggcg caaacaggc 
ggccaggcg cacgcattt gtgaggccc cctcgtact 
ccgagcccc gctcagggc acggcatgg ctcaccaac 
acgtcgaac gggtctcag attaagggg gcaacgact 
gtgttgagt tcaccagtg cggggtgca agtgtcacc 
gggaagccc caacttgtc tctcggtca caagccggg 
cttcaaaac gtgtcaaca attcgtcca ggaacgaca 
attttgcat tcagctatc acgattgga cactcgttc 
aagcctgga caaaacgcg tccgggatt cagggatta 
ggcaatact gtgactata gcacaggta cttccgtcg 
aggacccag gctgtggtt tatagtgct aatactagt 
ggccagttt acggcaaca cccagactt acagtgtcg 
agttcggcg caaaatcaa agacagagc actgcggct 
agacctatg gtaacgacg gcacgtttg acgattcct 
gttaatgtt acgcaaact ggggcgcgg ttggtggcc 
ccccaagcg actgttttg acttctggg gctaggatc 
actgctgtg tctcaagcc tcgacagtg atcggtact 
acaccgaat agaattgtg acaacgcag cctaatgtt 
acgataggg cgattgtct gtggctgca agtccggca 
caagtctca aactccaat attatcggc cagacccgg 
acacttaat cttcttgct gtagctaat ccttcgcag 
cctagaagt gtgcatacg cagcaagct actaaggtt 
ataacgcaa cctgctcaa ggtgccatt cattttact 
ccaatatca gcccctgtg aagacgacg caaactgtc 
gtcacggcg gctaatcga actgttaat gttccagct 
gcaatagtt agtcagagg caaccagcg gttgtttct 
tcgcaaact ataccaata gctaatgtg tattctcaa 
caaggcgat aatcaacaa ggacaaact ccagccagt 
gtttttatt ccgttgtcg tctgtgcct aggagaacc 
tctccaagt cctacaagt gcaccccaa accagcatc 
aacacaaca actagcagc gtaacaaca tattcgctc 
gccgcaagt tcgtatttt tacgatggc cgttctttc 
ggccaacaa ccgacatct ttcaccgct cttccacaa 
tccactcaa caaatacgg ccaacgtct ctaaacaca 
caagtccac ggtattgtg accaatcaa caaatgcgc 
tttaaccca gtcatggta gtcgaccag aaccgtact 
caacaattc cccacccaa tcggcggcg gagctaaat 
tcggaacaa tcccaaacc gttccaacc aaaatgaca 
tcgtcacca cgtcccagc attctacga aagcgagac 
cacgagggg tcgcccctc aaagcggcc aaaaatcta 
actccggtc ctgactaat ctcacccaa cagccgcta 
ccgtcgatt tcaccacct tcgaggccg gattcacga 
ggaaatgga cacagttct ggcggaagt acgactatt 
tctgcaacg tccagtccc ggattggcc gaagtgaac 
gaggatagc atgccccac gcccccatg aataaggag 
gaggagaac gtgaagccg cccatggag atgagccca 
aggaaaaaa cccagaaag cagcaattg actgggagc 
aatgatatt gatgagcat aacgatgac atgcagttt 
ataactgac agttcgctg aagaaggag caggaggac 
tccgatggg aatcaaagt gatgagccg agagatggc 
gctccggag gctgggcaa gtgactacg gttcggaaa 
ccggcctct gcgagtctg ttgaatagt tatcgacag 
acttggaag gctacacac aaccactat ttaaggtat 
tcagatgtg aggcctaaa gacgagcgg aggcctacc 
atcatggac ttggccaat caatacaga gtgcaagaa 
aaagtgaac ggatggaag atttatcat ctttcgact 
caaatggag gatttggcc gagcaagag caacaagtc 
tacaaccag ttgaatgag ctgcttaaa aacaccgaa 
tctcaagag gagctagat tttgagaag gatataaac 
cgaatcaac gaactcatc aagggtaat ttacagaga 
attaaaatt atcaacgat ggaatgatt gaggcgaag 
acccaaatt atgaagatc ttcgaccat aagggccat 
gtgaccgat ataatcaat agatgtgcc agtaaacgt 
aacttcaag aaacgagat aaatcgtaa attaagttt 
gttgtgatt ttgtgtttt ttgatcttg tgcttttat 
aattatcga cattaggtc aaagatcga aagaaaaag 
tagttttat acaattcgc ttgtatatt tttctgagt 
tttcattgt atttattta tttgatgtt gatattttg 
aattataaa aagatctaa aagtggaca aatggtttt 
gtaataaat aaaagtgtg caggttttg tacacggct 
tgtatttat attattgca tccattggt ggatgagac 
aacttttcc agtgaacct actgttgat gtttgtaat 
aaagttgtt ttaaatctc gacagtcta agttttcct 
tgtccttgt gtgcagata gattatatt attataaaa 
ttgtttctt aaataaatg gtttctaaa gaa

    If you use iBeetle-Base, please cite: Dönitz J et al.: Expanded and updated data and a query pipeline for iBeetle-Base,
    Nucleic Acids Res. 2018 Jan 4;46(D1):D831-D835. doi: 10.1093/nar/gkx984.

    The data is licensed under a Creative Commons Attribution 3.0 Unported License. (CC-BY) CC-BY