Status
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Gene information
General information
TC004159 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_007416.3: 1812999..1816050
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
    		TC004159
    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
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    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 *
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    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
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    * : mandatory fields
    For help on how to submit larger datasets or non experimental data please contact us.
    iBeetle screen iB_00670

    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: 40.0% (includes death as pupa, adult)

    eclosion not fulfilled (with pupal and adult features) - Number of animals showing the phenotype: 2 (3 dpi)
    Days post injection

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

    Fertility
    vitellarium thinner - Number of animals showing the phenotype: 4
    ovary size decreased - Number of animals showing the phenotype: 4
    vitellarium shortened - Number of animals showing the phenotype: 4
    egg chamber not present - Number of animals showing the phenotype: 4

    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: 20.0% (includes death as larva, prepupa, pupa)
    Lethalities 22 days after larval injection: 100.0% (includes death as larva, prepupa, pupa, adult)

    larva lethality early (L5/6) - Number of animals showing the phenotype: 2 (11 dpi)
    Days post injection

    pupal molt delayed (still larva) - Number of animals showing the phenotype: 8 (11 dpi)
    Days post injection

    larva lethality late (L7) - Number of animals showing the phenotype: 8 (16 dpi)
    Days post injection

    RNAi sequence
    Primers
    Left: Right:
    Protein sequence
    • >TC004159 RA
      MGRWVWSRA ECGSSGDCL EEVSKSAVC ARGPITDDL 
MCLKMMTFG LAKCTITGV DGHGPRDGG TPILLVAGA 
ATGHLQANL QIAAAPPGG AREGSCHWS RTNSVNLSV 
LGADMLALL CLCVVLLVW WFSRPKKSP STIPGPRPW 
PLIGSMHLL AGHETPFQA FTALSRVYG DIFSIHLGS 
ASCVVVNNF KLIKEVLIA KGGDFGGRP DFARFHKLF 
GGDRNNSLA LCDWSSLQK TRRSIARTY CSPRFTSLQ 
YDRVNNVGE EELKSFLHQ LDQLPHGQP CNVKPAVLM 
VCANMFTQY MCSTSFAYE DKGFQKIVR YFDEIFWEI 
NQGYAVDFL PWLLPVYTG HMKKISNWA TEIRQFILS 
RIIDKHRAT LDTNSPPRD FTDALLMHL EEDPNMNWQ 
HIIFELEDF LGGHSAIGN LVMVTLAAV VDHPEVAKR 
IQEEVDQVT GGTRCPNLF DKAAMPYTE ATILETLRT 
ASSPIVPHV ASKDTEIDG HEVSKGTIV FINNYELNQ 
GDAYWDEPG LFKPERFLS STGNIVKPA HFIPFSTGK 
RTCIGQRLV QCFSFVVLA TLLQYYDVS TKESVKVQP 
GCVAVPPDC FKLVLTPRK
    CDS sequence
    • >TC004159 RA
      atgggccga tgggtttgg tctcgtgca gagtgtgga 
tcaagtggg gactgtttg gaggaggtc tccaaaagc 
gcggtctgc gcgcggggt cctattact gatgacttg 
atgtgcttg aaaatgatg accttcggt ctggcgaag 
tgtaccatc acgggcgta gacggtcac gggccgcga 
gacggtggg actcctatt ttgctagtg gcgggggcg 
gccacaggc catcttcag gccaatctc cagatcgca 
gctgcaccc cctggtggg gcaagagag gggagctgt 
cattggtcg cgcaccaac tccgtcaat ctaagtgta 
ctcggtgca gacatgctc gcgctcctc tgtctgtgt 
gtggtgctg ctggtgtgg tggttctcg cggccgaag 
aagtccccg agtacgatt ccggggccg cggccctgg 
cccctcatc ggcagcatg cacctcctg gccgggcac 
gagacgccc ttccaggcc ttcaccgcg ctcagtcgg 
gtctacgga gacatcttc agcatccac ctcgggtcg 
gcttcctgt gtcgtcgtc aacaacttc aagctgatc 
aaagaggtg ctcatcgcc aaggggggc gacttcggg 
ggccggccc gacttcgct cgcttccat aagctcttc 
ggcggcgat cgcaacaat tcgctcgcc ctgtgtgac 
tggtcctcg ctgcagaag acgcgccgc agcatcgcc 
cgcacttac tgctcgccc agattcact tcgctccag 
tacgacaga gtcaacaac gtcggcgaa gaggagctc 
aagtccttc ctccaccaa ctggaccaa ctcccccac 
ggccagccc tgcaacgtc aagccggcc gtcctcatg 
gtctgcgcc aacatgttc acccagtac atgtgctcc 
acaagcttc gcctacgag gacaaaggc ttccagaag 
atcgtccgg tatttcgat gagatcttc tgggagatc 
aatcaaggc tatgccgtc gacttcctc ccctggctc 
ctcccggtc tacaccggc cacatgaag aaaatctcc 
aactgggcc acggaaatc cgacagttt atcttgtcg 
aggatcatt gacaaacac cgcgcgacc ttagacacc 
aactcccca ccgagagac ttcaccgat gctcttttg 
atgcacttg gaggaagac ccaaatatg aattggcaa 
catatcata ttcgaattg gaagatttc ctcggggga 
cactcggcc atcggtaac ttggtcatg gtaactcta 
gccgcagtc gtcgatcat ccggaagtc gcgaaacgt 
attcaggaa gaagtcgac caagtgact ggcggtact 
cgctgcccg aaccttttc gacaaagct gcgatgccc 
tacacggaa gccaccatc ttggaaact ctccgaaca 
gcctcttcg cccattgtc ccacacgtc gcgagtaaa 
gacaccgaa atcgacgga cacgaagtc agcaaaggc 
acgattgta ttcattaac aactacgag ctgaatcaa 
ggcgatgct tattgggac gagcctgga ctgttcaag 
cctgaacga ttcctttcg agcaccggc aatatcgtc 
aaaccggca catttcatt cctttcagc acgggaaag 
aggacgtgc atcggccaa aggctcgtc caatgtttc 
agtttcgtg gttttagca acacttctg cagtattat 
gacgtcagt acaaaagaa agcgtaaag gtacaacct 
ggctgcgtt gcggtcccg cctgattgt ttcaagcta 
gtattgaca ccaagaaaa taa
    mRNA sequence
    • >TC004159 RA
      aagtcgaag acggcggtg atgggccga tgggtttgg 
tctcgtgca gagtgtgga tcaagtggg gactgtttg 
gaggaggtc tccaaaagc gcggtctgc gcgcggggt 
cctattact gatgacttg atgtgcttg aaaatgatg 
accttcggt ctggcgaag tgtaccatc acgggcgta 
gacggtcac gggccgcga gacggtggg actcctatt 
ttgctagtg gcgggggcg gccacaggc catcttcag 
gccaatctc cagatcgca gctgcaccc cctggtggg 
gcaagagag gggagctgt cattggtcg cgcaccaac 
tccgtcaat ctaagtgta ctcggtgca gacatgctc 
gcgctcctc tgtctgtgt gtggtgctg ctggtgtgg 
tggttctcg cggccgaag aagtccccg agtacgatt 
ccggggccg cggccctgg cccctcatc ggcagcatg 
cacctcctg gccgggcac gagacgccc ttccaggcc 
ttcaccgcg ctcagtcgg gtctacgga gacatcttc 
agcatccac ctcgggtcg gcttcctgt gtcgtcgtc 
aacaacttc aagctgatc aaagaggtg ctcatcgcc 
aaggggggc gacttcggg ggccggccc gacttcgct 
cgcttccat aagctcttc ggcggcgat cgcaacaat 
tcgctcgcc ctgtgtgac tggtcctcg ctgcagaag 
acgcgccgc agcatcgcc cgcacttac tgctcgccc 
agattcact tcgctccag tacgacaga gtcaacaac 
gtcggcgaa gaggagctc aagtccttc ctccaccaa 
ctggaccaa ctcccccac ggccagccc tgcaacgtc 
aagccggcc gtcctcatg gtctgcgcc aacatgttc 
acccagtac atgtgctcc acaagcttc gcctacgag 
gacaaaggc ttccagaag atcgtccgg tatttcgat 
gagatcttc tgggagatc aatcaaggc tatgccgtc 
gacttcctc ccctggctc ctcccggtc tacaccggc 
cacatgaag aaaatctcc aactgggcc acggaaatc 
cgacagttt atcttgtcg aggatcatt gacaaacac 
cgcgcgacc ttagacacc aactcccca ccgagagac 
ttcaccgat gctcttttg atgcacttg gaggaagac 
ccaaatatg aattggcaa catatcata ttcgaattg 
gaagatttc ctcggggga cactcggcc atcggtaac 
ttggtcatg gtaactcta gccgcagtc gtcgatcat 
ccggaagtc gcgaaacgt attcaggaa gaagtcgac 
caagtgact ggcggtact cgctgcccg aaccttttc 
gacaaagct gcgatgccc tacacggaa gccaccatc 
ttggaaact ctccgaaca gcctcttcg cccattgtc 
ccacacgtc gcgagtaaa gacaccgaa atcgacgga 
cacgaagtc agcaaaggc acgattgta ttcattaac 
aactacgag ctgaatcaa ggcgatgct tattgggac 
gagcctgga ctgttcaag cctgaacga ttcctttcg 
agcaccggc aatatcgtc aaaccggca catttcatt 
cctttcagc acgggaaag aggacgtgc atcggccaa 
aggctcgtc caatgtttc agtttcgtg gttttagca 
acacttctg cagtattat gacgtcagt acaaaagaa 
agcgtaaag gtacaacct ggctgcgtt gcggtcccg 
cctgattgt ttcaagcta gtattgaca ccaagaaaa 
taaacgatg tgtagtact gaaccggtg agcgattag 
gcgatgctt atcggaggg tattttgta agattgcgg 
ctgtaatca caggtagtt tgtatgaca gtggagagg 
gcgggcgcc ctgccggaa cttgtacgg ccactaaaa 
gacgaggct ttaagccaa acatcacct tcatatttt 
ttcccattt attttatta tcgttattt tatcacgca 
ttcattgta tatatatca ttatgtgaa tttattgta 
aagatgttc taataattt atccttaat tgtagtctc 
ccagtttta agtccaata taatgagac tgaataaag 
tgtgtattt tatt

    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