Status
Please wait ...
Gene information
General information
TC004004 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_007418.3: 28614463..28652151
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
    		TC004004
    Gene ontology

    GO terms for Tribolium

    • {{ goTerm.term }}
      ({{ goTerm.evidence }}){{ goTerm.evidenceTooltip }}
      {{goTerm.showAll ? '[-]' : '[+]'}}
      Status: {{ goTerm.status }}
      Evidence: {{ goTerm.evidence }} ({{ goTerm.evidenceTooltip }})
      Reference: {{ goTerm.referenceText }}
      Quotation: {{ goTerm.quotation }}
      Submitter: {{ goTerm.name }}

    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 *
    {{ blurIdResult }}
    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.
      {{ unavailableText }}

    * : mandatory fields
    For help on how to submit larger datasets or non experimental data please contact us.
    iBeetle screen iB_00651

    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: 10.0% (includes death as pupa, adult)

    adult lethality - Number of animals showing the phenotype: 1 (9 dpi)
    Days post injection

    Analysis of larval stage 1 cuticle
    number of eggs/embryos/larvae on slide: < 50
    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: 30.0% (includes death as larva, prepupa, pupa)
    Lethalities 22 days after larval injection: 40.0% (includes death as larva, prepupa, pupa, adult)

    larva lethality - Number of animals showing the phenotype: 3 (11 dpi)
    Days post injection

    eclosion not fulfilled (died as pupa) - Number of animals showing the phenotype: 1 (16 dpi)
    Days post injection

    RNAi sequence
    Primers
    Left: Right:
    Protein sequence
    • >TC004004 RA
      MGCLREQYL FNVFEAIIS TLESKLQRI ENLDKAVEH 
LMRRVEGLD NRVNNNIDK TESVIAKLS LLDSKLFNF 
DSKKPDGSN DGNVGRRLV ALDQKVSDI DNKLNVLKS 
QLDNNLLQG EDINAEASE KKPVSMNVV EITKALNTE 
VINHVTKEL GQLREATGS VDRKLQFHI TLVSENLGK 
VLTMMTDIH HAIVDDITS HYNRTTTPA PEPKNNKID 
ALVQQIRPI ISVSEKMDE VWDVVVGTK SSVDDLVPK 
SDELLTQTQ RQERAIGEI HNDLRTKTN KIIANLDKV 
EKRLKKQED DVATLAQRP VPAELLLDP TIDRLVEYD 
PSRYVDEYS TDTTLPATF TTLPPPTTA TQASTLNQS 
STTPVSSST QATTEKRAE KRKSGLIFP SVKNKPSPA 
NTTFATEVL ANVKDVKGY SCVDLLNAG MRDSGVYYL 
QIRGTTYWF LKVYCEQEI ADGGWTVIQ RRDDFGDPR 
ENFNRDWND YKNGFGDPA KEFWLGNEN IYMLTNNEE 
YILRVELED FEGNKRFAQ YSHFKIFSE GEYYKLEID 
GYEGNAGDS LNDPWYGSN NSPFSTYNR DNDRSSLNC 
ASMLKGGWW WKSCGRGLN GLYLNDPQD LTARQGIVW 
FRWRGWDYT LKKAMMMIK PKGPVTTT
    CDS sequence
    • >TC004004 RA
      atgggttgt ttaagagag caatacctc ttcaacgta 
ttcgaagcc ataatctca accctcgaa tccaaactc 
cagcggatc gaaaacttg gacaaagcc gtcgagcat 
ttgatgcga agggtggaa ggtttggac aatcgtgtt 
aacaacaac attgacaaa actgaatca gtgatcgca 
aaactgtcg ctccttgac tccaaactg ttcaatttc 
gattcgaaa aaaccagat gggtcaaat gatggcaac 
gtgggtcga cgattggtc gcccttgac cagaaagtg 
agtgacatt gacaataaa ctgaacgtt ttgaagagc 
cagctcgac aacaacttg ctccaaggc gaagacatc 
aatgctgaa gcaagcgag aagaaacca gtgagcatg 
aacgtggtg gaaatcacc aaggcgttg aacacggaa 
gtgataaac cacgtgacc aaagagttg ggccaattg 
agggaagcc acgggaagt gttgaccgg aaactgcaa 
tttcatatc actttagtc tcggagaat ttgggcaaa 
gtgttgact atgatgact gatattcac cacgccata 
gttgatgat attacaagt cattataat agaaccaca 
actccggcc ccggaaccc aaaaacaac aaaatcgac 
gctttggtg caacaaatc cgcccgatt atctccgtg 
tcggagaaa atggacgag gtttgggac gttgttgtt 
gggactaaa tcgtcggtt gacgatttg gtgccgaaa 
tctgacgaa ctgctgacg cagacgcag cgacaggag 
cgagcgatc ggcgaaatc cacaacgat ttgaggact 
aagaccaat aaaattatc gcgaatttg gataaggtt 
gagaagagg ttgaagaag caggaggat gatgtggcc 
acgttggcc cagagacct gtcccagct gagttgtta 
ttggatccg actattgat cgtttggtt gagtatgat 
cccagtcgg tatgttgat gagtattca actgatacg 
actcttccg gcgactttc accactttg ccgcccccg 
actaccgcc actcaagcg tcaacgttg aatcagagt 
agtacaact ccggtgagt tcttcaact caggccaca 
acagagaaa agggcggag aagaggaaa agtggcttg 
attttcccg agtgtgaaa aataagcct tcgccggcg 
aataccacg tttgcgacc gaagttttg gccaatgtc 
aaggatgtt aaggggtat tcttgcgtg gacctgctg 
aacgctgga atgcgtgat tccggtgtt tactacttg 
caaatccgg ggaaccacc tactggttc ttgaaggtg 
tattgcgag caagaaatc gccgatggt ggatggacg 
gtgatccag cgcagagac gacttcggc gaccctcga 
gagaacttc aacagggac tggaacgac tacaagaac 
ggcttcggc gacccggcc aaggagttc tggctcggc 
aacgaaaac atctacatg ctgaccaac aacgaggag 
tacatcctg cgcgtggag ctcgaggac tttgaagga 
aataaaaga tttgcccaa tactcgcac ttcaagata 
ttctcagaa ggggaatat tacaagttg gagatcgat 
ggttacgaa ggcaatgct ggggattcg ctgaacgat 
ccgtggtat ggaagcaac aacagtccg ttctcaaca 
tacaacaga gacaacgat aggtcgagc ctcaactgc 
gcctccatg ttgaagggc ggctggtgg tggaagtcc 
tgtggacgg ggccttaac ggcctctac ctcaacgat 
ccgcaagat cttacagca cggcaaggt atagtctgg 
ttccggtgg agaggctgg gactacacg ctgaagaag 
gccatgatg atgatcaaa ccgaaagga ccagttaca 
acaacataa
    mRNA sequence
    • >TC004004 RA
      gtataaaaa aattaacct taataaaaa aacttattt 
cctcaaaaa agtaaataa ataaaaaat aaaaaatgg 
atacaatat ttaattttt acgaagata taaaaataa 
atgaaacat gggttgttt aagagagca atacctctt 
caacgtatt cgaagccat aatctcaac cctcgaatc 
caaactcca gcggatcga aaacttgga caaagccgt 
cgagcattt gatgcgaag ggtggaagg tttggacaa 
tcgtgttaa caacaacat tgacaaaac tgaatcagt 
gatcgcaaa actgtcgct ccttgactc caaactgtt 
caatttcga ttcgaaaaa accagatgg gtcaaatga 
tggcaacgt gggtcgacg attggtcgc ccttgacca 
gaaagtgag tgacattga caataaact gaacgtttt 
gaagagcca gctcgacaa caacttgct ccaaggcga 
agacatcaa tgctgaagc aagcgagaa gaaaccagt 
gagcatgaa cgtggtgga aatcaccaa ggcgttgaa 
cacggaagt gataaacca cgtgaccaa agagttggg 
ccaattgag ggaagccac gggaagtgt tgaccggaa 
actgcaatt tcatatcac tttagtctc ggagaattt 
gggcaaagt gttgactat gatgactga tattcacca 
cgccatagt tgatgatat tacaagtca ttataatag 
aaccacaac tccggcccc ggaacccaa aaacaacaa 
aatcgacgc tttggtgca acaaatccg cccgattat 
ctccgtgtc ggagaaaat ggacgaggt ttgggacgt 
tgttgttgg gactaaatc gtcggttga cgatttggt 
gccgaaatc tgacgaact gctgacgca gacgcagcg 
acaggagcg agcgatcgg cgaaatcca caacgattt 
gaggactaa gaccaataa aattatcgc gaatttgga 
taaggttga gaagaggtt gaagaagca ggaggatga 
tgtggccac gttggccca gagacctgt cccagctga 
gttgttatt ggatccgac tattgatcg tttggttga 
gtatgatcc cagtcggta tgttgatga gtattcaac 
tgatacgac tcttccggc gactttcac cactttgcc 
gcccccgac taccgccac tcaagcgtc aacgttgaa 
tcagagtag tacaactcc ggtgagttc ttcaactca 
ggccacaac agagaaaag ggcggagaa gaggaaaag 
tggcttgat tttcccgag tgtgaaaaa taagccttc 
gccggcgaa taccacgtt tgcgaccga agttttggc 
caatgtcaa ggatgttaa ggggtattc ttgcgtgga 
cctgctgaa cgctggaat gcgtgattc cggtgttta 
ctacttgca aatccgggg aaccaccta ctggttctt 
gaaggtgta ttgcgagca agaaatcgc cgatggtgg 
atggacggt gatccagcg cagagacga cttcggcga 
ccctcgaga gaacttcaa cagggactg gaacgacta 
caagaacgg cttcggcga cccggccaa ggagttctg 
gctcggcaa cgaaaacat ctacatgct gaccaacaa 
cgaggagta catcctgcg cgtggagct cgaggactt 
tgaaggaaa taaaagatt tgcccaata ctcgcactt 
caagatatt ctcagaagg ggaatatta caagttgga 
gatcgatgg ttacgaagg caatgctgg ggattcgct 
gaacgatcc gtggtatgg aagcaacaa cagtccgtt 
ctcaacata caacagaga caacgatag gtcgagcct 
caactgcgc ctccatgtt gaagggcgg ctggtggtg 
gaagtcctg tggacgggg ccttaacgg cctctacct 
caacgatcc gcaagatct tacagcacg gcaaggtat 
agtctggtt ccggtggag aggctggga ctacacgct 
gaagaaggc catgatgat gatcaaacc gaaaggacc 
agttacaac aacataaaa agtggaaga aaactagcc 
aatttataa tcaccggtc catttaatc ataaaattc 
atcaatcat aaatcaata tttatttcg acacatccg 
acacttacc tattttaaa ttacctcat agtatagta 
tactgaaaa tgatttttc acagaaata ttgcctaga 
acggttcta tcgaccaac gaattttcc ccagttgta 
tgtaaatat aaatgatag aattgttcc taatgtagg 
ttaagattg tacatttgc gctcccatc ttagttttg 
taaggaggt gtatttgca tgtagttac actaataca 
tacacagag acgcacaca catttcctg cacgatttt 
tgcaaaaac taacattta ctaatagcg aggcaaaat 
gtgtttaaa atttccgct gattataaa ttgggaaaa 
cacgaaaat gttgaggaa atttaagac tgtgtcgct 
tatcggagg aaagtttcg tcgataagt ttgtattaa 
tgtaaggta ttttgttgt gaggctaat gggacatga 
aatgcaatg ttcgtatta ggcaggtta aaatcaaat 
cttaccgta ggtcttgta ccttaagcg ttttacatg 
gttgttgta aatattcta tttcagagt tgtataaat 
taaatatat tttaatata ataaattat gttaagtat 
t

    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