Status
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Gene information
General information
TC000960 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_007417.3: 8955980..8958414
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
    		TC000960
    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_00197

    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: 1 (3 dpi)
    Days post injection

    adult lethality - Number of animals showing the phenotype: 4 (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: 20.0% (includes death as larva, prepupa, pupa)
    Lethalities 22 days after larval injection: 20.0% (includes death as larva, prepupa, pupa, adult)

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

    pupal molt delayed (still larva) - Number of animals showing the phenotype: 3 (11 dpi)
    Days post injection

    eclosion delayed (still pupa) - Number of animals showing the phenotype: 2 (16 dpi)
    Days post injection

    remarks: later than schedule, eclosion delayed (still pupa) - Number of animals showing the phenotype: 2 (19 dpi)
    Days post injection

    Pupal morphology
    remarks: later than schedule,
    Adult morphology
    remarks: later than schedule,
    RNAi sequence
    Primers
    Left: Right:
    Protein sequence
    • >TC000960 RA
      MLRLARSAF GRVQKCNFS AAAVPAPQE SPNVMYSGI 
FINNEWHKS KSGKTFPTV NPTTGEIIT EVQQGAKED 
IDLAVDAAN EAFRFNSPW RTMDASDRG LLLNRLADL 
MERDAAYLA SLETLDNGK PYHVAYPVD IMGSIKVIR 
YMAGWADKN HGRVIPLDG PFMCYTRHE PVGVCGQII 
PWNFPLLMM AWKIGPALS MGNTVVLKP AEQTPLTAL 
YTAQLIKEA GFPPGVFNL VPGFGDAGA ALVSNPKVD 
KIAFTGSTE VGLKIQQMS GVGNLKRTT LELGGKSPN 
IILADVDIE KAVEQAHFG LFFNQGQVC CAGSRTFIE 
DKIYDEFVE RSVERAKKR TVGNPFDPK TEQGPQIDE 
TQMTKILGL VKEGVNQGA KLLVGGKRV GDKGYFVEP 
TVFANVEDN HVIAKEEIF GPVQQLMRF KDLDEIIER 
ANNTNYGLA AAVFSKDLD KVNYLVQGI RAGTVWVNT 
YNILGAQTP FGGFKDSGH GREMGIYGL NQYTEVKSI 
ITSVARKNS
    CDS sequence
    • >TC000960 RA
      atgctccgt ttagcaaga tcagccttt ggcagggtc 
cagaaatgt aatttctcg gcagcggcg gtcccggcg 
cctcaagag agccccaat gtgatgtac tcggggatt 
tttatcaat aacgaatgg cacaaatcg aaatcgggc 
aaaaccttc cccaccgtg aaccccacc accggtgaa 
atcatcacc gaggtgcag caaggggcc aaggaagac 
atcgacttg gctgttgat gccgccaat gaggccttc 
cgcttcaac tccccctgg cgcaccatg gacgcctcc 
gaccggggg ctgctcctg aaccgcctg gcggacctg 
atggagcgc gacgccgcg tacttggcg agtctcgaa 
accttagac aacggtaaa ccgtaccat gtggcctac 
cctgtcgac atcatgggc agtatcaaa gtgataagg 
tacatggcc ggctgggct gacaaaaac cacggcagg 
gtcataccc ctggacggc cccttcatg tgctacacg 
cgccacgag cccgtcgga gtctgcggg caaatcatc 
ccctggaac ttccccctg ctgatgatg gcgtggaag 
atcggccct gccttgagc atggggaac acggtggtg 
ctcaagccc gccgagcaa acccccctg acagccctc 
tacacggcg cagttgatc aaagaggcc gggttcccc 
ccaggcgtc ttcaatcta gtgcccggg ttcggcgac 
gcgggggcc gcacttgtc tccaacccc aaagtcgat 
aaaatcgca tttacggga tcgaccgaa gtggggctg 
aaaatccag caaatgtca ggcgttggt aacttgaaa 
cggaccacc ttggaattg gggggcaaa agccccaac 
attatcctg gccgatgtt gatatcgag aaggccgtg 
gaacaagcc cacttcggg ctgttcttc aatcaagga 
caagtgtgc tgtgcgggc tcacggacc ttcatcgag 
gacaaaatc tacgacgag tttgtcgaa aggtcggtc 
gaacgggcg aaaaagcgc accgttggc aaccccttt 
gaccccaaa acggagcaa gggccccag attgatgaa 
acccaaatg acgaaaatc ctgggtttg gttaaagaa 
ggggtgaac caaggggca aaattgttg gttgggggt 
aagagagtt ggggataag ggatatttc gttgaaccg 
acagttttc gccaatgtt gaggataac cacgtgatt 
gccaaagaa gaaattttt gggccagtg caacaattg 
atgcggttc aaggacttg gatgagatt atagaacgg 
gcgaataat accaattat gggcttgcg gcagctgtt 
ttctcgaaa gatttggat aaagtcaat tatctggtt 
caagggata agggctggg actgtctgg gtcaacacg 
tacaatatt ttgggggcg caaacgccg tttggaggg 
ttcaaggat tcgggacat gggcgtgag atgggaatt 
tatggcttg aatcaatac actgaagtt aaaagtatt 
attacatcg gttgcacga aaaaactcg taa
    mRNA sequence
    • >TC000960 RA
      tgtcaatgt cgacgaacg tcaatgtca catttttgc 
gcacatgtt ttttaactg ggataaaaa tacagaatt 
ttaattaat accccgttt aatttcgat aaaccaacc 
gtaaacact gtatatcac tcgctacaa gcgctattt 
caaggttat caagcctat tttcgtgca taccaaacc 
aatgattac cggtaacca gttgatgaa ttgtagttt 
ttgatttat ctaaaatcc cgcgataaa gtccgtgcg 
gggggtatt tagtgataa tatcctgac cctgctaag 
tgttataag cgtaactgg aatagcaga cgttcattt 
ggtgccgaa gcgtcgaac gatctcaac aagatgctc 
cgtttagca agatcagcc tttggcagg gtccagaaa 
tgtaatttc tcggcagcg gcggtcccg gcgcctcaa 
gagagcccc aatgtgatg tactcgggg atttttatc 
aataacgaa tggcacaaa tcgaaatcg ggcaaaacc 
ttccccacc gtgaacccc accaccggt gaaatcatc 
accgaggtg cagcaaggg gccaaggaa gacatcgac 
ttggctgtt gatgccgcc aatgaggcc ttccgcttc 
aactccccc tggcgcacc atggacgcc tccgaccgg 
gggctgctc ctgaaccgc ctggcggac ctgatggag 
cgcgacgcc gcgtacttg gcgagtctc gaaacctta 
gacaacggt aaaccgtac catgtggcc taccctgtc 
gacatcatg ggcagtatc aaagtgata aggtacatg 
gccggctgg gctgacaaa aaccacggc agggtcata 
cccctggac ggccccttc atgtgctac acgcgccac 
gagcccgtc ggagtctgc gggcaaatc atcccctgg 
aacttcccc ctgctgatg atggcgtgg aagatcggc 
cctgccttg agcatgggg aacacggtg gtgctcaag 
cccgccgag caaaccccc ctgacagcc ctctacacg 
gcgcagttg atcaaagag gccgggttc cccccaggc 
gtcttcaat ctagtgccc gggttcggc gacgcgggg 
gccgcactt gtctccaac cccaaagtc gataaaatc 
gcatttacg ggatcgacc gaagtgggg ctgaaaatc 
cagcaaatg tcaggcgtt ggtaacttg aaacggacc 
accttggaa ttggggggc aaaagcccc aacattatc 
ctggccgat gttgatatc gagaaggcc gtggaacaa 
gcccacttc gggctgttc ttcaatcaa ggacaagtg 
tgctgtgcg ggctcacgg accttcatc gaggacaaa 
atctacgac gagtttgtc gaaaggtcg gtcgaacgg 
gcgaaaaag cgcaccgtt ggcaacccc tttgacccc 
aaaacggag caagggccc cagattgat gaaacccaa 
atgacgaaa atcctgggt ttggttaaa gaaggggtg 
aaccaaggg gcaaaattg ttggttggg ggtaagaga 
gttggggat aagggatat ttcgttgaa ccgacagtt 
ttcgccaat gttgaggat aaccacgtg attgccaaa 
gaagaaatt tttgggcca gtgcaacaa ttgatgcgg 
ttcaaggac ttggatgag attatagaa cgggcgaat 
aataccaat tatgggctt gcggcagct gttttctcg 
aaagatttg gataaagtc aattatctg gttcaaggg 
ataagggct gggactgtc tgggtcaac acgtacaat 
attttgggg gcgcaaacg ccgtttgga gggttcaag 
gattcggga catgggcgt gagatggga atttatggc 
ttgaatcaa tacactgaa gttaaaagt attattaca 
tcggttgca cgaaaaaac tcgtaattg ataaccttt 
aaaaatggt atcggttat tatgtaacg tttttccat 
tgaaaagtg ctttttcat catacattt taaggtcaa 
atttgattg tgtgttgcc ataaattgt tacgattgt 
ttgtattca taataaagt ttctatatt ttt

    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