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Gene information
General information
TC009993 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_007422.5: 10606194..10608642
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
    		TC009993
    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
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    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
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    Name
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    Email
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    * : mandatory fields
    For help on how to submit larger datasets or non experimental data please contact us.
    iBeetle screen iB_06281

    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: 20.0% (includes death as pupa, adult)

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

    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

    RNAi sequence
    Primers
    Left: Right:
    Protein sequence
    • >TC009993 RA
      MMEIHLPIK NSWKTVNNL KENLKKEAQ ERKRNILHL 
IFKYLVDNN LLSVAEVLQ NETQTGIHY QVCDNIDLE 
IVLQEYQSY YYTKFQKQP KILRKTAEN EQVAPLKKE 
RKSTAKEKQ TLKQEKNDD TFQFEIVTL SKDSSLSDI 
QSKPLIDFE NYSSEWREM ADQIIKQIV PKTLGITFK 
DCISLSSTI ETLKEAIIY PLSYPQLFE KACTWRGVL 
LYGPPGTGK TLLARALAC ESSSTLINV TSSAFISKW 
RGESEKMVK VLFDVAKFY SPTTIFIDE IDALASTSH 
DSNHEASRR FKSELLTQI DGIMKTEVF VLATTNNPW 
SIDNALLRR FEKRILVPL PDKDSRSEL FQYYFSKNG 
YDFRNEDLA VFVNQTENF SGSDVKNVC KEAEMIVIR 
EKLEQIRRG DKKKCTRQV KSGDVLNAL KKIKPCIEQ 
NDYKKYLDW GRKYGAT
    CDS sequence
    • >TC009993 RA
      atgatggaa atccatcta cctatcaaa aacagttgg 
aaaaccgtc aataacttg aaagaaaac ttgaaaaaa 
gaggcccaa gagcgcaag cgaaacatt ctccaccta 
atcttcaaa tacctcgtc gacaacaac ttactctca 
gtcgccgaa gtgcttcaa aacgaaacc caaaccgga 
atccactac caagtctgc gacaacatc gacttggag 
atagtcctc caagaatac caaagttac tattacaca 
aaattccaa aaacaacca aaaatctta cgaaaaact 
gccgaaaac gaacaagtg gccccttta aaaaaagag 
cgaaaatca acagccaaa gaaaaacaa accctaaag 
caagaaaaa aatgacgac actttccaa ttcgaaatt 
gtcacatta tcaaaagac tcgagcttg agcgacatc 
cagtcaaaa ccgctgatc gattttgaa aactactca 
tcagaatgg cgcgaaatg gccgaccaa ataatcaaa 
caaatcgta ccgaaaaca ctggggata actttcaag 
gattgtatc agcctcagc tccactatt gagacgctg 
aaagaggcg ataatttac cccttgagc tacccccag 
ctgtttgaa aaagcctgc acttggcga ggcgtcctc 
ctctacggc cctccaggc accggcaaa accttacta 
gccagagct ttagcatgc gaatcctcg tccacgctc 
atcaacgtc accagtagc gcatttatc agcaaatgg 
cgcggagag tcggaaaaa atggttaaa gtactattc 
gacgttgcc aaattctat tcaccaacg acgattttc 
atcgacgaa atcgacgcc ctcgcctcc acatcgcac 
gattcgaat cacgaagct tcgcgtcgt ttcaaaagc 
gagcttttg acacagatc gatggtatt atgaaaact 
gaagtattt gttttggcc accacaaat aatccctgg 
agtatagat aacgcgctt ttgagacgg tttgaaaaa 
cgaattttg gtgccacta ccagataaa gactcaaga 
agtgaattg tttcaatac tacttttcc aaaaatgga 
tacgatttt agaaacgaa gacttggcg gtgtttgtt 
aatcagact gaaaatttc tcaggctct gatgtgaaa 
aacgtgtgc aaggaagct gaaatgatt gtaattcgg 
gaaaaactg gaacaaatc agaagaggg gataagaaa 
aagtgtacg agacaggtg aaaagtggg gacgtttta 
aacgctctc aagaaaatc aaaccgtgt attgaacaa 
aatgattac aagaagtat cttgactgg gggcggaaa 
tatggggcc acgtga
    mRNA sequence
    • >TC009993 RA
      actcaatgg tgtgtggta gagaagtgg ttacatata 
aagcaacac gctgttaat ttattacta aaaatgatg 
gaaatccat ctacctatc aaaaacagt tggaaaacc 
gtcaataac ttgaaagaa aacttgaaa aaagaggcc 
caagagcgc aagcgaaac attctccac ctaatcttc 
aaatacctc gtcgacaac aacttactc tcagtcgcc 
gaagtgctt caaaacgaa acccaaacc ggaatccac 
taccaagtc tgcgacaac atcgacttg gagatagtc 
ctccaagaa taccaaagt tactattac acaaaattc 
caaaaacaa ccaaaaatc ttacgaaaa actgccgaa 
aacgaacaa gtggcccct ttaaaaaaa gagcgaaaa 
tcaacagcc aaagaaaaa caaacccta aagcaagaa 
aaaaatgac gacactttc caattcgaa attgtcaca 
ttatcaaaa gactcgagc ttgagcgac atccagtca 
aaaccgctg atcgatttt gaaaactac tcatcagaa 
tggcgcgaa atggccgac caaataatc aaacaaatc 
gtaccgaaa acactgggg ataactttc aaggattgt 
atcagcctc agctccact attgagacg ctgaaagag 
gcgataatt taccccttg agctacccc cagctgttt 
gaaaaagcc tgcacttgg cgaggcgtc ctcctctac 
ggccctcca ggcaccggc aaaacctta ctagccaga 
gctttagca tgcgaatcc tcgtccacg ctcatcaac 
gtcaccagt agcgcattt atcagcaaa tggcgcgga 
gagtcggaa aaaatggtt aaagtacta ttcgacgtt 
gccaaattc tattcacca acgacgatt ttcatcgac 
gaaatcgac gccctcgcc tccacatcg cacgattcg 
aatcacgaa gcttcgcgt cgtttcaaa agcgagctt 
ttgacacag atcgatggt attatgaaa actgaagta 
tttgttttg gccaccaca aataatccc tggagtata 
gataacgcg cttttgaga cggtttgaa aaacgaatt 
ttggtgcca ctaccagat aaagactca agaagtgaa 
ttgtttcaa tactacttt tccaaaaat ggatacgat 
tttagaaac gaagacttg gcggtgttt gttaatcag 
actgaaaat ttctcaggc tctgatgtg aaaaacgtg 
tgcaaggaa gctgaaatg attgtaatt cgggaaaaa 
ctggaacaa atcagaaga ggggataag aaaaagtgt 
acgagacag gtgaaaagt ggggacgtt ttaaacgct 
ctcaagaaa atcaaaccg tgtattgaa caaaatgat 
tacaagaag tatcttgac tgggggcgg aaatatggg 
gccacgtga cagtgaatt taatgtaat taataatta 
ttcaagaat cttcataaa tgtaacgac tacgagtat 
aataaaagt cccaaaact aa

    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