Status
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Gene information
General information
TC004297 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.

NW_015451971.1: 37189..46903
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
    		TC004297
    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_03721

    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)

    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: 1 (9 dpi)
    Days post injection

    Analysis of larval stage 1 cuticle
    number of eggs/embryos/larvae on slide: < 50
     head not present - Penetrance (percentage of animals/eggs on slide): 30% - 50%

    thorax not present - Penetrance (percentage of animals/eggs on slide): 30% - 50%
    abdomen not present - Penetrance (percentage of animals/eggs on slide): 30% - 50%
    affected eggs/embryos/larvae total percentage of affected eggs/embryos/larvae on slide - Penetrance (percentage of animals/eggs on slide): 30% - 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: 10.0% (includes death as larva, prepupa, pupa)
    Lethalities 22 days after larval injection: 50.0% (includes death as larva, prepupa, pupa, adult)

    larva lethality - Number of animals showing the phenotype: 1 (11 dpi)
    Days post injection

    adult lethality - Number of animals showing the phenotype: 3 (16 dpi)
    Days post injection

    adult lethality - Number of animals showing the phenotype: 1 (19 dpi)
    Days post injection

    adult lethality - Number of animals showing the phenotype: 1 (41 dpi)
    Days post injection

    Fertility
    egg production: number <50% of expected -
    ovary without detectable defects - Number of animals showing the phenotype: 4
    RNAi sequence
    Primers
    Left: Right:
    Protein sequence
    • >TC004297 RA
      MGTRAVLVL LIFLSVGRS DRSLRSVFG AIFVPGTQF 
SQSENSVSQ SAPPEAPPM AYSVTEKEF TALRIEYIK 
NQILKKLRL KEKPTVALA ELPKPVKEY DNLIPDQED 
NLHSGYSED FYGKTTQAI IFPYEDEAR CLRKIRFPS 
VCVPFQMPT DIHSTDVST AELWFHKVP DNLDSHNQT 
FVVSEVAHW DTNKSFQKT KPIAIQETS LTEGWLKVD 
VTYVVKNWL DFQDSPTHA ISVACKTCG MDKNQSPIS 
FSSEFKPFL VVYTHSQQR RSLHRRPKR ATKCSAGRN 
ECCRESFYV SFADIGWDD WIMSPAGYD AYFCKGSCV 
TASALTLSA TQHNSILQK VMYGQNKNR GSRPELTPC 
CAATQFQPL QLVYMDNNK TMMTKVLSN MIVESCGCW
    CDS sequence
    • >TC004297 RA
      atgggcacc agagccgtt ttggtgttg ctgattttc 
ctctcggtc ggtcgcagt gatcgaagt ttgcggtcg 
gtttttggc gcaattttc gttccgggc acgcagttc 
agccaatcg gagaacagt gtgagccag agcgcgccc 
ccagaagcc cccccgatg gcctattcg gtcaccgag 
aaggagttc accgcgttg cggatcgaa tacatcaaa 
aaccaaatc ctgaagaag ctcaggctg aaggagaag 
cccacggtg gctttggcc gagctgccc aagccagtc 
aaggagtac gacaatttg ataccggac caggaggat 
aatttgcac agtggatac tcggaggac ttctacggg 
aagaccacg caagccatc atcttcccc tatgaagat 
gaggctcga tgtttgcga aaaattcgc ttcccctca 
gtttgcgtc cctttccaa atgcccact gatatccac 
tcgaccgat gttagcacg gctgaactt tggtttcac 
aaagtgcct gataatctg gactcccat aatcaaact 
ttcgtggta tcggaagtt gcccattgg gacaccaat 
aagagtttc caaaaaacg aagcctata gccatccag 
gaaacgagt ctcacagag ggttggctg aaggtggac 
gtgacgtac gtggtgaaa aactggctc gatttccaa 
gactcgcca acgcacgcc atcagcgtg gcttgcaag 
acctgcggc atggacaag aaccagtct cccatttcg 
ttttcgagc gaatttaag ccgtttttg gtggtctac 
acccactcg cagcagagg aggtcgctg caccgccgg 
ccgaagagg gcaacgaag tgctccgca ggccggaac 
gagtgctgc agggagagc ttctacgtc tcgtttgcg 
gacatcggc tgggacgac tggatcatg agtcctgca 
ggatacgac gcctacttc tgcaaaggc tcgtgtgtc 
acagcctcc gcgctgacg ctcagcgcc acgcaacat 
aacagtata ttacagaaa gtcatgtac gggcagaat 
aaaaatcgc ggctcgcga cccgaattg actccctgt 
tgcgctgca acgcagttt cagccgctg cagctggtt 
tatatggac aataataaa actatgatg acgaaagtt 
ctgtcgaat atgatagtg gaaagttgt ggttgttgg 
tga
    mRNA sequence
    • >TC004297 RA
      tccaacaga atgagagtc acaatagaa cgtcttata 
aaactcgta taataatgt gacgtacca agatgtatt 
gaacaattg atttcattt gatctgttt aatgttgca 
ctaatgtta aataaagca aatgtttct taaaaatat 
atattagaa attatacaa tacaaaaaa aaacaatct 
taaacagga aataaacaa cttcgcaaa ataattatt 
aatttttaa tgaaaaaat aaatctaac caacaacta 
gataaaatt aggaaatgt ttacacgga aaaagacaa 
acaaaatgg aactatcat gtcttgaag cgccaatgg 
atttaaatc cggtagaca ataaaaaca aaattgaat 
ctcaatttt ttaataggt gatttataa actcaatat 
cagtgtcgt agaattcgt tgcaaaagt gaccgggct 
tgttattta gttgaaaac ttagtccag caaaaagtt 
tgttttatc ctgtatggc taggtggtg aactggtta 
gcttgcgat tgagtgaat tttcggggc ttgcttcca 
agtgccaag ttcgacatt ggggttgtg gttgtggct 
ccaagccgt tcagatttt cattactta aaacttgag 
cggaagtac gtccagttc atattctcg tattatttc 
taaataagt gatatatca gtagcttgt taacgcaat 
ctactctct ataagcaga ttagtttct tcgctgtta 
catgtttta ttttgaatg atgaaattt taatatttg 
actaggaat acttacaag ttttataca acattgtat 
aggattttc aaagtgata gctatacat atatatcgg 
ttacgttgg tgtgctgtg cttacggat cagttaggt 
tattgaagg tgttatatt tagtactac gcgatcatt 
tctattact gctaggagc gttttccgc aagaatcaa 
acatgttca tattacctt tgttcttta ataataaac 
atgcaaatg tgatatggt ttttaattc tactaattt 
tgtattgct ttgtttacg ttttacaca tattttaac 
aatcctacc aacaataaa ttgtacagt ttctattct 
gagtgttga tacaatttc atacaaaat aaatatcta 
ataataaca ttacgaaac atgactcgt ttttctgcc 
cttccgaat ccctcaggt cattcacac aattcgtgt 
ttatgtgtt aattaatga ctaatactg aaaacatcc 
gaagatatt ttttaattt gattagttg tggagaaat 
aaacaatat tttatagta cggcatttg attatgaat 
ttgttttgc tcccgctat ctgattcaa accgaagga 
aagttacga gataaaaaa ctgataaac cacactact 
accgctgat tttgcttct agaaatagt ttttcattg 
ataaaaaac aagcgtgtg cgccgttac gtttggaca 
tgcggatac gccttggag gccacctca tgaagtact 
taacatttt ctgaaagct gttccttcc tacgtgaca 
tagcacgtg ctgaaacca ccgaatcgg tatcatcta 
aatttgaca taacggcta ctctagttc tgatagaac 
ctcaggttc aaggttcat ttctatcat ccgttacag 
aaatgccaa gaactcgag agtggggaa ttaaatcgc 
tgtgtttta agagtgcac ttctcggca ccaatctag 
tttaaaatc atctgtaaa caacgcaaa atgggcacc 
agagccgtt ttggtgttg ctgattttc ctctcggtc 
ggtcgcagt gatcgaagt ttgcggtcg gtttttggc 
gcaattttc gttccgggc acgcagttc agccaatcg 
gagaacagt gtgagccag agcgcgccc ccagaagcc 
cccccgatg gcctattcg gtcaccgag aaggagttc 
accgcgttg cggatcgaa tacatcaaa aaccaaatc 
ctgaagaag ctcaggctg aaggagaag cccacggtg 
gctttggcc gagctgccc aagccagtc aaggagtac 
gacaatttg ataccggac caggaggat aatttgcac 
agtggatac tcggaggac ttctacggg aagaccacg 
caagccatc atcttcccc tatgaagat gaggctcga 
tgtttgcga aaaattcgc ttcccctca gtttgcgtc 
cctttccaa atgcccact gatatccac tcgaccgat 
gttagcacg gctgaactt tggtttcac aaagtgcct 
gataatctg gactcccat aatcaaact ttcgtggta 
tcggaagtt gcccattgg gacaccaat aagagtttc 
caaaaaacg aagcctata gccatccag gaaacgagt 
ctcacagag ggttggctg aaggtggac gtgacgtac 
gtggtgaaa aactggctc gatttccaa gactcgcca 
acgcacgcc atcagcgtg gcttgcaag acctgcggc 
atggacaag aaccagtct cccatttcg ttttcgagc 
gaatttaag ccgtttttg gtggtctac acccactcg 
cagcagagg aggtcgctg caccgccgg ccgaagagg 
gcaacgaag tgctccgca ggccggaac gagtgctgc 
agggagagc ttctacgtc tcgtttgcg gacatcggc 
tgggacgac tggatcatg agtcctgca ggatacgac 
gcctacttc tgcaaaggc tcgtgtgtc acagcctcc 
gcgctgacg ctcagcgcc acgcaacat aacagtata 
ttacagaaa gtcatgtac gggcagaat aaaaatcgc 
ggctcgcga cccgaattg actccctgt tgcgctgca 
acgcagttt cagccgctg cagctggtt tatatggac 
aataataaa actatgatg acgaaagtt ctgtcgaat 
atgatagtg gaaagttgt ggttgttgg tgatgacac 
tgtaacagt aacagtatt ttgtttcgt gatttttca 
cgtgcaact aaccaaagc gagagatac caaaaattg 
gggaaattt tcgttttag aatttttcg ccaggcgag 
gattttcta cgtcaattt aatttattt cttagttaa 
ttttatgtc aagctatgt tatatttat tttatgtgt 
attttttaa ttttataag taaaccaat tgagcaaat 
atgcgtgtt tttatcctt cctcttcca aataattcc 
aaataaaca gtcctgaaa tta

    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