Status
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Gene information
General information
TC004489 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: 3809491..3814978
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
    		TC004489
    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_03768

    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: 90.0% (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

    adult lethality - Number of animals showing the phenotype: 4 (11 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: 80.0% (includes death as larva, prepupa, pupa)
    Lethalities 22 days after larval injection: 100.0% (includes death as larva, prepupa, pupa, adult)

    larva lethality - Number of animals showing the phenotype: 8 (11 dpi)
    Days post injection

    pupal molt delayed (still larva) - Number of animals showing the phenotype: 2 (11 dpi)
    Days post injection

    pupal molt not fulfilled (died as L7 or prepupa) - Number of animals showing the phenotype: 2 (16 dpi)
    Days post injection

    RNAi sequence
    Primers
    Left: Right:
    Protein sequence
    • >TC004489 RA
      MSGEETSAD RNVEIWKIK KLIKSLELA RGNGTSMIS 
LIIPPKDQI SRVSKMLAD EFGTASNIK SRVNRLSVL 
GAITSVQHR LKLYTKVPP NGLVIYCGT IVTDEGKEK 
KVNIDFEPF KPINTSLYL CDNKFHTEA LTALLADDN 
KFGFIVMDG NGALFGTLQ GNTREVLHK FTVDLPKKH 
GRGGQSALR FARLRMEKR HNYVRKVAE VATQLFITN 
DKPNIAGLI LAGSADFKT ELSQSDMFD PRLQAKVIK 
LVDVSYGGE NGFNQAIEL AAESLQNVK FIQEKKLIG 
RYFDEISQD TGKYCFGVE DTLRGLELG AVETLICWE 
NLDIQRYVL KNHTTGTET VLHLTPEQE KDKSHFTDK 
DSGVELELV ECQPLLEWL ANNYKNFGA TLEIITDKS 
QEGSQFVRG FGGIGGLLR YKVDFQNLQ LDEELDNGD 
DFDLDDY
    CDS sequence
    • >TC004489 RA
      atgtcagga gaggagact tcagccgac cgtaatgta 
gaaatctgg aaaataaag aaactgatc aaaagtttg 
gaactggcg agaggcaat ggaaccagc atgatttcg 
ttaattata ccgcccaaa gatcaaatc tcgagagtt 
agcaaaatg ttagctgat gaattcggc acagcctcc 
aatatcaag tcgagagtt aacagattg tcagtcttg 
ggggctatc acctcagtc cagcatcgc ctcaaactc 
tacacaaaa gtgccgcca aacggctta gtcatctac 
tgtggtacg atcgtgacg gatgaaggt aaagaaaag 
aaagtcaac atcgatttc gaaccgttc aaacctatc 
aatacctct ctgtactta tgcgacaat aagttccac 
acggaagct ctaacggcc ttactggca gacgataat 
aaattcggc tttatcgta atggacggt aacggagca 
ttattcggt acattacaa ggcaacact cgagaggtc 
ctccataag ttcaccgtc gatctacca aaaaagcac 
ggacgtggt ggtcaatcc gcgctgcgt ttcgcccgt 
ttgcgaatg gaaaaacgg cacaattac gtgcgaaaa 
gtggccgaa gtggcaaca caactcttt atcaccaat 
gataagccc aatatcgct ggcttgata ttggcggga 
agtgctgat tttaagact gaacttagt caatccgat 
atgtttgat cctagattg caagcgaaa gttataaaa 
ttagtcgat gtgtcgtac gggggcgaa aacgggttc 
aatcaagcg attgaactg gcggctgaa tcgctccaa 
aacgtcaaa ttcatccaa gaaaagaaa ctgattggc 
cgatacttt gacgaaatc agtcaagac accggcaaa 
tactgtttc ggtgttgaa gatacgcta agagggctc 
gaattaggt gctgttgaa acgctgatt tgttgggag 
aatcttgat attcaacga tacgtcttg aagaatcac 
acgactggt acagaaacc gtattacac ctaacacca 
gaacaggaa aaggacaag tcacatttc actgacaaa 
gacagcggc gtggaactg gaattggtg gagtgtcag 
cctttgctt gaatggctt gcaaacaac tataagaat 
tttggtgct actttagaa attattacc gataagtcg 
caagaaggg tcgcagttc gttcgaggt tttggagga 
attggaggt ttgttacga tacaaagtg gatttccag 
aatttacag ttagatgaa gaactagac aacggcgat 
gattttgat ctagacgat tattaa
    mRNA sequence
    • >TC004489 RA
      ccagtttga ttgaataaa tgggaaatt ccggtcgga 
aagttggga aatcgtagg gtccttttc gaatttcct 
tctgcgaga ggctgtcac ctgccagtt ttattttgt 
gatcccctt tgtttcggc atgtgagtg actggaata 
ttttttccc gcactaacc aagtctccg ggtcgcgca 
tttctggtt ataaccagt taaagtggt taagttacc 
tgcataacc agtgaaaag tgactcaat caagtagtt 
cgtcggcat tggagaccg cgccatttt gcatcgggt 
cacattttt cgtattttt agttcatac gaaatccag 
cagaaatgt caggagagg agacttcag ccgaccgta 
atgtagaaa tctggaaaa taaagaaac tgatcaaaa 
gtttggaac tggcgagag gcaatggaa ccagcatga 
tttcgttaa ttataccgc ccaaagatc aaatctcga 
gagttagca aaatgttag ctgatgaat tcggcacag 
cctccaata tcaagtcga gagttaaca gattgtcag 
tcttggggg ctatcacct cagtccagc atcgcctca 
aactctaca caaaagtgc cgccaaacg gcttagtca 
tctactgtg gtacgatcg tgacggatg aaggtaaag 
aaaagaaag tcaacatcg atttcgaac cgttcaaac 
ctatcaata cctctctgt acttatgcg acaataagt 
tccacacgg aagctctaa cggccttac tggcagacg 
ataataaat tcggcttta tcgtaatgg acggtaacg 
gagcattat tcggtacat tacaaggca acactcgag 
aggtcctcc ataagttca ccgtcgatc taccaaaaa 
agcacggac gtggtggtc aatccgcgc tgcgtttcg 
cccgtttgc gaatggaaa aacggcaca attacgtgc 
gaaaagtgg ccgaagtgg caacacaac tctttatca 
ccaatgata agcccaata tcgctggct tgatattgg 
cgggaagtg ctgatttta agactgaac ttagtcaat 
ccgatatgt ttgatccta gattgcaag cgaaagtta 
taaaattag tcgatgtgt cgtacgggg gcgaaaacg 
ggttcaatc aagcgattg aactggcgg ctgaatcgc 
tccaaaacg tcaaattca tccaagaaa agaaactga 
ttggccgat actttgacg aaatcagtc aagacaccg 
gcaaatact gtttcggtg ttgaagata cgctaagag 
ggctcgaat taggtgctg ttgaaacgc tgatttgtt 
gggagaatc ttgatattc aacgatacg tcttgaaga 
atcacacga ctggtacag aaaccgtat tacacctaa 
caccagaac aggaaaagg acaagtcac atttcactg 
acaaagaca gcggcgtgg aactggaat tggtggagt 
gtcagcctt tgcttgaat ggcttgcaa acaactata 
agaattttg gtgctactt tagaaatta ttaccgata 
agtcgcaag aagggtcgc agttcgttc gaggttttg 
gaggaattg gaggtttgt tacgataca aagtggatt 
tccagaatt tacagttag atgaagaac tagacaacg 
gcgatgatt ttgatctag acgattatt aaattcctt 
gtaaggaca attaaacca gcattttgt aggagtggt 
gccgtttaa tataacgtg aagtggccg tattttgct 
catattaaa tgtgttgtt acaaatgat tgatataca 
taatttttt agttaattg ttaatttat gtaaatttc 
tgatcatag gtgattttg tacaagcct tgttttatt 
ttccagttt tgcgcagta aaatggatt tgagaattg 
atacttttc ataattatt ttaaattca agggtcaaa 
gttccccgg ggatatatt cttgtatgt ttgcatgat 
ctgtgagtt tttaccaag atatttttt attttatca 
aactaaatg gaattgttt aaagtacta aatataagt 
ttttctttt taaataatt ggatttgtt ccttttgac 
agttcctca acctccacg ttgtagtat agtagattt 
acattcctt aaaaattca aaggcaact acttctatg 
aaagcttgc gtctgtttt accagtttg tatcaagcc 
gcataattt tacatacaa attgtctaa atacgaatt 
tttacgtaa tagccactc attgtactt tttaacgaa 
attaaggat cttgtgcag gggttagtg accgcagaa 
gacccttaa ttgggccaa cgacctgtc accacatgt 
tgtaatttt gtttgtaat aaaattacc accatacaa 
gaaactgca gtttatttg ctgtttcta ccgagtgat 
caagaatga ctgtcagct ggcaacaat tcagttgta 
ttaaaacaa aattcaaag ctgccaact cacagtcct 
tgattattt tgtat

    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