Status
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Gene information
General information
TC003404 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: 4331472..4336984
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
    		TC003404
    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_03550

    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: 0.0% (includes death as pupa, adult)

    Fertility
    ovary without detectable defects - Number of animals showing the phenotype: 3
    Analysis of larval stage 1 cuticle
    number of eggs/embryos/larvae on slide: < 20
    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: 30.0% (includes death as larva, prepupa, pupa, adult)

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

    eclosion not fulfilled (not completely eclosed) - Number of animals showing the phenotype: 1 (16 dpi)
    Days post injection

    Adult morphology
    legs tarsus partially necrotic - Number of animals showing the phenotype: 8


    legs tarsus distal cuticularisation lighter - Number of animals showing the phenotype: 8


    RNAi sequence
    Primers
    Left: Right:
    Protein sequence
    • >TC003404 RA
      MWKTLSILL LCLLLEPSW SRLAEDITY SSLDNCVTD 
HCFHQPAEA CPSPDSKCR CRKLPYCKS AAVCCNVNK 
FQLTEGLAC ANISGNGHV ESLHIRNAS LDILNVEDW 
RKLKYLRYM TITDGQINS VVGEFAKHT IVSCLNLSS 
NGIVNFENR SLVNLYNLS FLDLSHNNL SDVPRFKKD 
GNITLDISA NQHMLCSNL FDALKRTEL HFSNINNSF 
CLFARTFHW FNTTETVPL TQVIGTHKL RKDCRKNCT 
CEPSRLDLV SGKQATIAV AVNCSGQSW TSLPSPLPP 
NTIALNVSN NNITSLELF STDSSYQNI RELYADNNQ 
ITSILPLEG SQFLSSFAV LSLRNNKLK SLPTYIFSN 
ILDRNNYVR YVFLGLNRL QCDCNTAKV LKVWLLTKQ 
KNIPDFEEI YCDNMDMKV IDLNPSKLC QTQQDWTDY 
IYYIITIEV VLLVGLIAK VVYDYCVFK TSGYLPWPA 
SKMPKLPCD WLCE
    CDS sequence
    • >TC003404 RA
      atgtggaag acactaagc attttgctg ctctgtctt 
ctgctcgaa ccctcatgg agtcgctta gccgaagac 
atcacctac tcatccctg gacaactgc gtaaccgac 
cactgtttc catcaacca gcagaggca tgccctagc 
cctgacagc aagtgccgt tgtcgcaaa ctcccatac 
tgcaaaagt gcggccgtt tgctgcaac gttaataaa 
ttccaacta acggaaggc ttggcatgc gcaaacatc 
agtggcaac ggtcatgtg gagtcgctg cacatacgg 
aacgccagt ctggacatc ctaaacgtg gaggactgg 
aggaaactc aaatatctg agatacatg accataaca 
gacggccaa ataaacagc gtagtcggg gaattcgcc 
aaacacacc atagtctcc tgtttgaat ttatcctca 
aacgggatc gtcaatttt gaaaataga tctctggtc 
aatttgtac aatctgagc ttcttggat ctttcacac 
aacaattta tcggacgtc cctcggttc aaaaaagat 
gggaatata actctagac atatcagct aatcagcac 
atgttatgc tcaaaccta ttcgacgct ttaaagcgc 
accgaactc cacttcagc aacataaac aattccttt 
tgtctattt gcccgaacc tttcactgg ttcaatacg 
actgaaact gtccctctt acacaagtg attggaaca 
cataagttg cgtaaagat tgccgcaaa aattgcact 
tgtgagccc tcaagactg gacctagtg tcaggaaaa 
caagcaacg attgcagtg gctgttaac tgctccgga 
cagagctgg acatcactg ccttcacct ctgccaccc 
aacactata gctctgaac gtttcgaat aataacata 
acttcgctg gaactgttc agtaccgac tcctcctac 
cagaatatt agggagctg tatgctgat aataaccag 
attacgtcc attctcccg ctggagggg tcgcagttt 
ttgagcagt ttcgcagtc ctgagtctt agaaacaac 
aagttgaaa tcgctccca acttacata ttctcgaac 
atactggac cggaataat tacgtccgg tacgttttt 
ctcggtctg aacagactc cagtgtgat tgtaacacg 
gccaaagtt ttgaaggtg tggctgttg acgaagcag 
aaaaacatc cccgatttc gaagaaatc tactgtgat 
aacatggat atgaaagtg atagatttg aacccttcc 
aagctctgt cagacgcaa caagactgg actgactac 
atctactac atcatcacc atagaggtg gtgcttctc 
gtgggtctg attgccaaa gtcgtttac gattactgt 
gtttttaaa acctccggt tatttgccg tggccggcg 
agcaaaatg ccaaagtta ccatgcgat tggttatgt 
gaatag
    mRNA sequence
    • >TC003404 RA
      taaaagtag agtgtgagg aaatattca aaatatttg 
attttcctt gaatggggt cttttgaaa tggagtaat 
ggaagtttg tttgaggtg tgggcagcg agtttcatt 
gatccaatt actgaataa agtttaatt aacaataat 
aattgggag taaagagtg gagaacaaa tagatggcg 
ccttgatat caacattag tagtttact atatttatc 
tgttattat gttcatttt atgttcacg tttccgtgt 
gcctcatca aggccgtac caaggccat agcaaaagc 
tatagtagt gtgttatgt ttaggttaa ttctgttaa 
aaacatctc gtcccatag tgtctttgt gtaactttg 
tagtaaagg cttaaaaca gttctatgg ccaaagaat 
aatgtgtac cgttgattg tgttcctct acctgagtg 
aaaagatgt ggaagacac taagcattt tgctgctct 
gtcttctgc tcgaaccct catggagtc gcttagccg 
aagacatca cctactcat ccctggaca actgcgtaa 
ccgaccact gtttccatc aaccagcag aggcatgcc 
ctagccctg acagcaagt gccgttgtc gcaaactcc 
catactgca aaagtgcgg ccgtttgct gcaacgtta 
ataaattcc aactaacgg aaggcttgg catgcgcaa 
acatcagtg gcaacggtc atgtggagt cgctgcaca 
tacggaacg ccagtctgg acatcctaa acgtggagg 
actggagga aactcaaat atctgagat acatgacca 
taacagacg gccaaataa acagcgtag tcggggaat 
tcgccaaac acaccatag tctcctgtt tgaatttat 
cctcaaacg ggatcgtca attttgaaa atagatctc 
tggtcaatt tgtacaatc tgagcttct tggatcttt 
cacacaaca atttatcgg acgtccctc ggttcaaaa 
aagatggga atataactc tagacatat cagctaatc 
agcacatgt tatgctcaa acctattcg acgctttaa 
agcgcaccg aactccact tcagcaaca taaacaatt 
ccttttgtc tatttgccc gaacctttc actggttca 
atacgactg aaactgtcc ctcttacac aagtgattg 
gaacacata agttgcgta aagattgcc gcaaaaatt 
gcacttgtg agccctcaa gactggacc tagtgtcag 
gaaaacaag caacgattg cagtggctg ttaactgct 
ccggacaga gctggacat cactgcctt cacctctgc 
cacccaaca ctatagctc tgaacgttt cgaataata 
acataactt cgctggaac tgttcagta ccgactcct 
cctaccaga atattaggg agctgtatg ctgataata 
accagatta cgtccattc tcccgctgg aggggtcgc 
agtttttga gcagtttcg cagtcctga gtcttagaa 
acaacaagt tgaaatcgc tcccaactt acatattct 
cgaacatac tggaccgga ataattacg tccggtacg 
tttttctcg gtctgaaca gactccagt gtgattgta 
acacggcca aagttttga aggtgtggc tgttgacga 
agcagaaaa acatccccg atttcgaag aaatctact 
gtgataaca tggatatga aagtgatag atttgaacc 
cttccaagc tctgtcaga cgcaacaag actggactg 
actacatct actacatca tcaccatag aggtggtgc 
ttctcgtgg gtctgattg ccaaagtcg tttacgatt 
actgtgttt ttaaaacct ccggttatt tgccgtggc 
cggcgagca aaatgccaa agttaccat gcgattggt 
tatgtgaat agttttatt ttagtcgca acgatgtgc 
ctgttaatg cttccgcct tgtatcatg gttgtgaaa 
tgtttactg tagtaggga ttagtgtag gaagttttg 
tgctctcaa tcaagtttg aaacgaaaa gtctgacac 
accaacagt catattagt tttctagac tcaaatcta 
atacgaaaa gacagtaca attgcggaa atttaaata 
aattcgcga atttatttt aaattttct atcttattt 
acaaattat gaactatgg ctttatatg tcttttact 
gtaaactat ttttcttca ttaggttta tgcaacttt 
agctccgta tgtgttttt atttattgt cttcttttg 
aaaacactg tttttaaca tcactttca gaatattaa 
tcctctaat atgttattc ccttttatt tgcttatgc 
aaatatttt cctaataat gtgcaattg tatatattt 
catttttta cattatcta cggtatgtc tttatttgt 
gcaactctt ccctttata tttttgttg tttaattgc 
tcaatttat agtagttgt ttgtgtttt ttgttttga 
tatttattt tatttattt ttttccaaa ttgtggtaa 
aagacaata tatcaagta taccaattg atttacaat 
aattccggt gtgtattta ctatttgtt gtaaaatac 
atgaaccgc ctaagtatg ggtagcaac aaaatgaac 
tctgtaatc attaatact ttttggaat gtaatttaa 
ttgtgttta ctgtaagca cgtccaaat atttaattg 
tagtcgttt tacagtttt tatactatt aagtaatac 
tcatccaag gacaaaatc aaaaatcgt ctacgaatt 
atcaaaacg tgtcacagc tttttagtt tttacaaat 
gtatggtca aaaattgtt tgaaatctc tttacccaa 
aatttttat tttatttag catatttta cttacttta 
agtacaata tcttgtttg ctaatgtat agataaata 
ttgtttctt ttgtaatat tgtttcgta taataaagt 
gtcttatca aac

    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