Status
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Gene information
General information
TC001328 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: 14546685..14548549
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
    		TC001328
    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
    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
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    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_00240

    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: 70.0% (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: 3 (9 dpi)
    Days post injection

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

    Adult morphology
    low validity due to technical reasons - should be repeated: ovary phenotype not scorable,
    animals lost
    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: 75.0% (includes death as larva, prepupa, pupa, adult)

    pupal molt not fulfilled (died as L7 or prepupa) - Number of animals showing the phenotype: 6 (11 dpi)
    Days post injection


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

    pupal molt delayed (still larva) - Number of animals showing the phenotype: 1 (19 dpi)
    Days post injection

    delayed (still larva) - Number of animals showing the phenotype: 1 (22 dpi)
    Days post injection

    RNAi sequence
    Primers
    Left: Right:
    Protein sequence
    • >TC001328 RA
      MVIRNLHRL SRLFQPVSV VPKNAEVKR HDITSKSQR 
LMLELGIIR QASPGCFHF LPLGVKSLE KLTRLVDEE 
MKKIGGQKI IFPTLTNAK LWEKTGRLE TVSSELFQI 
KDRHDQSYI LSPTHEEAA SNLLASLAP ISYKHLPLK 
LYQITSKYR DEMKPRFGL MRGKQFLMK DMYSFDTDL 
ETAKHTYDE ICKSYDRIF RRIGIDFVK VVGCSGHMG 
GELSHEYHY KADVGEDKI LTCNKCNYS ANTEVSGEE 
KCPNCGNTS VKIHLGIEV GHTFLLGEK YSKPLNATF 
LNNHGKPDV LQMGSYGLG LSRILAAVI EVMSSEQEI 
RWPQILSPY SVIILPPKS GSKEETHIK DSGLVDSLY 
EKIETTCNL QDNVLIDDR TNFTIGRRF LEAKKNGYP 
FIVTLGKKI VENPLLYEI TNLKTNETL FLSENDLMN 
YLRSQLSSF SSDSDNK
    CDS sequence
    • >TC001328 RA
      atggttatt cggaacttg caccgactc tcccgcctt 
ttccagccg gtttcggtg gtccccaaa aatgcggaa 
gtcaagcgg cacgatatc acttcgaag agtcaacga 
ttaatgcta gagcttggg attataaga caagcgagt 
ccgggttgt ttccatttt ttgccatta ggggtcaag 
tctttggag aaactaaca aggcttgtt gatgaggaa 
atgaaaaaa attgggggg caaaaaatt atttttccc 
acgttaact aacgcgaaa ctgtgggaa aaaacaggc 
agattggag actgtttcc agtgagctt ttccaaatt 
aaagaccgg catgaccag agttatatt ttaagccct 
acacatgag gaggccgcg agtaattta cttgcgtcg 
ttggcgccg atttcgtac aagcactta cctttaaaa 
ctgtatcag attacaagt aaatatagg gacgagatg 
aaacccaga tttgggtta atgagggga aagcagttt 
cttatgaaa gacatgtat tcgtttgat accgacctc 
gaaacggcc aaacacact tacgatgaa atttgtaaa 
agttacgat cggattttt aggagaatt gggattgat 
tttgtcaaa gtggtgggt tgttcggga catatgggg 
ggcgaatta tcgcacgaa taccactac aaagcggac 
gtaggcgaa gataaaatt ttaacgtgc aacaaatgc 
aactattcg gcaaatacc gaagtttca ggggaggaa 
aaatgcccc aattgtggg aacacttca gtcaaaatt 
cacttaggg atagaagtt ggtcacact tttcttttg 
ggcgaaaaa tactcaaaa ccgcttaat gccactttt 
ttgaataat cacggcaaa ccggacgtg ttacaaatg 
ggcagttat ggactgggg ttatcacgg attttagct 
gccgtaatt gaagtcatg tcaagtgaa caagaaatc 
aggtggccc cagatttta tcaccttac agcgtcatt 
attttgcct ccgaaaagc ggaagtaag gaagaaaca 
cacattaag gattcgggt ctagttgac tcactttac 
gaaaaaatt gaaacgact tgcaattta caagacaat 
gttttaatc gacgacagg acgaatttt acgatcggt 
cgccggttt ctagaagca aagaaaaac ggatatcct 
tttatcgta actttaggt aaaaaaatc gtagaaaac 
ccactttta tacgaaatt actaattta aaaacgaat 
gaaacgcta tttctaagt gagaatgat ttaatgaat 
tatcttagg agtcagtta tcgtcgttt tcgagcgac 
tctgataat aaataa
    mRNA sequence
    • >TC001328 RA
      aatttttcg aaaaatggt tattcggaa cttgcaccg 
actctcccg ccttttcca gccggtttc ggtggtccc 
caaaaatgc ggaagtcaa gcggcacga tatcacttc 
gaagagtca acgattaat gctagagct tgggattat 
aagacaagc gagtccggg ttgtttcca ttttttgcc 
attaggggt caagtcttt ggagaaact aacaaggct 
tgttgatga ggaaatgaa aaaaattgg ggggcaaaa 
aattatttt tcccacgtt aactaacgc gaaactgtg 
ggaaaaaac aggcagatt ggagactgt ttccagtga 
gcttttcca aattaaaga ccggcatga ccagagtta 
tattttaag ccctacaca tgaggaggc cgcgagtaa 
tttacttgc gtcgttggc gccgatttc gtacaagca 
cttaccttt aaaactgta tcagattac aagtaaata 
tagggacga gatgaaacc cagatttgg gttaatgag 
gggaaagca gtttcttat gaaagacat gtattcgtt 
tgataccga cctcgaaac ggccaaaca cacttacga 
tgaaatttg taaaagtta cgatcggat ttttaggag 
aattgggat tgattttgt caaagtggt gggttgttc 
gggacatat ggggggcga attatcgca cgaatacca 
ctacaaagc ggacgtagg cgaagataa aattttaac 
gtgcaacaa atgcaacta ttcggcaaa taccgaagt 
ttcagggga ggaaaaatg ccccaattg tgggaacac 
ttcagtcaa aattcactt agggataga agttggtca 
cacttttct tttgggcga aaaatactc aaaaccgct 
taatgccac ttttttgaa taatcacgg caaaccgga 
cgtgttaca aatgggcag ttatggact ggggttatc 
acggatttt agctgccgt aattgaagt catgtcaag 
tgaacaaga aatcaggtg gccccagat tttatcacc 
ttacagcgt cattatttt gcctccgaa aagcggaag 
taaggaaga aacacacat taaggattc gggtctagt 
tgactcact ttacgaaaa aattgaaac gacttgcaa 
tttacaaga caatgtttt aatcgacga caggacgaa 
ttttacgat cggtcgccg gtttctaga agcaaagaa 
aaacggata tccttttat cgtaacttt aggtaaaaa 
aatcgtaga aaacccact tttatacga aattactaa 
tttaaaaac gaatgaaac gctatttct aagtgagaa 
tgatttaat gaattatct taggagtca gttatcgtc 
gttttcgag cgactctga taataaata acttccaga 
aggtgattc aatgtttgc acttaacat atccggtat 
tttcattaa cagcccggc agcgtaacg acgccacat 
tttcccttg tcttatcct cgcactcct cgcttgctc 
cgtttcggt ccatttagg gggcacttc cggcaaagt 
ctcggtcac tatatccca cctaaagcc cctcaagtc 
aaagattta aatcgtaaa atgat

    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