Status
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Gene information
General information
TC001412 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_015451510.1: 9033..14223
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
    		TC001412
    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
    If you have entered your name and agree by marking the checkbox. we might show your name on this page to honor your contribution.
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    * : mandatory fields
    For help on how to submit larger datasets or non experimental data please contact us.
    iBeetle screen iB_03179

    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: 30.0% (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: 2 (9 dpi)
    Days post injection

    Analysis of embryonic musculature and early development
    number of eggs/embryos/larvae on slide: > 50 embryo/egg not developed/not fertilized - Penetrance (percentage of animals/eggs on slide): 50% - 80%

    affected eggs/embryos/larvae - Penetrance (percentage of animals/eggs on slide): 50% - 80%
    Analysis of larval stage 1 cuticle
    number of eggs/embryos/larvae on slide: > 50
     embryo/egg without visible larval cuticle in cuticle preparation - Penetrance (percentage of animals/eggs on slide): 50% - 80%
    affected eggs/embryos/larvae - Penetrance (percentage of animals/eggs on slide): 50% - 80%
    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: % (includes death as larva, prepupa, pupa)
    Lethalities 22 days after larval injection: % (includes death as larva, prepupa, pupa, adult)

    RNAi sequence
    Primers
    Left: Right:
    Protein sequence
    • >TC001412 RA
      MTTKEEYEY TPVAGTEES ETTFNVTNG EVTIQSNKM 
TSESAEPTN RKFLYVAAC VANLAGFVC GTSFGWTSP 
EIPKMKISH EAGNPLALA LTKSEESWI GSLLPVGAT 
LGPFIAGLT ADKIGRKNT LLAGTVPFI VAFAIAAYA 
TNPLLFFLM RFLCGLAVG VVFTVLPMY IGEIAEDEV 
RDSLGSFMQ LFIVVGLLF SYALGPYMS IMAFNIACV 
VSPCVFLVV FYLFIPESP YFLIRENKD QAAQALMKL 
RSKSEEAIQ EELEEIKAS VEETLANKA SFADIFKSK 
GLTKALTIS VGLVSLQQL SGINIVLFY AQDIFTDAG 
STIPADIST IIIGIVQVF ASGATPIVV EKKGKRYLL 
LLSAVGMAV SQGALAVFF HVKSGGSDV SAISWLPVT 
CLVVYIITY CLGFGPLPW AVMGELFPG NIKSVASTV 
TAAGCWFLG FILTKYFSL VSDLIGQAG SFGIFAACC 
VGAGVFVYK YLPDTSGKS LQEIQDMLS GKSSSSDA
    CDS sequence
    • >TC001412 RA
      atgaccact aaggaagaa tatgagtac acaccagtg 
gcggggacg gaagaatcc gaaacaaca ttcaatgtt 
acaaatggc gaagtcacc attcagtcg aacaaaatg 
accagtgag agtgccgaa cccacaaac cgaaaattt 
ttgtacgtt gcggcatgt gtcgcaaac ttggccggc 
ttcgtgtgc ggcacgagc ttcggctgg acttccccc 
gaaatcccc aagatgaaa atctcgcac gaggccggc 
aaccccctc gccctagcc ctcaccaag agcgaggag 
tcctggatc ggctccctc ctcccggtt ggggcgacc 
ctcggcccc ttcatcgcc ggcctcaca gccgacaaa 
atcgggcga aaaaacacc ctcctggcc ggaaccgtg 
cccttcatc gtcgctttc gcaatcgcc gcttacgcc 
accaacccc cttctattc ttcctgatg cggtttctg 
tgcggtctg gccgtggga gtggtgttc accgtcctg 
ccgatgtac attggggag atcgcagag gacgaagtc 
cgggactcg ctcggctcc ttcatgcag cttttcatc 
gtcgtgggg ctgcttttc tcgtacgcc ctggggccc 
tacatgtcc atcatggcg ttcaacatc gcgtgcgtc 
gtgtcaccg tgcgtgttt ttggtggtt ttctacttg 
tttatcccg gagagtccc tattttctg attcgggag 
aacaaggat caagcggcg caagcgctg atgaagctg 
aggtcgaag tcggaggag gcgattcag gaggagttg 
gaggagatt aaggccagc gttgaggaa actctagcc 
aacaaagcc tcgttcgct gatattttc aaatcgaag 
ggtttgacc aaagccttg acgatctcg gtcgggtta 
gtgtccttg cagcaatta tcagggatc aatattgtc 
ctgttttac gcccaggat attttcact gacgctgga 
agcacgatc cctgctgac atttcgacg atcattatc 
gggattgtc caggttttc gccagtggg gccactccg 
atcgttgtg gaaaaaaag ggcaaaagg taccttctg 
ctgctctcc gccgtgggc atggcggtg tctcaaggg 
gccctagct gtgttcttc cacgtcaaa agtgggggc 
agtgatgtt agcgccatt tcctggctc cctgttacg 
tgtcttgtg gtctacatt atcacctat tgtcttggc 
tttgggcct ctgccatgg gccgtgatg ggcgagctt 
ttccccggg aacattaaa tcagtggcg tccacggtc 
acagcagct gggtgctgg tttcttggt tttattctg 
accaaatat ttctcgctg gtttcggat ttgattgga 
caggcgggg tctttcggg attttcgcc gcgtgttgc 
gtgggggct ggcgttttt gtctacaag tatttgcca 
gatacgtca ggaaagagt ctgcaggag attcaggat 
atgctgagt gggaagagt tcgtcgagt gatgcttga
    mRNA sequence
    • >TC001412 RA
      gaagtgaca tcctcgaaa gacaaatcc ttgtgccta 
gtttccgcg ctcaaaatg accactaag gaagaatat 
gagtacaca ccagtggcg gggacggaa gaatccgaa 
acaacattc aatgttaca aatggcgaa gtcaccatt 
cagtcgaac aaaatgacc agtgagagt gccgaaccc 
acaaaccga aaatttttg tacgttgcg gcatgtgtc 
gcaaacttg gccggcttc gtgtgcggc acgagcttc 
ggctggact tcccccgaa atccccaag atgaaaatc 
tcgcacgag gccggcaac cccctcgcc ctagccctc 
accaagagc gaggagtcc tggatcggc tccctcctc 
ccggttggg gcgaccctc ggccccttc atcgccggc 
ctcacagcc gacaaaatc gggcgaaaa aacaccctc 
ctggccgga accgtgccc ttcatcgtc gctttcgca 
atcgccgct tacgccacc aaccccctt ctattcttc 
ctgatgcgg tttctgtgc ggtctggcc gtgggagtg 
gtgttcacc gtcctgccg atgtacatt ggggagatc 
gcagaggac gaagtccgg gactcgctc ggctccttc 
atgcagctt ttcatcgtc gtggggctg cttttctcg 
tacgccctg gggccctac atgtccatc atggcgttc 
aacatcgcg tgcgtcgtg tcaccgtgc gtgtttttg 
gtggttttc tacttgttt atcccggag agtccctat 
tttctgatt cgggagaac aaggatcaa gcggcgcaa 
gcgctgatg aagctgagg tcgaagtcg gaggaggcg 
attcaggag gagttggag gagattaag gccagcgtt 
gaggaaact ctagccaac aaagcctcg ttcgctgat 
attttcaaa tcgaagggt ttgaccaaa gccttgacg 
atctcggtc gggttagtg tccttgcag caattatca 
gggatcaat attgtcctg ttttacgcc caggatatt 
ttcactgac gctggaagc acgatccct gctgacatt 
tcgacgatc attatcggg attgtccag gttttcgcc 
agtggggcc actccgatc gttgtggaa aaaaagggc 
aaaaggtac cttctgctg ctctccgcc gtgggcatg 
gcggtgtct caaggggcc ctagctgtg ttcttccac 
gtcaaaagt gggggcagt gatgttagc gccatttcc 
tggctccct gttacgtgt cttgtggtc tacattatc 
acctattgt cttggcttt gggcctctg ccatgggcc 
gtgatgggc gagcttttc cccgggaac attaaatca 
gtggcgtcc acggtcaca gcagctggg tgctggttt 
cttggtttt attctgacc aaatatttc tcgctggtt 
tcggatttg attggacag gcggggtct ttcgggatt 
ttcgccgcg tgttgcgtg ggggctggc gtttttgtc 
tacaagtat ttgccagat acgtcagga aagagtctg 
caggagatt caggatatg ctgagtggg aagagttcg 
tcgagtgat gcttgaatg tagtgatag ttatttatt 
gttttatac ttttacgtt gtttgtagt cttgtcatt 
aatttattt aacgtttca tgttttatt atacagtat 
tattgaact gaaatctac aagtcgtac aaatgtaca 
aagtaatac ttaaataat taataaagt ttttacaat 
tgg

    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