Status
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Gene information
General information
TC001440 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_007416.3: 3893417..3897196
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
    		TC001440
    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
    {{ blurEvidenceResult }}
    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 *
    {{ blurReferenceResult }}
    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_03188

    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: 10.0% (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

    Analysis of embryonic musculature and early development
    number of eggs/embryos/larvae on slide: > 50 embryo/egg with embryonic tissue, no cuticle, no fluorescence - Penetrance (percentage of animals/eggs on slide): 50% - 80%

    larval musculature pattern irregular - Penetrance (percentage of animals/eggs on slide): 30% - 50%

    affected eggs/embryos/larvae - Penetrance (percentage of animals/eggs on slide): 50% - 80%
    remarks: muscle pattern potentially obscured by segmentation defect,
    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%
    larva partially dorsalnot fused - Penetrance (percentage of animals/eggs on slide): less than 30%

    abdomen segment potentially partiallyfused - Penetrance (percentage of animals/eggs on slide): less than 30%

    abdomen circumference irregular - Penetrance (percentage of animals/eggs on slide): less than 30%

    abdomen segment number decreased - Penetrance (percentage of animals/eggs on slide): less than 30%

    abdomen irregular - Penetrance (percentage of animals/eggs on slide): 30% - 50%
    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
    • >TC001440 RA
      MTMSLKLFT FGILTGLIW TEIRCDAPL SDSASLPLE 
HRGVYGPPL SGPGYAPPA ILQGAGGGS SDDPWPLAT 
PDMPQIKHL QVQCEKTHM RVNIEFDRP FYGMIFSKG 
FYSDPHCVH LKPGTGHLS ATFEIFLNS CGMSSSANH 
NAGNYGGPT PSGSYVENT IIIQYDPYV QEVWDQARK 
LRCTWYDFY EKAVTFRPF QVDMLHAVT ANFLGDNLQ 
CWMQIQVGK GPWASEVSG IVKIGQTMT MVLAIKDDE 
NKFDMLVRN CVAHDGKRA PIQLVDQYG CVVRPKIMS 
KFQKIKNFG PSASVVSFA YFQAFKFPD SMNVHFQCV 
IQVCRYNCP EPKCGNHGL SLSSEYGPP PLGNSLGSG 
DFGGHAEYA SQSLSEYGV PPAFPDPRH PSGPTGAYS 
DNNPDVVPA PQSQISSSS TSNPPNLSS PAPQISAQN 
GGDVHLPPP PPPGHHGVY NTVKRKSSV PEEFEGNLA 
TLGGRPRSV ENIPELQGA RKRRSLDSI NIVVNHVYK 
REAQEMTDV NTSRTIQVV APGDVNFAL NPSQSNETV 
VIQSASSSD PETICMSVP SFVAGLVML LLVLIVASL 
VAAFLFVRV RAIDRKGIA TVFAGARGY DNAEFVKVA 
N
    CDS sequence
    • >TC001440 RA
      atgactatg tcattaaag cttttcacc tttgggata 
ttaaccgga ctgatttgg acggagata cggtgtgat 
gccccactt tcggattcg gcgtctctg cctttagag 
caccggggc gtgtacggg ccccccttg tcagggccg 
gggtacgcg cccccggcg attctgcaa ggggctggg 
ggcggctcc tcggatgac ccctggccc ttggcaacc 
cccgacatg ccccagatc aagcaccta caagtgcag 
tgcgaaaag actcacatg cgagtcaac atcgagttt 
gaccggccg ttttacgga atgattttc tcgaaggga 
ttctacagc gacccgcac tgcgtgcac ctgaagccc 
gggaccggg catttgagt gcgacgttc gaaatattt 
ctgaatagt tgcgggatg tcctcatcc gcaaaccac 
aatgcgggc aattacggg gggccgacg cctagcggc 
agctacgtc gagaacacc atcataatc cagtacgac 
ccttacgtg caagaagtt tgggaccaa gcgcgcaaa 
ttgcgctgc acttggtac gatttttac gaaaaggcg 
gtcacgttc cgaccgttc caagtggat atgttgcac 
gcggtcact gccaatttc ctaggcgat aatttgcaa 
tgctggatg cagattcaa gtcggcaaa ggtccgtgg 
gcgtcggaa gtgtcggga atcgtcaaa attggacaa 
accatgacc atggtcttg gctatcaaa gacgacgaa 
aacaaattc gacatgttg gtacgcaat tgcgtggcg 
catgatgga aaacgcgcc cctatccag cttgtggac 
caatacggt tgtgtcgta cggccaaag atcatgagc 
aagttccag aaaattaaa aacttcggg ccttcggcc 
tccgtggtc tcgttcgcc tatttccaa gctttcaaa 
ttccccgat tccatgaac gtgcacttc caatgcgtg 
attcaagtt tgtcggtac aattgtcca gaacccaaa 
tgtggaaac cacggtttg agtttaagt agcgaatac 
gggcctcca ccgctaggc aattcgctt ggtagcgga 
gactttggt ggtcacgct gaatacgcg tctcagtct 
ttgtccgaa tacggcgtt ccgccggcg ttcccagac 
cctagacac ccttctggg cccaccgga gcgtactcg 
gataacaac cctgatgtt gttccagcc ccacagtca 
caaatctcc tcgtcttcg acgtcaaat ccgccgaat 
ttgtcgtca ccagctccg caaatttcc gcccaaaac 
ggcggcgac gtccacttg ccgcccccg ccgccgccg 
ggccaccac ggagtgtac aacacagtg aagcggaaa 
agcagtgtt ccggaggag tttgaaggg aatctcgcg 
actctcggg ggacgaccg cgttcggtt gaaaacatc 
ccggaattg caaggtgcc agaaagagg cgcagtctt 
gactcgata aacattgta gttaaccat gtttacaaa 
cgagaagct caagaaatg actgatgtc aatactagt 
cgaacgatt caagtcgta gctcccggt gatgtcaat 
tttgcgctg aacccgtca caaagcaac gaaactgtg 
gtcattcag tcggcgtcc tcgtcggac ccagagaca 
atttgcatg tctgttccc agttttgtg gctgggtta 
gttatgttg ctcttggta ctcattgtt gctagttta 
gtagctgcg tttttgttt gttcgcgtt cgggctatt 
gatcgaaaa ggcatcgca acggtcttt gcaggagct 
cggggttat gataacgcc gagtttgtg aaagtggct 
aattga
    mRNA sequence
    • >TC001440 RA
      tattacttt tcacccaac tgttgtact cggttaatg 
tgttgagaa aaactgtgc ttgaggggg attgcagtg 
ctggtgtta gtgttcggt gactgggat ttatgactt 
ttttgtgtt aatctgagc gacaatttc ggattagta 
aaagctggc acagcaaag acgatgact atgtcatta 
aagcttttc acctttggg atattaacc ggactgatt 
tggacggag atacggtgt gatgcccca ctttcggat 
tcggcgtct ctgccttta gagcaccgg ggcgtgtac 
gggcccccc ttgtcaggg ccggggtac gcgcccccg 
gcgattctg caaggggct gggggcggc tcctcggat 
gacccctgg cccttggca acccccgac atgccccag 
atcaagcac ctacaagtg cagtgcgaa aagactcac 
atgcgagtc aacatcgag tttgaccgg ccgttttac 
ggaatgatt ttctcgaag ggattctac agcgacccg 
cactgcgtg cacctgaag cccgggacc gggcatttg 
agtgcgacg ttcgaaata tttctgaat agttgcggg 
atgtcctca tccgcaaac cacaatgcg ggcaattac 
ggggggccg acgcctagc ggcagctac gtcgagaac 
accatcata atccagtac gacccttac gtgcaagaa 
gtttgggac caagcgcgc aaattgcgc tgcacttgg 
tacgatttt tacgaaaag gcggtcacg ttccgaccg 
ttccaagtg gatatgttg cacgcggtc actgccaat 
ttcctaggc gataatttg caatgctgg atgcagatt 
caagtcggc aaaggtccg tgggcgtcg gaagtgtcg 
ggaatcgtc aaaattgga caaaccatg accatggtc 
ttggctatc aaagacgac gaaaacaaa ttcgacatg 
ttggtacgc aattgcgtg gcgcatgat ggaaaacgc 
gcccctatc cagcttgtg gaccaatac ggttgtgtc 
gtacggcca aagatcatg agcaagttc cagaaaatt 
aaaaacttc gggccttcg gcctccgtg gtctcgttc 
gcctatttc caagctttc aaattcccc gattccatg 
aacgtgcac ttccaatgc gtgattcaa gtttgtcgg 
tacaattgt ccagaaccc aaatgtgga aaccacggt 
ttgagttta agtagcgaa tacgggcct ccaccgcta 
ggcaattcg cttggtagc ggagacttt ggtggtcac 
gctgaatac gcgtctcag tctttgtcc gaatacggc 
gttccgccg gcgttccca gaccctaga cacccttct 
gggcccacc ggagcgtac tcggataac aaccctgat 
gttgttcca gccccacag tcacaaatc tcctcgtct 
tcgacgtca aatccgccg aatttgtcg tcaccagct 
ccgcaaatt tccgcccaa aacggcggc gacgtccac 
ttgccgccc ccgccgccg ccgggccac cacggagtg 
tacaacaca gtgaagcgg aaaagcagt gttccggag 
gagtttgaa gggaatctc gcgactctc gggggacga 
ccgcgttcg gttgaaaac atcccggaa ttgcaaggt 
gccagaaag aggcgcagt cttgactcg ataaacatt 
gtagttaac catgtttac aaacgagaa gctcaagaa 
atgactgat gtcaatact agtcgaacg attcaagtc 
gtagctccc ggtgatgtc aattttgcg ctgaacccg 
tcacaaagc aacgaaact gtggtcatt cagtcggcg 
tcctcgtcg gacccagag acaatttgc atgtctgtt 
cccagtttt gtggctggg ttagttatg ttgctcttg 
gtactcatt gttgctagt ttagtagct gcgtttttg 
tttgttcgc gttcgggct attgatcga aaaggcatc 
gcaacggtc tttgcagga gctcggggt tatgataac 
gccgagttt gtgaaagtg gctaattga caatctgtt 
tacaaatca gcaaagtac attccgaag attccaaag 
atgttcagg tcaatcaag tgattgtgc gtatgaatc 
taccggcca atgtgcggt catttttca ccctccctc 
gcaccccct ctcgagaac tgttttcaa cattacaca 
tatttcgtt aattattta ttatctcat taaacactt 
gtgctcaca agcggcgct cgacgccgt tgtcagcat 
gacctacct aatgtttgt tattattta taatactta 
ggctatttt tttattact taggttact taagtgtaa 
tttaacact gtataatgt actacttga gagtatgat 
tgtaagata tttgtttga aaaacatat taattattt 
attaatact tctaagttt attttgctc gtgttagag 
caactgttt ccactgccc cgaacatgc tacatcaac 
aggtgcaga aactagtct cgtagttag aacatagtc 
ttcatgtaa atacatatt tgtatcaaa atactcaat 
aaaatcaag caaattgag attattaac actgcattt 
ttagcacac cattcgcct gtaacggtt gttaaaagt 
gccgccatt tgcatgaat ctttaacgg tgtgataat 
ctgataatc caaaaaccg aaagaaagt taatacttt 
tcaaggaca gggaccttc aaactggca tatttagtt 
tacgtacta gatataaaa tattgtatg tatgaggac 
tcataaaac aatttcaaa ttaaatctt gtttttctt 
t

    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