Status
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Gene information
General information
TC004311 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_007424.3: 1091988..1123130
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
    		TC004311
    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_03725

    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: 20.0% (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: 1 (11 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%

    embryo/egg with embryonic tissue, no cuticle, but muscle fluorescence - Penetrance (percentage of animals/eggs on slide): less than 30%

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

    affected eggs/embryos/larvae total percentage of affected eggs/embryos/larvae on slide - Penetrance (percentage of animals/eggs on slide): more than 80%
    remarks: muscle pattern potentially obscured by segmentation defect,
    Analysis of larval stage 1 cuticle
    number of eggs/embryos/larvae on slide: > 50
     egg without cuticle embryo/egg without visible larval cuticle in cuticle preparation - Penetrance (percentage of animals/eggs on slide): 30% - 50%
    cuticle remnants cuticle remnants with unidentifyable segments - Penetrance (percentage of animals/eggs on slide): less than 30%

    larva partially dorsalnot closed - Penetrance (percentage of animals/eggs on slide): less than 30%

    head appendages size decreased - Penetrance (percentage of animals/eggs on slide): 30% - 50%

    head appendages orientation irregular - Penetrance (percentage of animals/eggs on slide): less than 30%
    head appendages shape irregular - Penetrance (percentage of animals/eggs on slide): less than 30%
    head capsule mostly not present - Penetrance (percentage of animals/eggs on slide): less than 30%
    head irregular - Penetrance (percentage of animals/eggs on slide): less than 30%
    legs sometimesshape irregular - Penetrance (percentage of animals/eggs on slide): 30% - 50%

    thorax not present - Penetrance (percentage of animals/eggs on slide): less than 30%
    thorax irregular - Penetrance (percentage of animals/eggs on slide): less than 30%
    abdomen shortened - Penetrance (percentage of animals/eggs on slide): 30% - 50%
    abdomen not present - Penetrance (percentage of animals/eggs on slide): less than 30%
    abdomen not present - Penetrance (percentage of animals/eggs on slide): less than 30%
    affected eggs/embryos/larvae total percentage of affected eggs/embryos/larvae on slide - 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: 20.0% (includes death as larva, prepupa, pupa)
    Lethalities 22 days after larval injection: 80.0% (includes death as larva, prepupa, pupa, adult)

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

    eclosion not fulfilled (died as pupa) - Number of animals showing the phenotype: 2 (16 dpi)
    Days post injection

    eclosion not fulfilled (with pupal and adult features) - Number of animals showing the phenotype: 3 (16 dpi)
    Days post injection

    adult lethality - Number of animals showing the phenotype: 1 (19 dpi)
    Days post injection

    adult lethality - Number of animals showing the phenotype: 1 (41 dpi)
    Days post injection

    Pupal morphology
    wings shortened - Number of animals showing the phenotype: 8

    Adult morphology
    elytra not closed - Number of animals showing the phenotype: 3


    RNAi sequence
    Primers
    Left: Right:
    Protein sequence
    • >TC004311 RA
      MLAPSQTKP EKNGNTITT KTRTVAIVA PQRSNSLDY 
LNFEEKRRL IASSLSLSD FLNAGNNAT KEVKEVVTA 
KKQNGSVFR TNSLGSGTR TPSLERKSK FSIGKLLRP 
WKWKRKKKS DKLEAVSRT LERKISVRA NRDELVQKG 
ILPPESPLT PPISEPGSG EPLSSPLPP SGCQQLTEK 
QAPQGPPPL YPTLPQMQH MPINPALLQ QQLLRNPHF 
NQANANNNQ TEPKKEKTD GAAHNGAVS PNGDTPSQV 
TQPGSEVGK PERPNTLGH GRLTRRLLC YHSEHFNDG 
QPSLLGNPP PSSEKESQN IPPPPMSDP GLMLSDLPE 
PPIPLSEIG PIPPPPMFS SPSPVPNRQ SPPPPQMAD 
YEYEENEDD DGEEIDFEN FDETSYMFR MPQPDPTID 
TSRIDEIPA KEPKFNAMP LKSALKKKS SGGGSGPGT 
PQNTPTQEN RPLTIRQAQ TENNSSFNS KPVRFGIGL 
PCTLENKEN ARPYVIKED GSDSDSNDG PINYRDEDG 
ELSEENRLA LKIARKESL SLKLSLRPD RQELINRNI 
LQIQSENER QEAKEAIGA RLIRRLSMR PTQEELEER 
NILKKQTPA EEKKQKEEK KRFLLRKLS FRPTVEELK 
EKKIIRFND YIEVTQAHD YDRRADKPW TRLTPKDKA 
AIRKELNEF KSSEMAVHE GSRHLTRFH RP
    CDS sequence
    • >TC004311 RA
      atgttggcg ccgtcgcaa accaagcct gagaagaat 
ggaaatacg atcaccacc aagacgcgg actgtcgcc 
atagtggcg cctcagagg agtaacagt ttggattat 
cttaatttt gaggaaaag aggcgtttg attgcatcg 
tccttatct ctttcggat tttcttaat gcgggaaat 
aatgccacc aaagaggtc aaggaggtt gttactgct 
aagaaacaa aatggttct gtattccga acgaacagt 
ttgggtagt ggaacaagg actccgtcc ctagaacga 
aaaagcaaa ttctccata ggaaaatta cttagacca 
tggaaatgg aaaagaaaa aagaagtcg gataaattg 
gaagcagtt tcgagaacg ttagaaaga aaaatttca 
gttcgtgct aatagagac gaattagtt cagaaaggt 
atccttcct ccagaaagc cctttaact ccgcctata 
tccgagcca ggttcaggt gaaccctta tcatcacca 
cttcctccc agcgggtgt caacaattg accgaaaaa 
caagcacca cagggacca ccacctctt tatccaaca 
cttccacag atgcagcat atgcctatt aatccggca 
ttactgcag caacaactt cttcgaaac ccacacttt 
aaccaagcg aatgccaac aataatcaa accgagcca 
aaaaaagaa aagactgat ggagcggca cataacggc 
gccgtttct cccaacgga gacacgcct tcgcaagtt 
acccagcct ggaagtgaa gtcggaaaa ccagaaaga 
cccaacact ttaggccac gggaggttg acgagacga 
ttattgtgc taccacagt gaacatttt aatgatgga 
cagccaagt cttctcggc aatccaccg ccttcatct 
gagaaagag tcccagaat atacctccg cccccaatg 
tccgatcct ggtcttatg ctctctgac ttaccagag 
ccgcctatt cccttatca gaaatcggg cctatccct 
ccaccaccc atgtttagc tctcctagt ccagtgccc 
aatcggcag tcgccgcct ccgccacaa atggccgat 
tacgaatac gaagaaaac gaagacgat gacggcgaa 
gaaatcgat tttgaaaat ttcgacgaa acctcgtac 
atgtttcgc atgcctcaa ccggatcct accatcgac 
acaagtcga atagatgag attcccgct aaagaacca 
aaattcaat gccatgcct ctgaaatca gctttgaaa 
aagaagagt agtggtggt ggtagtggt cctggaaca 
ccgcaaaat acaccaaca caagaaaat agaccatta 
acaattcga caagcgcaa acggaaaat aattccagt 
tttaactcg aagcccgtg aggtttggc ataggcttg 
ccatgcact ttagaaaac aaagaaaat gccaggccg 
tatgtaatc aaggaggac ggtagtgac agcgactct 
aatgatggt ccaatcaat tacagagat gaagatggg 
gaattgtcg gaagagaac agactggct cttaaaatt 
gccagaaaa gagagtctt tcgctgaaa ttatcattg 
aggccagat cgtcaagag ctcattaac cgaaatatt 
ttgcaaata caatcggaa aacgaacga caagaagcc 
aaggaagca atcggagcg agattgata agaagatta 
agtatgaga cctactcaa gaagagttg gaagagagg 
aatattttg aaaaaacaa actccagct gaagaaaag 
aaacaaaaa gaagagaaa aaacgattt ttgttgcga 
aaattgagc ttccgaccg actgttgaa gaattaaaa 
gaaaagaag attatcaga tttaatgat tatattgaa 
gtaacacaa gcacatgat tatgatcgt agggcagac 
aagccatgg actaggtta acaccaaaa gacaaagct 
gctattagg aaggaatta aacgagttc aaaagctca 
gagatggca gtacatgag ggcagccgt catttaacg 
aggtttcat aggccttga
    mRNA sequence
    • >TC004311 RA
      tggcagagc agcagcagt gagtgtgtg ttatgttat 
acatagatt tgtatgcgt gtgtgtgtg tgtgagaga 
gatatttta aaatactag tgttattag tttggattt 
ctattgaat ccaaatgaa attaaacgt aatagtaat 
agatggtgg tagttagta gtagaagag gcaacgtcg 
cgtcgctcc gattaacgg acacactac ctgtgaagg 
gccaaaggt gtaataata ataatgacc ctacctgct 
ggtggtgta caggtatgt ggtgtgagt tgtgtcgga 
cctgctcca agttgtttt ggttattgt tgtgagtga 
agtgaagtg atgttggcg ccgtcgcaa accaagcct 
gagaagaat ggaaatacg atcaccacc aagacgcgg 
actgtcgcc atagtggcg cctcagagg agtaacagt 
ttggattat cttaatttt gaggaaaag aggcgtttg 
attgcatcg tccttatct ctttcggat tttcttaat 
gcgggaaat aatgccacc aaagaggtc aaggaggtt 
gttactgct aagaaacaa aatggttct gtattccga 
acgaacagt ttgggtagt ggaacaagg actccgtcc 
ctagaacga aaaagcaaa ttctccata ggaaaatta 
cttagacca tggaaatgg aaaagaaaa aagaagtcg 
gataaattg gaagcagtt tcgagaacg ttagaaaga 
aaaatttca gttcgtgct aatagagac gaattagtt 
cagaaaggt atccttcct ccagaaagc cctttaact 
ccgcctata tccgagcca ggttcaggt gaaccctta 
tcatcacca cttcctccc agcgggtgt caacaattg 
accgaaaaa caagcacca cagggacca ccacctctt 
tatccaaca cttccacag atgcagcat atgcctatt 
aatccggca ttactgcag caacaactt cttcgaaac 
ccacacttt aaccaagcg aatgccaac aataatcaa 
accgagcca aaaaaagaa aagactgat ggagcggca 
cataacggc gccgtttct cccaacgga gacacgcct 
tcgcaagtt acccagcct ggaagtgaa gtcggaaaa 
ccagaaaga cccaacact ttaggccac gggaggttg 
acgagacga ttattgtgc taccacagt gaacatttt 
aatgatgga cagccaagt cttctcggc aatccaccg 
ccttcatct gagaaagag tcccagaat atacctccg 
cccccaatg tccgatcct ggtcttatg ctctctgac 
ttaccagag ccgcctatt cccttatca gaaatcggg 
cctatccct ccaccaccc atgtttagc tctcctagt 
ccagtgccc aatcggcag tcgccgcct ccgccacaa 
atggccgat tacgaatac gaagaaaac gaagacgat 
gacggcgaa gaaatcgat tttgaaaat ttcgacgaa 
acctcgtac atgtttcgc atgcctcaa ccggatcct 
accatcgac acaagtcga atagatgag attcccgct 
aaagaacca aaattcaat gccatgcct ctgaaatca 
gctttgaaa aagaagagt agtggtggt ggtagtggt 
cctggaaca ccgcaaaat acaccaaca caagaaaat 
agaccatta acaattcga caagcgcaa acggaaaat 
aattccagt tttaactcg aagcccgtg aggtttggc 
ataggcttg ccatgcact ttagaaaac aaagaaaat 
gccaggccg tatgtaatc aaggaggac ggtagtgac 
agcgactct aatgatggt ccaatcaat tacagagat 
gaagatggg gaattgtcg gaagagaac agactggct 
cttaaaatt gccagaaaa gagagtctt tcgctgaaa 
ttatcattg aggccagat cgtcaagag ctcattaac 
cgaaatatt ttgcaaata caatcggaa aacgaacga 
caagaagcc aaggaagca atcggagcg agattgata 
agaagatta agtatgaga cctactcaa gaagagttg 
gaagagagg aatattttg aaaaaacaa actccagct 
gaagaaaag aaacaaaaa gaagagaaa aaacgattt 
ttgttgcga aaattgagc ttccgaccg actgttgaa 
gaattaaaa gaaaagaag attatcaga tttaatgat 
tatattgaa gtaacacaa gcacatgat tatgatcgt 
agggcagac aagccatgg actaggtta acaccaaaa 
gacaaagct gctattagg aaggaatta aacgagttc 
aaaagctca gagatggca gtacatgag ggcagccgt 
catttaacg aggtttcat aggccttga caattccag 
agtttgtta aaacaaaaa caaaaaact gtgatggac 
gtagccgta gaaattaac gttcccgta ttcgcttat 
taattgagt cagattgtg ttaaatctg gctgagttt 
gtgtaggac attgcacag gattataac tgtataatt 
gttttgtac atacgtgat ttttaatac acaaagttt 
ttatggata attattata aataatatg tgtacattt 
tttgtttga agcacttga tcaagttgt aaatatttt 
gtgtaatta tagtgcagg ttttaattt aaaattcaa 
gttgcatta cagtgtgta taactactg taggtgtat 
ttgttaatg tagaaattt tgtttgagt tactgtcta 
acactaaac attgactta gagacttta ttttatccc 
atacgacac gatttattt cgtttggaa aaattattt 
ttattggat ataaataag tagccaatc aaagttgta 
aaattagaa atcttgtat aaggacctt gtgcaaaag 
aggaaccgt tggtctagc ttgtaacat agtttcctt 
cgcttctaa aggcaatat gctctatgt atactgtaa 
gaaattgta ttcatactc aatcaattt atactggtt 
ttaataaca agaaatgtc ttccaaata g

    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