Status
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Gene information
General information
TC004640 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: 4264674..4272731
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
    		TC004640
    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_02947

    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)

    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 larval musculature fluorescence decreased - Penetrance (percentage of animals/eggs on slide): less than 30%

    affected eggs/embryos/larvae - Penetrance (percentage of animals/eggs on slide): less than 30%
    Analysis of larval stage 1 cuticle
    number of eggs/embryos/larvae on slide: < 50
    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
    • >TC004640 RA
      MTSGTSSPT PTDSPSLSQ RPLLTAITP IPKKTVEFE 
TMPAKRSDA AAKDPESLT LRQKRGRLT QPRMSLLGR 
PLNYRASRR DARYRRIQS RVYNFLERP RGVAIFYHM 
IVFLMVFTC LTLSVFSTI ETYEDMTVQ VLTYMESFV 
VIWFAIEFS LRLWSSGCR SRYQGYIGR LKFLRRPFC 
IIDVITIVA SIVVLVMRS RGQVLATSA LRGLRFFQI 
LRMVRMDRR GGTWKLLGS VVYAHRQEL ITTLYIGFL 
GLIFASFLV FLAEKDVNK NFSNFAQAL WWGVITLCT 
VGYGDMVPE TWQGKIIAS FCALLGISF FALPAGILG 
SGFALKVQQ QQRQKHMIR RRQPAAMLI QSLWRCYAA 
DEHSLSVAT WKIHQVPLP SPPSRVSSS FKHNASFVS 
RLPTIRRHK STSLHSPSM HKGPPRSGR SFVDLNASA 
ENLGGVSNN GSRNLSHSE DSVAETMLS KKNSDDEDD 
EPRYIQLTN QHKGAIRAI RKLKYFVAR KKFREALKP 
YDVKDVIEQ YSSGHADLL NRVKNLQFR LDQILGKQG 
SKAKDVYAS KISLASRVV KVERQVDDI ESKIDQLLE 
LYMEDRKRF LSLPYIQPS AEKNTTSSS TTVNLCSSN 
MTNPSSTIL KPKPILVEK QSSEPSSPI TKSFKEHST 
AAVTKRPMH RGFSDLGNR IKKRVTLSS ISSNYVCPP 
DGMSYDGEV VIVVPPINN TPSTVGASA QEPDLGSPK 
TATESSGVK KLTRNRNCE EDEDDAAEK PLLCRSKST 
EILITPTTL ETTREEFYD NKTNQQSKN KFLKDDV
    CDS sequence
    • >TC004640 RA
      atgacatct gggacttct tcgccaaca ccaacggat 
tcgccgtcc ttatcacaa cgaccttta ctcactgca 
ataactcca ataccgaag aaaactgtt gaatttgaa 
accatgcca gcgaaacgg tccgatgct gcagccaag 
gatccggaa agtttgacg ttgcggcaa aaacgcggc 
cgtctcaca caaccccgg atgagtctt cttggtaga 
ccgctcaat tatagagct tcacgccga gatgctcgc 
tatcgtcga attcaaagt cgggtttat aacttccta 
gagagacct cggggggtc gctatcttc taccacatg 
atagtcttc ttgatggtt tttacatgt ttaactttg 
agtgtgttt tcaacgatt gagacttac gaagacatg 
actgttcaa gtcctaact tacatggaa tcgttcgtc 
gttatttgg tttgctatt gaattcagc ctaaggctt 
tggtcttcg ggatgtcgc tcccgctac caaggctac 
atcggccgc cttaaattt cttagacgt ccgttctgt 
attattgat gttataaca attgtggct tccattgtt 
gttctggtt atgaggtct cgcggtcaa gttttagcg 
actagcgcc cttcgtggt ttacgattt ttccaaatt 
ttgcggatg gtccgaatg gacagacgt ggagggact 
tggaaactg ttgggctca gtcgtgtac gcacatcga 
caagaactt ataactacg ttatacata ggatttttg 
ggcttgatt ttcgcttca tttttggtc ttcctggcg 
gaaaaagac gtgaacaaa aatttctcc aattttgca 
caagctttg tggtggggt gttattaca ttgtgcact 
gttggctat ggggatatg gttccggaa acatggcaa 
ggcaaaatc attgcttcg ttttgtgct ttacttggt 
atatcgttt tttgcattg ccggctgga attttagga 
tccggtttt gctttaaaa gttcagcaa caacaaagg 
caaaagcat atgatcagg aggagacaa ccagccgca 
atgctaatt cagtcgctt tggcgatgt tacgcagcc 
gatgagcac tccctatct gtggctacg tggaaaata 
catcaagtt cccttaccc agcccgccc tcacgagtt 
tcgagcagt tttaagcac aatgcatct tttgtaagt 
cgattaccg acaattcgt cgccacaaa agcacttca 
cttcattcc ccgtcgatg cataaagga ccaccaaga 
agtggtagg agtttcgtg gatttaaac gcatcagca 
gaaaattta ggcggagtc agcaacaac ggatcgcgg 
aatttgagc catagcgag gattcggtt gcagagacg 
atgctttcg aaaaaaaat tccgacgat gaggacgac 
gagccgaga tatatacag ttaacgaat cagcacaaa 
ggggcaatc cgggccatc cgtaagctc aagtatttt 
gtggcacga aagaagttt agagaggcc ttgaagcca 
tatgacgtt aaagacgtt atagaacaa tattcgtct 
gggcatgca gatcttttg aatagagtg aaaaactta 
cagttcaga ttagatcaa atcctaggg aaacaaggc 
tccaaggcg aaagatgtt tatgcttcc aaaatcagt 
ttagcatcg cgcgtagtc aaagttgaa agacaagta 
gatgacata gagtctaag attgaccag cttttagag 
ctttacatg gaagaccgt aaacgcttc ctctctctt 
ccttacatc cagccaagc gccgaaaaa aacaccact 
tcctctagt acaaccgtc aatctatgt tcttcaaac 
atgacaaat ccgtcgagt acaatcctt aaacctaaa 
ccaatactt gtagagaaa caatcatcc gaaccaagt 
tcgccaatc acaaaaagt tttaaagaa cattcaacg 
gccgcagta acaaaacga ccaatgcat cgcggattt 
tccgacctc ggcaatcgg attaaaaaa agagtgaca 
ttaagttca atttcgtcg aattatgtg tgcccaccg 
gatggcatg tcctacgac ggcgaagtc gtgattgtg 
gttcccccc atcaacaac acgccatcg acagttggt 
gcttcggca caggagccg gacttaggg agcccaaag 
acagccaca gaaagctct ggggtgaaa aagttaacg 
agaaatcga aattgtgaa gaagatgaa gacgacgca 
gcggagaag ccgttacta tgccgttcg aaatcaaca 
gaaatactc atcacgcca acgacttta gaaaccacc 
agagaagaa ttttatgat aataaaact aatcaacaa 
tcaaaaaac aaattttta aaagacgat gtatga
    mRNA sequence
    • >TC004640 RA
      ccgtccgtt tttcgggtt aatccgttt atatctcca 
attctattg atttattaa ctccttgat gatgccgga 
gatgccgaa aatttttca ctctttcga tattgccgc 
tcccccaca acaccctca tgaatactt aaatgccgc 
tttgagagg agagtaaca cgcttgagg caaaatgac 
atctgggac ttcttcgcc aacaccaac ggattcgcc 
gtccttatc acaacgacc tttactcac tgcaataac 
tccaatacc gaagaaaac tgttgaatt tgaaaccat 
gccagcgaa acggtccga tgctgcagc caaggatcc 
ggaaagttt gacgttgcg gcaaaaacg cggccgtct 
cacacaacc ccggatgag tcttcttgg tagaccgct 
caattatag agcttcacg ccgagatgc tcgctatcg 
tcgaattca aagtcgggt ttataactt cctagagag 
acctcgggg ggtcgctat cttctacca catgatagt 
cttcttgat ggtttttac atgtttaac tttgagtgt 
gttttcaac gattgagac ttacgaaga catgactgt 
tcaagtcct aacttacat ggaatcgtt cgtcgttat 
ttggtttgc tattgaatt cagcctaag gctttggtc 
ttcgggatg tcgctcccg ctaccaagg ctacatcgg 
ccgccttaa atttcttag acgtccgtt ctgtattat 
tgatgttat aacaattgt ggcttccat tgttgttct 
ggttatgag gtctcgcgg tcaagtttt agcgactag 
cgcccttcg tggtttacg atttttcca aattttgcg 
gatggtccg aatggacag acgtggagg gacttggaa 
actgttggg ctcagtcgt gtacgcaca tcgacaaga 
acttataac tacgttata cataggatt tttgggctt 
gattttcgc ttcattttt ggtcttcct ggcggaaaa 
agacgtgaa caaaaattt ctccaattt tgcacaagc 
tttgtggtg gggtgttat tacattgtg cactgttgg 
ctatgggga tatggttcc ggaaacatg gcaaggcaa 
aatcattgc ttcgttttg tgctttact tggtatatc 
gttttttgc attgccggc tggaatttt aggatccgg 
ttttgcttt aaaagttca gcaacaaca aaggcaaaa 
gcatatgat caggaggag acaaccagc cgcaatgct 
aattcagtc gctttggcg atgttacgc agccgatga 
gcactccct atctgtggc tacgtggaa aatacatca 
agttccctt acccagccc gccctcacg agtttcgag 
cagttttaa gcacaatgc atcttttgt aagtcgatt 
accgacaat tcgtcgcca caaaagcac ttcacttca 
ttccccgtc gatgcataa aggaccacc aagaagtgg 
taggagttt cgtggattt aaacgcatc agcagaaaa 
tttaggcgg agtcagcaa caacggatc gcggaattt 
gagccatag cgaggattc ggttgcaga gacgatgct 
ttcgaaaaa aaattccga cgatgagga cgacgagcc 
gagatatat acagttaac gaatcagca caaaggggc 
aatccgggc catccgtaa gctcaagta ttttgtggc 
acgaaagaa gtttagaga ggccttgaa gccatatga 
cgttaaaga cgttataga acaatattc gtctgggca 
tgcagatct tttgaatag agtgaaaaa cttacagtt 
cagattaga tcaaatcct agggaaaca aggctccaa 
ggcgaaaga tgtttatgc ttccaaaat cagtttagc 
atcgcgcgt agtcaaagt tgaaagaca agtagatga 
catagagtc taagattga ccagctttt agagcttta 
catggaaga ccgtaaacg cttcctctc tcttcctta 
catccagcc aagcgccga aaaaaacac cacttcctc 
tagtacaac cgtcaatct atgttcttc aaacatgac 
aaatccgtc gagtacaat ccttaaacc taaaccaat 
acttgtaga gaaacaatc atccgaacc aagttcgcc 
aatcacaaa aagttttaa agaacattc aacggccgc 
agtaacaaa acgaccaat gcatcgcgg attttccga 
cctcggcaa tcggattaa aaaaagagt gacattaag 
ttcaatttc gtcgaatta tgtgtgccc accggatgg 
catgtccta cgacggcga agtcgtgat tgtggttcc 
ccccatcaa caacacgcc atcgacagt tggtgcttc 
ggcacagga gccggactt agggagccc aaagacagc 
cacagaaag ctctggggt gaaaaagtt aacgagaaa 
tcgaaattg tgaagaaga tgaagacga cgcagcgga 
gaagccgtt actatgccg ttcgaaatc aacagaaat 
actcatcac gccaacgac tttagaaac caccagaga 
agaatttta tgataataa aactaatca acaatcaaa 
aaacaaatt tttaaaaga cgatgtatg acataattt 
aaatttgtt attagttta tatattatg accgttaaa 
tattcaaaa taatgtaaa tgattatag atttttgga 
cctaaaact tgcgaatat ttttaacat gtactgaac 
ttagggcac aataatgac gcttattaa tataaaaat 
atatttgaa aagtttgta cttcttcac ttaggatta 
aaatttgct gtagcatgt tttagctgt gatttgttt 
cgacgtttt atactgaaa ctttacagg gacattggc 
caatgcttg tagattaat tcagttacg tttcacaag 
tgaatttta acggcaact tgtacttac aacgaccac 
actataatc ctaacgttt ttataatat caagtagaa 
aaaaacgcc taacaaaca atcaacgac tttaaaaat 
gtgctgctg aaattcact tttaatcag tagactata 
ctataaaat ttagctatt taaaaatgt acgtaaaat 
aatgtgatt aatttatag atacgacag taatatttt 
ttgacccga cccattgcc tactgttgt tacaataag 
tatttgttt gcttaaaaa tgatgtgga acatctata 
ctgtacggg atttttaat aaaac

    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