Status
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Gene information
General information
TC001243 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: 13153732..13155696
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
    		TC001243
    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
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    * : mandatory fields
    For help on how to submit larger datasets or non experimental data please contact us.
    iBeetle screen iB_07900

    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: 2 (3 dpi)
    Days post injection

    adult lethality - Number of animals showing the phenotype: 1 (9 dpi)
    Days post injection

    Adult morphology
    abdominal odoriferous glands colour lighter - Number of animals showing the phenotype: 4 (13 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): 30% - 50%

    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
    embryo/egg without visible larval cuticle in cuticle preparation - Penetrance (percentage of animals/eggs on slide): 50% - 80%
    larva everted (inside-out) - Penetrance (percentage of animals/eggs on slide): less than 30%

    head capsule size decreased - Penetrance (percentage of animals/eggs on slide): less than 30%

    head appendages partially not present - Penetrance (percentage of animals/eggs on slide): less than 30%
    affected eggs/embryos/larvae - Penetrance (percentage of animals/eggs on slide): more than 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
    • >TC001243 RA
      MDVNQRLSS FQEISKTLL SKIFSSVPR TKHIVIEPS 
VIRPLERVC SVSWLKGNG IEKIFKLEG KCPNFGNSP 
VFYMIFNQR ATFRRVVDQ IRSQIDQEN PVKNRFHVI 
IVPHYQRCF DDMLEALGL CSIIKLHCF LWFPVHLDT 
GILSLELPH IYKKLFLVH DYTALHPLA RALWNMFSV 
IGLPKFQIA VGEYSNKIL RQIDLLAAE KGETERLNP 
EVGALIIID RSVDYPSAL LTPGTYSAL LNEVYGVTT 
GMVECKESE DEVRLNPVV KKQPVKFTL DSNLDSIYS 
EIKNLYFTE VTSSLRTMT RKLKSEALE SRDMGLNEM 
RHFVQKLLQ PAQTRKKLI ANHLLAAET IANVLGPRY 
ETQREIEAN IIQNTNRAS NFSHLEESL CTEDDPCVT 
LRLFCLLCV TQKLTDSEI KNFWRKFLH QFGFASSSA 
MRYLINANF VPEAGVSGL PKIRFPKFT TKEFYANAN 
KFKQIPANP EFADLGHPG CASYVFGGI YIPLVTKIA 
GMIVSGTPI EEIRSKLEG LGMVTLRSG DAYPLERRT 
VLIYFVGGV TYAEIAACN LLETFTRAT IVVMSDRIV 
SGNDLMKQM LS
    CDS sequence
    • >TC001243 RA
      atggatgta aaccaaaga ttatcgtct tttcaagag 
atttccaag accctgctt tcgaaaatc ttcagttct 
gtccctcgg acgaaacat atcgttatc gaaccgagt 
gtgattcgc ccccttgag cgcgtttgt agcgtgagc 
tggctgaag ggaaacggc attgagaag atatttaaa 
ctggaaggg aaatgcccg aattttggc aacagcccc 
gttttttac atgattttc aatcaaagg gctacattc 
cgacgagtg gttgatcag attcggtca cagatcgac 
caagagaat ccagttaag aataggttt cacgtaatc 
attgtccca cactatcag cgttgtttt gacgacatg 
ttagaagca ctgggcttg tgttccatt atcaagtta 
cactgcttc ctttggttt cctgtccac ttggacacg 
gggatttta agtttggaa ttgccccac atttacaag 
aaactgttt ttggtgcat gactacacg gccttgcac 
cccttggcc agagcccta tggaacatg ttcagtgtg 
attggttta ccaaagttc cagatagct gtaggcgaa 
tattcgaat aaaattttg cgccagatt gacttgctc 
gccgccgag aagggcgaa accgagcga cttaatccc 
gaggtgggg gctttaatc ataattgac aggagcgta 
gattaccca agtgcctta ctaacacct ggtacctat 
tccgcttta ctaaacgaa gtgtacgga gttactact 
gggatggtc gagtgcaag gaaagcgag gatgaagtc 
cgccttaat ccagtcgta aaaaaacag ccggtgaaa 
ttcaccctc gatagcaat ctcgactca atttactcc 
gagataaaa aacctgtat ttcacggaa gttacgtca 
agtttgagg accatgacg cgcaaatta aaatccgag 
gcgctcgag tcgcgtgac atgggctta aacgaaatg 
cgccacttc gtgcaaaag ctcctccag cccgcacaa 
actcgtaaa aaactaatc gccaatcat ttgcttgcc 
gccgagacc atagccaat gtcctcggc ccgcgctac 
gaaacgcag cgcgagatc gaggcgaac atcatccag 
aacacgaac cgcgcctcc aacttctcc cacctggag 
gagagtctg tgcacggaa gacgacccg tgtgtcaca 
ctgcggctc ttttgtttg ctctgtgtc acgcagaaa 
ctcaccgac agcgaaatt aaaaacttc tggaggaag 
tttctacac cagttcggg ttcgcctcc agttcggct 
atgcgttat ttgatcaac gctaatttc gtgccggag 
gcgggggtt tcgggactg ccgaaaata cgcttcccg 
aagttcaca acgaaggag ttttacgcc aatgcgaat 
aagtttaaa cagattccg gctaatccg gagtttgcc 
gatttgggg catccgggg tgtgcgagt tatgtcttt 
ggggggatt tacataccg ttggttacg aaaatcgcg 
ggtatgatc gttagtggc actccgatt gaggagatt 
aggagtaaa ttggagggg cttgggatg gtcacgttg 
aggagtggt gacgcctat cctttggaa aggcggact 
gtgctcatt tatttcgtt ggaggggtc acgtatgcc 
gaaattgca gcttgtaat cttttggag actttcacg 
agggctaca attgtcgtt atgagcgac aggattgtc 
tcaggaaac gatttgatg aagcaaatg ctgtcttaa
    mRNA sequence
    • >TC001243 RA
      tgataagtt atttactaa taatggatg taaaccaaa 
gattatcgt cttttcaag agatttcca agaccctgc 
tttcgaaaa tcttcagtt ctgtccctc ggacgaaac 
atatcgtta tcgaaccga gtgtgattc gcccccttg 
agcgcgttt gtagcgtga gctggctga agggaaacg 
gcattgaga agatattta aactggaag ggaaatgcc 
cgaattttg gcaacagcc ccgtttttt acatgattt 
tcaatcaaa gggctacat tccgacgag tggttgatc 
agattcggt cacagatcg accaagaga atccagtta 
agaataggt ttcacgtaa tcattgtcc cacactatc 
agcgttgtt ttgacgaca tgttagaag cactgggct 
tgtgttcca ttatcaagt tacactgct tcctttggt 
ttcctgtcc acttggaca cggggattt taagtttgg 
aattgcccc acatttaca agaaactgt ttttggtgc 
atgactaca cggccttgc accccttgg ccagagccc 
tatggaaca tgttcagtg tgattggtt taccaaagt 
tccagatag ctgtaggcg aatattcga ataaaattt 
tgcgccaga ttgacttgc tcgccgccg agaagggcg 
aaaccgagc gacttaatc ccgaggtgg gggctttaa 
tcataattg acaggagcg tagattacc caagtgcct 
tactaacac ctggtacct attccgctt tactaaacg 
aagtgtacg gagttacta ctgggatgg tcgagtgca 
aggaaagcg aggatgaag tccgcctta atccagtcg 
taaaaaaac agccggtga aattcaccc tcgatagca 
atctcgact caatttact ccgagataa aaaacctgt 
atttcacgg aagttacgt caagtttga ggaccatga 
cgcgcaaat taaaatccg aggcgctcg agtcgcgtg 
acatgggct taaacgaaa tgcgccact tcgtgcaaa 
agctcctcc agcccgcac aaactcgta aaaaactaa 
tcgccaatc atttgcttg ccgccgaga ccatagcca 
atgtcctcg gcccgcgct acgaaacgc agcgcgaga 
tcgaggcga acatcatcc agaacacga accgcgcct 
ccaacttct cccacctgg aggagagtc tgtgcacgg 
aagacgacc cgtgtgtca cactgcggc tcttttgtt 
tgctctgtg tcacgcaga aactcaccg acagcgaaa 
ttaaaaact tctggagga agtttctac accagttcg 
ggttcgcct ccagttcgg ctatgcgtt atttgatca 
acgctaatt tcgtgccgg aggcggggg tttcgggac 
tgccgaaaa tacgcttcc cgaagttca caacgaagg 
agttttacg ccaatgcga ataagttta aacagattc 
cggctaatc cggagtttg ccgatttgg ggcatccgg 
ggtgtgcga gttatgtct ttgggggga tttacatac 
cgttggtta cgaaaatcg cgggtatga tcgttagtg 
gcactccga ttgaggaga ttaggagta aattggagg 
ggcttggga tggtcacgt tgaggagtg gtgacgcct 
atcctttgg aaaggcgga ctgtgctca tttatttcg 
ttggagggg tcacgtatg ccgaaattg cagcttgta 
atcttttgg agactttca cgagggcta caattgtcg 
ttatgagcg acaggattg tctcaggaa acgatttga 
tgaagcaaa tgctgtctt aaaccattt tgtattatt 
ttttctaca aaaacagtc aaaaaatca cgtttttgt 
ttcaataac ttgtacgac tgttttgtt tgccaaatt 
ctatatttt gtaccgttg tttttatta aaataaacg 
aaaaaaagt tca

    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