Status
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Gene information
General information
TC000561 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: 9763362..9765957
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
    		TC000561
    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_00127

    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: 2 (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): 30% - 50%

    affected eggs/embryos/larvae - Penetrance (percentage of animals/eggs on slide): 30% - 50%
    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
    • >TC000561 RA
      MKKFDLDDI LISIGGWGK FQTLYYAVL CTAIIFSVF 
PAMNYIFIA RDIKYRCKI DSCDRENGD FNPDWLKNA 
VPFEQNVPS KCSYYQPEE NDTCTSFVK NETLTCHDD 
FVYERLETT IVHDFNIKC DENLWKLTI IGTINVVGK 
LVCLPLAGF FSDRFGRKS MVIVSVFLS TIVGLVRSF 
SVNYYMYVG LEFLNTVVG SGIYSGAFI LALELVDSK 
RRNLGNSII CLAFTVGHI LLGAAAWVS PTWQFMTQI 
MYGPGILVT ILLWFVPES VRWLIARNK IEKAEGVLK 
SIAKINGKE LTEETIKTI PYLEDSKSD GDEAIPLMA 
ILKKKSLLI RIIHCSFTW ICCNFPYYG LTIQSVALS 
QDIYVNYMC VSVVEIPAY ILAYGALDR IGRKKTLAL 
SLILTGVAC LSVDFIRAG SPLALVVFL SGKLFVTVS 
YMTIYIYTA ELFPTSSRH SAFAVCSMF GCVGSMLAP 
QVPLLAKVY KPLPLMVFS ALAFTAGLL AFLFPETKD 
TKNPDEIDK S
    CDS sequence
    • >TC000561 RA
      atgaagaag ttcgatctc gacgatata ctcatatct 
ataggagga tggggaaaa tttcaaact ttgtactat 
gccgttttg tgcaccgcg attattttc tcagttttt 
ccggctatg aattatatt ttcatcgcg agggacatc 
aagtacagg tgtaaaatt gattcttgt gatagagaa 
aacggcgat tttaaccca gattggttg aaaaacgcc 
gttcctttc gaacaaaat gttccgagc aaatgttcc 
tactatcaa cctgaagag aatgacact tgtactagt 
tttgtaaaa aacgagact ttaacatgt catgatgac 
tttgtttac gaaagacta gaaacgaca attgtccac 
gattttaat ataaaatgc gatgaaaat ctttggaag 
ttgacaatt ataggaaca atcaatgta gtaggaaaa 
cttgtgtgt ttgcctctt gctgggttt ttctccgac 
cgatttggt cgaaagtct atggtcatc gttagcgta 
tttttaagc acgattgtg ggtcttgtg cggtcgttt 
tccgtaaat tactacatg tatgtcggt ttggagttt 
ttaaataca gtcgtgggc tcaggaata tacagcggg 
gcctttatt ttagcttta gaattagtc gattcaaaa 
cgccgtaat ttgggcaac agtatcata tgtttggcc 
ttcaccgtg ggccatatt ttgttaggg gccgctgct 
tgggtgtcc ccaacttgg caatttatg actcagata 
atgtacggt cctgggatt ttggtcaca attcttttg 
tggtttgtc cccgagtcc gtccgatgg ctgatcgcg 
cgcaacaaa atcgaaaag gctgaaggc gtcctaaaa 
tcaatcgcg aaaatcaac ggcaaagaa ctgaccgaa 
gaaacgatt aaaacaatt ccgtatctt gaggacagc 
aagagtgac ggtgacgaa gcgattcct ttgatggca 
attctgaaa aagaaaagc ctcctcatt cgaatcatc 
cattgttcg ttcacttgg atctgctgc aatttccct 
tactacggc ttaaccatt caatcagtg gctttatct 
caggacatt tatgtaaat tatatgtgc gtctcggtg 
gttgaaatt cctgcttat atattagcc tacggggct 
ttggatcga atcgggcga aagaaaacc ctcgctctg 
agcctcatc ctcacagga gtggcgtgt ctcagtgtc 
gattttatc agagcagga agtccactc gcactcgta 
gtcttcctc tccggaaaa ctctttgtt accgtgtct 
tacatgact atttacatt tacacggct gaactattc 
cccactagc tccagacat tccgccttt gccgtgtgc 
tccatgttt ggatgcgtc ggctcgatg ctggcgccc 
caagtgccc ttattggcc aaagtttac aagcccctg 
ccgctgatg gtcttctcg gctctcgcc ttcacggcc 
ggactgctc gccttcctg tttccggag acgaaagac 
acgaaaaac ccagacgaa atagacaaa tcctga
    mRNA sequence
    • >TC000561 RA
      cgtccttcc attgaggtc aaataagat tgaaactaa 
tgccggcgt ccagtaatc tcagttttt gagcacttc 
ttagagcgg caacacagt cagttatcg ctagtagaa 
gcatctttc gcgccatga agaagttcg atctcgacg 
atatactca tatctatag gaggatggg gaaaatttc 
aaactttgt actatgccg ttttgtgca ccgcgatta 
ttttctcag tttttccgg ctatgaatt atattttca 
tcgcgaggg acatcaagt acaggtgta aaattgatt 
cttgtgata gagaaaacg gcgatttta acccagatt 
ggttgaaaa acgccgttc ctttcgaac aaaatgttc 
cgagcaaat gttcctact atcaacctg aagagaatg 
acacttgta ctagttttg taaaaaacg agactttaa 
catgtcatg atgactttg tttacgaaa gactagaaa 
cgacaattg tccacgatt ttaatataa aatgcgatg 
aaaatcttt ggaagttga caattatag gaacaatca 
atgtagtag gaaaacttg tgtgtttgc ctcttgctg 
ggtttttct ccgaccgat ttggtcgaa agtctatgg 
tcatcgtta gcgtatttt taagcacga ttgtgggtc 
ttgtgcggt cgttttccg taaattact acatgtatg 
tcggtttgg agtttttaa atacagtcg tgggctcag 
gaatataca gcggggcct ttattttag ctttagaat 
tagtcgatt caaaacgcc gtaatttgg gcaacagta 
tcatatgtt tggccttca ccgtgggcc atattttgt 
taggggccg ctgcttggg tgtccccaa cttggcaat 
ttatgactc agataatgt acggtcctg ggattttgg 
tcacaattc ttttgtggt ttgtccccg agtccgtcc 
gatggctga tcgcgcgca acaaaatcg aaaaggctg 
aaggcgtcc taaaatcaa tcgcgaaaa tcaacggca 
aagaactga ccgaagaaa cgattaaaa caattccgt 
atcttgagg acagcaaga gtgacggtg acgaagcga 
ttcctttga tggcaattc tgaaaaaga aaagcctcc 
tcattcgaa tcatccatt gttcgttca cttggatct 
gctgcaatt tcccttact acggcttaa ccattcaat 
cagtggctt tatctcagg acatttatg taaattata 
tgtgcgtct cggtggttg aaattcctg cttatatat 
tagcctacg gggctttgg atcgaatcg ggcgaaaga 
aaaccctcg ctctgagcc tcatcctca caggagtgg 
cgtgtctca gtgtcgatt ttatcagag caggaagtc 
cactcgcac tcgtagtct tcctctccg gaaaactct 
ttgttaccg tgtcttaca tgactattt acatttaca 
cggctgaac tattcccca ctagctcca gacattccg 
cctttgccg tgtgctcca tgtttggat gcgtcggct 
cgatgctgg cgccccaag tgcccttat tggccaaag 
tttacaagc ccctgccgc tgatggtct tctcggctc 
tcgccttca cggccggac tgctcgcct tcctgtttc 
cggagacga aagacacga aaaacccag acgaaatag 
acaaatcct gattttagc acattgtag ctgattatg 
taaatagtt caaaagtgt gcaagtttg tacgtaatt 
agactcatt tttgcgagt gttagaaac ggcaatgga 
tttttcacg gtcatcatt caataccct tgaagatat 
cgcggcgat tccagtttt cggcatttt aatgtgtct 
tgttgtttt ttaattgtt tccgctttt ttcacaacg 
aaaaaactg atgatttat ttatttcta aaacgtcta 
gaatcatcg ccaaaaatt ttgtttgat ttaacagtt 
tgttgataa ttcttgcaa atttattca aggaggaag 
tttgtactt tcatacagt tagtgcatc tcattgttg 
gattaactg ttccttatt tgtttacta taaaaggtc 
aaaacgacc tcggactgc acctcggag tgtaaaatt 
gatttgtta ttaaaattg tcttttaat acatttata 
ttatgtac

    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