Status
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Gene information
General information
TC001944 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: 1469455..1478708
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
    		TC001944
    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_03274

    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: 40.0% (includes death as pupa, adult)

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

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

    Analysis of larval stage 1 cuticle
    number of eggs/embryos/larvae on slide: < 20
    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
    • >TC001944 RA
      MGAGVSAGE NNDDLIDNL IEANYIKTA SVERVFRAV 
DRGAYLLPE PPADAYRDV AWKNGNFHI SAPCIYSEV 
MEGLKLRPG LSFLNLGSG TGYLNTVAG LILGSYGIN 
HGIELHDDV IQYAYLRLE EFKKHSGAI DEYDFCEPK 
FMQGNCLCL VSGYHLYDR VYCGAACPE KYLSHIKNL 
IKVGGILVV PINERLVEM RRVSETSWS THYLLPVSF 
TSLVKPEQG SQEIVPTFD IEPLSLQEL CRTTIRNLL 
RKIIEIEHP AVKNVRKTR KTSKKKKPL KKNGRKDTN 
PKTSEELLD FFLLTIARK KRRDTATAD RDNSSSSAN 
NDDDSDGPS SDSDDSSLD DPLETMQEA FHVLDRQTN 
HVVPSTSNS DEAGSSKQS DDVKIESNV IIHREAGEE 
RAENKVSYN ITVEPMLVE EQNERKNNR DKFDSGLGD 
ELLISELPV DMVEAMSSS SDDEQSSKR CKRGLKEKE 
KRLSSKWRK IERVDTPKK CDSDDSSDN DDKSDSESD 
YVDAMNRMK MYMSPYSGH MKSKIQQLP LPSNVKKFL 
NFYREF
    CDS sequence
    • >TC001944 RA
      atgggggcc ggcgtgagc gcaggtgag aataacgac 
gatctcatc gataacctc atcgaggcc aattacatc 
aagacggca tcggtggaa agggtgttc cgggctgtg 
gacaggggg gcctattta ctaccggag cccccagct 
gatgcctac agagatgtg gcgtggaaa aatggaaat 
tttcatatc tcggctcct tgtatctac agcgaggtt 
atggaggga ctgaagctc cgtcctgga ttgagtttt 
cttaatttg ggctcaggg acggggtat ttgaacacg 
gtggctgga cttattcta ggcagctac ggtatcaac 
cacggtatc gaactccac gatgacgtc atccaatac 
gcctacttg cgcctcgaa gagttcaaa aaacactcg 
ggcgcaatc gacgaatac gatttttgc gaaccaaaa 
ttcatgcaa ggcaattgt ctctgcttg gttagcggc 
taccacttg tacgatcgt gtctattgt ggagctgca 
tgtcccgaa aaataccta agccatata aaaaatttg 
atcaaagtt ggtggcatt ctggtggtg ccaatcaat 
gaacgtctc gttgaaatg cgaagagtt tcggagaca 
agttggtca acgcattat ttgttgcct gtttcgttt 
acgagtctc gttaaaccg gaacaaggt tctcaggaa 
attgtgccg acatttgac attgaacct ttgtcattg 
caagaattg tgcaggact acgattcgg aatttgttg 
aggaagatt attgaaatt gagcatccg gctgttaag 
aatgttaga aagacgagg aagacgtcc aagaagaaa 
aaaccactc aaaaaaaat ggtagaaag gacactaat 
ccgaaaacc tccgaagag ctcctcgac ttcttcttg 
ttaacaatc gctcgtaaa aaaagacgt gatacggcc 
acagccgac cgcgataac tcatcaagt tcagccaac 
aacgacgac gattcagac ggtccttcg tcagacagt 
gatgattca tcattagac gatccgctt gaaacaatg 
caggaagct ttccacgtt ttagaccgt caaactaat 
cacgttgtt ccatcgaca agcaattcg gacgaagcc 
ggcagtagc aaacaatcc gatgatgtg aaaatcgaa 
agcaacgtc attattcac agagaggcc ggtgaagag 
cgagccgaa aacaaagtg agctacaat atcacggtt 
gaaccgatg cttgtcgag gaacaaaac gagcgtaaa 
aataaccga gataagttc gatagtggc ttaggagat 
gagctgctt atttcggaa ttgcccgtg gatatggtc 
gaggcaatg tcgagcagt agcgacgat gagcagagt 
agcaagagg tgcaaaaga ggcttgaag gagaaagag 
aaaagattg agctcgaaa tggcgcaaa atcgaacgg 
gtcgatacg ccgaaaaaa tgtgatagt gatgatagt 
tcagacaat gatgataaa agtgatagt gagagtgat 
tatgtagat gctatgaat agaatgaag atgtacatg 
agtccgtac agtggacac atgaagagt aagatccaa 
caactgcct ctgccatcc aatgtcaag aaatttctc 
aacttttat cgggaattt taa
    mRNA sequence
    • >TC001944 RA
      acttcaatc tcagctgat tttgtgtcg actttgttg 
tcgttccgt atttacaaa acttgtcat aaaacgccc 
caaacttcc gttgtcaca acataagaa ccagtgctg 
taatcaccc attacatca ttgttcctg atgaaccca 
taaatttgg taatcggtt cgcattttt cgcccgctt 
gtcgttcca aagatgggg gccggcgtg agcgcaggt 
gagaataac gacgatctc atcgataac ctcatcgag 
gccaattac atcaagacg gcatcggtg gaaagggtg 
ttccgggct gtggacagg ggggcctat ttactaccg 
gagccccca gctgatgcc tacagagat gtggcgtgg 
aaaaatgga aattttcat atctcggct ccttgtatc 
tacagcgag gttatggag ggactgaag ctccgtcct 
ggattgagt tttcttaat ttgggctca gggacgggg 
tatttgaac acggtggct ggacttatt ctaggcagc 
tacggtatc aaccacggt atcgaactc cacgatgac 
gtcatccaa tacgcctac ttgcgcctc gaagagttc 
aaaaaacac tcgggcgca atcgacgaa tacgatttt 
tgcgaacca aaattcatg caaggcaat tgtctctgc 
ttggttagc ggctaccac ttgtacgat cgtgtctat 
tgtggagct gcatgtccc gaaaaatac ctaagccat 
ataaaaaat ttgatcaaa gttggtggc attctggtg 
gtgccaatc aatgaacgt ctcgttgaa atgcgaaga 
gtttcggag acaagttgg tcaacgcat tatttgttg 
cctgtttcg tttacgagt ctcgttaaa ccggaacaa 
ggttctcag gaaattgtg ccgacattt gacattgaa 
cctttgtca ttgcaagaa ttgtgcagg actacgatt 
cggaatttg ttgaggaag attattgaa attgagcat 
ccggctgtt aagaatgtt agaaagacg aggaagacg 
tccaagaag aaaaaacca ctcaaaaaa aatggtaga 
aaggacact aatccgaaa acctccgaa gagctcctc 
gacttcttc ttgttaaca atcgctcgt aaaaaaaga 
cgtgatacg gccacagcc gaccgcgat aactcatca 
agttcagcc aacaacgac gacgattca gacggtcct 
tcgtcagac agtgatgat tcatcatta gacgatccg 
cttgaaaca atgcaggaa gctttccac gttttagac 
cgtcaaact aatcacgtt gttccatcg acaagcaat 
tcggacgaa gccggcagt agcaaacaa tccgatgat 
gtgaaaatc gaaagcaac gtcattatt cacagagag 
gccggtgaa gagcgagcc gaaaacaaa gtgagctac 
aatatcacg gttgaaccg atgcttgtc gaggaacaa 
aacgagcgt aaaaataac cgagataag ttcgatagt 
ggcttagga gatgagctg cttatttcg gaattgccc 
gtggatatg gtcgaggca atgtcgagc agtagcgac 
gatgagcag agtagcaag aggtgcaaa agaggcttg 
aaggagaaa gagaaaaga ttgagctcg aaatggcgc 
aaaatcgaa cgggtcgat acgccgaaa aaatgtgat 
agtgatgat agttcagac aatgatgat aaaagtgat 
agtgagagt gattatgta gatgctatg aatagaatg 
aagatgtac atgagtccg tacagtgga cacatgaag 
agtaagatc caacaactg cctctgcca tccaatgtc 
aagaaattt ctcaacttt tatcgggaa ttttaattt 
tgccctaaa accggtcag tggaggagg aggtctcgt 
atgttacga gtgttcaat tgaaaaaaa aaagattca 
gttcaattt tttttattt ggtcattcg ttagaattc 
gtaaatttg gtctaaccg tttttttgc tatcatctt 
ttgtttaag ttttaccga aaataaaaa attcatata 
ttc

    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