Status
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Gene information
General information
TC005415 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_007423.3: 13504553..13508791
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
    		TC005415
    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
    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_03946

    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: 10.0% (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

    Analysis of embryonic musculature and early development
    number of eggs/embryos/larvae on slide: > 50 larval musculature irregular - 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): less than 30%
    remarks: muscle pattern potentially obscured by segmentation defect,
    Analysis of larval stage 1 cuticle
    number of eggs/embryos/larvae on slide: > 50
     larva complete everted (inside-out) - 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 appendages orientation irregular - Penetrance (percentage of animals/eggs on slide): less than 30%
    head appendages random not present - Penetrance (percentage of animals/eggs on slide): less than 30%
    head irregular - Penetrance (percentage of animals/eggs on slide): less than 30%
    thorax segment number decreased - Penetrance (percentage of animals/eggs on slide): less than 30%
    legs podomer shortened - Penetrance (percentage of animals/eggs on slide): less than 30%
    thorax irregular - Penetrance (percentage of animals/eggs on slide): less than 30%
    abdomen everted (inside-out) - Penetrance (percentage of animals/eggs on slide): less than 30%
    abdomen posterior circumference decreased - 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: 30.0% (includes death as larva, prepupa, pupa)
    Lethalities 22 days after larval injection: 60.0% (includes death as larva, prepupa, pupa, adult)

    larva lethality - Number of animals showing the phenotype: 3 (11 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: 2 (41 dpi)
    Days post injection

    Adult morphology
    elytra dorsal orientation not closed - Number of animals showing the phenotype: 2


    RNAi sequence
    Primers
    Left: Right:
    Protein sequence
    • >TC005415 RA
      MAESKAVDD LLLGDGFSI VDSTKGDAP ESESKKRSS 
KDKDKEKKP EVKKEKSEE KKPKEEPPK DDTKVNGHD 
TKSDALLIT TEEDLDMTE KDKKSEAET KDEDSKPKK 
DSESGSKEK DKPVDKKKQ GDLWVSNIT RHVKATDLK 
KHFSRHGKV LTAKIVTNG KSFFGYILM ETSDIANKC 
VRSLHGSTL DGRKLTVSR QRPDQRRPM TERKPTVKS 
SKTERKTEK KSDEKKTDK KDDALAAAK RTEDRLRRE 
IDFHKREIT RLKRYLTDE QRRLRIEQQ KNRSLGREL 
QEAEAKLRD ERRKMDRER ELFEKNQRT DRVKLENDR 
SMIKKELEE VKKLREYLK RKLEEEARP VDRRPRASS 
PYAYSSKRF RESSGGDSK SKYVEERTR TPPSPPKLS 
SRSKRSPVN SFVEKDRRP HHYSMSERE EVRSLVIPA 
KPSAPAAPR NIWPSFHQE VWRVPPGTA TSSPFSGQS 
YSRQSEYSS STSKGPSYS SSQREFSKR DHYTSSSVR 
KY
    CDS sequence
    • >TC005415 RA
      atggccgag tccaaggct gttgacgat ttgctcctc 
ggtgatggc ttctccatt gtcgatagt acgaaaggg 
gacgctccc gaatccgaa tccaaaaag cgatcatcg 
aaggacaaa gacaaggag aagaagccc gaagtgaag 
aaagaaaaa tccgaggag aagaaacca aaggaagag 
cccccgaag gatgacacc aaagtcaac ggacacgac 
accaaaagt gacgccctc ctcatcaca acggaggaa 
gatttggac atgaccgag aaggacaag aagagcgaa 
gccgaaacc aaagacgaa gactccaag ccgaagaaa 
gactccgaa agcggcagc aaagagaag gacaaacca 
gtcgataag aagaaacaa ggcgacctc tgggtctcc 
aacatcacc cggcatgtc aaggccacc gacttgaag 
aaacacttc tcccgccat ggcaaggtc ctaaccgcc 
aaaatcgtc accaacggc aagtccttc ttcggctac 
attctcatg gagacgtcc gacatcgcc aacaagtgt 
gtgcggagt ctccacggc tcgaccctc gacggccgc 
aaactcacc gtgagccgt cagagaccc gaccagagg 
agacccatg accgagcgc aagcccaca gtcaagtcc 
agcaagacc gagcgcaaa accgaaaaa aagtccgac 
gagaagaaa accgacaag aaagacgac gccttggct 
gcggcgaaa cgcacggaa gaccgactt cgccgcgaa 
atcgacttc cacaagcgc gaaatcaca cgactaaag 
cgctacctc accgacgaa caacgacgc ttgcgaatc 
gaacaacag aagaatcgt tcgctgggt cgggaactg 
caagaagcc gaagccaaa ctccgcgac gaacgcaga 
aaaatggac cgcgaacgc gaactgttc gagaagaac 
caacgcacc gaccgggtc aagctcgaa aacgaccgc 
tccatgatc aagaaggag ctggaagaa gtgaagaaa 
ctccgcgag tatctcaag cgcaagctg gaggaagag 
gcgcgtccg gtggaccgg cggccgcgg gcttcgtca 
ccgtacgcc tactcgtcg aagaggttc cgggagtcg 
tcgggcggc gactccaag tccaagtac gtggaggag 
cggacgagg acgccgccg tcgcccccg aagctctcc 
tccaggtcc aaacgctcg ccggtcaat tccttcgtg 
gagaaggat cgaaggccg catcattat agcatgtcc 
gagagggag gaagtccgc tcgttggtg attccggcc 
aagccgtcg gcaccggcc gcccccagg aatatatgg 
ccgtcgttc caccaggaa gtttggagg gtgcctccg 
gggacggcg accagttcg ccgttttca ggccagtcg 
tatagcaga cagtccgag tatagtagc tccacgtcg 
aaggggcca agttattcg tcgtcgcag agggagttc 
agcaaacgc gatcattat acgagcagt tcagttagg 
aagtattaa
    mRNA sequence
    • >TC005415 RA
      catcgattt agcgattga ttttctttg tttgtttgc 
ttgttgtcg gaaaacagg catcgatcg ttgcatttt 
cacaatgct gtccgaaag gccgtaaac ttccaactc 
tccctaaaa acgtacgac tgcttttag cggccccga 
cggctttgc gggtgtaat tcactctct cgcccccgc 
ctttagcag aaggaaaac attctccac ggtcgggga 
ttatcgccg aattcactt tccatattc ggaaggaaa 
ctcggggaa attaatcga atcgcgtga tggaaataa 
caaaaacat gatgggttg ttttaacga gatttccgc 
gctcggaca ccgctcgta attgtaact ttttgacgg 
aatgtgaga ttttaaacg acttgacaa agttccgta 
tatatgaaa tgtttattt cttttaacc gtcctgagg 
tacagcgta tttttattt catcaagac ccagcattg 
gaatttaaa gctacgtcg aaaaaggct acgagggag 
ggagttgcc cgttttctt tgcaaatat gagtagttt 
agttgcaag gtgtcgcta ggtatagtc ttgtccccg 
tttcgacat taatggcgc ataaatatc cagctcggc 
tctttgttt tccgtcggg ggagcccct ctgtcagga 
gcccgcata attaggagc gctgagcgt ctgcggctg 
cacccgaca cgccatcgt ggacccggt gacttatgg 
cctacattt ccgcaactc ctgggggcg gccaccgcg 
ccgatcgaa gaggagaaa tagaggcaa gaggaggcc 
gccgccact ggacacgtt ttggggcat ttttcactt 
ggcgccata aatatgcac gctcgacgc gtctctaac 
gttgaataa taattaggg cggcggcgg cggcggcgg 
tggcgggct cccatgttt catttatac gccgtcgcc 
gcagatgtg tacaacttc cgatgccaa tcaactaaa 
ttactaaac aacttggac gatgaattt aatatgact 
ttgctttga aactcgcta tacccacct atcgttagt 
tttttgccg cgtctttca acttgttat cggagtaca 
aattgctac tggtggacg agatagcag gcgacgaaa 
ggaaaataa ccaccaaag tatacaagt cttatctgt 
ggactacaa tgattccgc tccggctta tccttgcaa 
ggaacctat ctgaatgtg tgtgctgtg tgttacaac 
aaaacgact cgaagctcc ccattttat tactgtgtc 
tgttggctg ttgtagcac aatagttga attttttgg 
tactagctt tgcccccgc taccaaaaa atttatttt 
gctacactg gccttgctt gtgttctaa caaaagtct 
gattttacg caggtaaat aataggatt tcctgcaat 
agtatttaa aaaataacc aatggccga gtccaaggc 
tgttgacga tttgctcct cggtgatgg cttctccat 
tgtcgatag tacgaaagg ggacgctcc cgaatccga 
atccaaaaa gcgatcatc gaaggacaa agacaagga 
gaagaagcc cgaagtgaa gaaagaaaa atccgagga 
gaagaaacc aaaggaaga gcccccgaa ggatgacac 
caaagtcaa cggacacga caccaaaag tgacgccct 
cctcatcac aacggagga agatttgga catgaccga 
gaaggacaa gaagagcga agccgaaac caaagacga 
agactccaa gccgaagaa agactccga aagcggcag 
caaagagaa ggacaaacc agtcgataa gaagaaaca 
aggcgacct ctgggtctc caacatcac ccggcatgt 
caaggccac cgacttgaa gaaacactt ctcccgcca 
tggcaaggt cctaaccgc caaaatcgt caccaacgg 
caagtcctt cttcggcta cattctcat ggagacgtc 
cgacatcgc caacaagtg tgtgcggag tctccacgg 
ctcgaccct cgacggccg caaactcac cgtgagccg 
tcagagacc cgaccagag gagacccat gaccgagcg 
caagcccac agtcaagtc cagcaagac cgagcgcaa 
aaccgaaaa aaagtccga cgagaagaa aaccgacaa 
gaaagacga cgccttggc tgcggcgaa acgcacgga 
agaccgact tcgccgcga aatcgactt ccacaagcg 
cgaaatcac acgactaaa gcgctacct caccgacga 
acaacgacg cttgcgaat cgaacaaca gaagaatcg 
ttcgctggg tcgggaact gcaagaagc cgaagccaa 
actccgcga cgaacgcag aaaaatgga ccgcgaacg 
cgaactgtt cgagaagaa ccaacgcac cgaccgggt 
caagctcga aaacgaccg ctccatgat caagaagga 
gctggaaga agtgaagaa actccgcga gtatctcaa 
gcgcaagct ggaggaaga ggcgcgtcc ggtggaccg 
gcggccgcg ggcttcgtc accgtacgc ctactcgtc 
gaagaggtt ccgggagtc gtcgggcgg cgactccaa 
gtccaagta cgtggagga gcggacgag gacgccgcc 
gtcgccccc gaagctctc ctccaggtc caaacgctc 
gccggtcaa ttccttcgt ggagaagga tcgaaggcc 
gcatcatta tagcatgtc cgagaggga ggaagtccg 
ctcgttggt gattccggc caagccgtc ggcaccggc 
cgcccccag gaatatatg gccgtcgtt ccaccagga 
agtttggag ggtgcctcc ggggacggc gaccagttc 
gccgttttc aggccagtc gtatagcag acagtccga 
gtatagtag ctccacgtc gaaggggcc aagttattc 
gtcgtcgca gagggagtt cagcaaacg cgatcatta 
tacgagcag ttcagttag gaagtatta attgtattg 
gtttagttg tagtgttgc gttttttgg aaataaagc 
cgtagatta gaagagaaa tttttaata aagtatcgt 
cgtaacctt atttgaagt cgtttcgtg taatttgcc 
aagtgcgaa atttaattt tgcgaagcg gaactttca 
tctcatctc tggataaaa tgagcaata tattccgac 
attacttat tttattaga ttaaaatct accagaaca 
aactaggat acgaattac caaactaat ggcggaatt 
attgtgcag acctttcac ttatctcga tttacattt 
ttaacaggg atttgcagg gcgagggta agtcgcgat 
tatatgcat cctcctgct cgaataaat ttttttctt 
ctct

    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