Status
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Gene information
General information
TC004404 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_007418.3: 19788411..19798457
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
      		TC004404
      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 *
      {{ blurIdResult }}
      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_06721

      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: 2 (3 dpi)
      Days post injection

      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 pattern irregular - Penetrance (percentage of animals/eggs on slide): 30% - 50%

      larval musculature fluorescence decreased - Penetrance (percentage of animals/eggs on slide): 30% - 50%

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

      affected eggs/embryos/larvae - Penetrance (percentage of animals/eggs on slide): 50% - 80%
      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): less than 30%
      cuticle remnants with unidentifyable segments - Penetrance (percentage of animals/eggs on slide): less than 30%

      labium not present - Penetrance (percentage of animals/eggs on slide): less than 30%

      labium structure irregular - Penetrance (percentage of animals/eggs on slide): 30% - 50%

      head capsule structure irregular - Penetrance (percentage of animals/eggs on slide): 30% - 50%

      head not present - Penetrance (percentage of animals/eggs on slide): 50% - 80%
      head fused - Penetrance (percentage of animals/eggs on slide): 50% - 80%

      thorax partially not present - Penetrance (percentage of animals/eggs on slide): 50% - 80%

      thorax not present - Penetrance (percentage of animals/eggs on slide): 50% - 80%
      thorax fused - Penetrance (percentage of animals/eggs on slide): 50% - 80%
      abdomen segment number decreased - Penetrance (percentage of animals/eggs on slide): less than 30%

      abdomen not present - Penetrance (percentage of animals/eggs on slide): less than 30%

      abdomen cuticle structure irregular - Penetrance (percentage of animals/eggs on slide): 30% - 50%

      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
      • >TC004404 RA
        MISLRYTRN LFLRSFCIV YLFAFISFY IQIPGLYGD 
NGILPAKSL LENSKHKTL SAKVHYQPT LLWLAPYLG 
LDVNYALDV LALLGSFLA FTGFISQKF CTIPLFAGL 
WSLYFSLYQ VGQVFVSNN YDEFLLEAG FLVLLVAPL 
LPGRRKGSK VLPSDSISF WLVRWLLFR FLLTCGLLK 
FISGCPKWW TLSAFNYYF ETLPLPTPL SWYFHQIPS 
WYLKLFGVI ANVCEIGIP FLFFVPIRA VRITSFMIQ 
IFLQISIVL TGNYNFTNL LMVTLLLSL LDDQFFYGR 
RKPFTKWTF IEKVINILT YGALLLAVV KLYSLKLDG 
TIIESNIAF TKDQFEYVL KQGLTITIY LGLISLAVT 
ILRALSISL FDVQGSKVF TIITTILYS GIAVLLFFA 
STVPLASLH TASNSTVHP SVRTVYNRL HKLHAVNQY 
GLFPKMMGV DGRPEVILE GSDNVEGPW LEYNFLYKP 
GNVNHSLPF VAPYSPRLD WQMFWAAYN TYDKQPWIL 
SLTHRLLTG KAEVLALLD RHHSPFNQK PPKYIRGIL 
YKYKYSSWS QRSQPSWWV RQKVGEYFP AYTKESPAL 
VDYLKARNL LPTSSKQTV NPIWKQILD GVRYITGHL 
EATLLLWSV FTAGCAIIT TSAKK
      CDS sequence
      • >TC004404 RA
        atgatatct ctgcgatac accaggaat ctctttctg 
agatcgttc tgcatagtc tacctcttt gcatttatt 
tcgttctac atccaaatc cccggattg tacggcgat 
aatggaata ttaccggca aaatcgttg ttggaaaac 
agtaaacac aagacttta tcagccaaa gtacattat 
caacccaca ttactgtgg cttgccccc tacttgggc 
ttggatgtg aattatgcg ttggatgtg ttggcactg 
cttgggagc tttttagca tttacaggg tttatctcc 
caaaagttt tgtacaatt ccactcttt gctgggttg 
tggtcttta tatttctct ctttatcaa gttgggcaa 
gtttttgtg agcaataat tacgacgaa tttttacta 
gaggccggt tttcttgtt ctcctggtg gccccttta 
ctccctggc aggagaaag ggttcgaaa gttttaccc 
agcgattct attagtttc tggctggtg cgttggtta 
ctgtttcga tttttgtta acctgtggc ctattaaaa 
ttcatcagt ggttgcccc aagtggtgg actttatct 
gcatttaat tactatttt gaaacttta ccattacca 
acaccactc tcttggtac ttccatcaa attccgagc 
tggtacttg aaactgttc ggcgttatt gccaatgtt 
tgtgagatt ggtattccg tttttattc ttcgtcccg 
attcgagcg gtgcgcatc accagtttt atgatacaa 
atattccta caaatatct attgtactt actggcaat 
tataacttt accaacttg ttgatggta actctactt 
ttatcttta ctggacgac cagttcttt tacggccgc 
cgcaaaccc ttcaccaag tggactttt atcgaaaaa 
gtcatcaat attttgaca tatggcgct cttttattg 
gccgttgtt aagttatat tctttgaaa ctcgacggg 
acgataatt gaatccaat attgcattt acgaaggac 
cagtttgag tatgtcctc aagcaaggt ctcacaatc 
accatatac ttgggtttg atctcattg gctgttaca 
attctgcga gccctctcg atctccttg tttgacgtt 
cagggatca aaagtattc acaattatt acaacaatt 
ctgtattcg ggaatcgcc gtacttcta tttttcgct 
agtaccgtt cctctcgcg tctttacac acagcatcc 
aattcaacc gttcatcca agtgtccgc actgtatat 
aaccgactt cataaactg catgctgtc aaccagtat 
ggacttttc ccaaaaatg atgggagtg gatggtcgt 
cctgaagtt atccttgaa ggttccgac aatgttgag 
ggcccatgg ctcgaatat aacttcctg tacaagccg 
ggaaatgtg aaccactcc ttacctttt gttgcacca 
tactctccc aggttggac tggcagatg ttctgggcg 
gcttacaac acttacgac aagcagcct tggattttg 
agtttaact caccgatta ttgacgggg aaagccgaa 
gttttggct cttttggac agacaccat tcaccgttc 
aaccaaaaa ccgccaaaa tacatccga ggaattctc 
tataaatac aagtattcg tcgtggagt caaaggtcg 
cagccctcg tggtgggtt cgccaaaaa gtgggtgaa 
tatttcccc gcctacaca aaagagtct ccagctttg 
gtggattac ttaaaggct aggaacctc ttgcctacg 
tcttcgaaa cagactgtc aaccccatt tggaagcag 
attttggat ggggtgagg tatattaca gggcattta 
gaagctact ttgcttttg tggtcagtt tttacggct 
ggttgtgcc attattaca acttctgcc aagaaataa
      mRNA sequence
      • >TC004404 RA
        aataatctg ttgattttt tcactaaac gtcattttt 
caaaatcca aaattttag tatgtcgag cttagaaag 
caagaaaaa gccctccaa acagtcaaa aaataagga 
aaagaaaga attaggtga caccgagct tccccgcaa 
accaaaaat taaaaagga acaaaaagg cacacaaga 
gacaaaagt gaagaaagg gaccccgaa gggttcttt 
ggttggtgg tggcattaa gaaaaagtc caacaagaa 
tgagtaaac aagacacac attattatt atcattaaa 
cacaaagtg tgtgcatat aatcaatac atggcatgt 
aaatatact gttacattt aaaaacgta tcaaatatt 
tacttttgc taaatttgt aattgtgtt cacatcatt 
gttgggaca ggaatttcc aaaattcag ctacttgtg 
ctagttttt aattaactt aatgcctag aagaatcca 
ccaattttc ataaaaccg aggaaatgt gatgatgtt 
aaacataaa aaacagtta ttttattcg gattcgatc 
attcctgtt tatattaca aactagcgc tccttgtcc 
cacctatgt tgaggtgca tgcttggct ggttgctgt 
gtccttgtc tcttgctgg gcgtttgtt ggttcgagt 
tggttgcgt tgcgtcgct ttattcttt cagatcaca 
tcatcacta tcatcaaat acgagagaa gtactcgtg 
ttaagttgt tattaatgt gttgtttat tgtttacat 
gttgagttc aatctccag aagtggatt tttttctat 
cggcttgtt aattatcgg tgaacaatg atatctctg 
cgatacacc aggaatctc tttctgaga tcgttctgc 
atagtctac ctctttgca tttatttcg ttctacatc 
caaatcccc ggattgtac ggcgataat ggaatatta 
ccggcaaaa tcgttgttg gaaaacagt aaacacaag 
actttatca gccaaagta cattatcaa cccacatta 
ctgtggctt gccccctac ttgggcttg gatgtgaat 
tatgcgttg gatgtgttg gcactgctt gggagcttt 
ttagcattt acagggttt atctcccaa aagttttgt 
acaattcca ctctttgct gggttgtgg tctttatat 
ttctctctt tatcaagtt gggcaagtt tttgtgagc 
aataattac gacgaattt ttactagag gccggtttt 
cttgttctc ctggtggcc cctttactc cctggcagg 
agaaagggt tcgaaagtt ttacccagc gattctatt 
agtttctgg ctggtgcgt tggttactg tttcgattt 
ttgttaacc tgtggccta ttaaaattc atcagtggt 
tgccccaag tggtggact ttatctgca tttaattac 
tattttgaa actttacca ttaccaaca ccactctct 
tggtacttc catcaaatt ccgagctgg tacttgaaa 
ctgttcggc gttattgcc aatgtttgt gagattggt 
attccgttt ttattcttc gtcccgatt cgagcggtg 
cgcatcacc agttttatg atacaaata ttcctacaa 
atatctatt gtacttact ggcaattat aactttacc 
aacttgttg atggtaact ctactttta tctttactg 
gacgaccag ttcttttac ggccgccgc aaacccttc 
accaagtgg acttttatc gaaaaagtc atcaatatt 
ttgacatat ggcgctctt ttattggcc gttgttaag 
ttatattct ttgaaactc gacgggacg ataattgaa 
tccaatatt gcatttacg aaggaccag tttgagtat 
gtcctcaag caaggtctc acaatcacc atatacttg 
ggtttgatc tcattggct gttacaatt ctgcgagcc 
ctctcgatc tccttgttt gacgttcag ggatcaaaa 
gtattcaca attattaca acaattctg tattcggga 
atcgccgta cttctattt ttcgctagt accgttcct 
ctcgcgtct ttacacaca gcatccaat tcaaccgtt 
catccaagt gtccgcact gtatataac cgacttcat 
aaactgcat gctgtcaac cagtatgga cttttccca 
aaaatgatg ggagtggat ggtcgtcct gaagttatc 
cttgaaggt tccgacaat gttgagggc ccatggctc 
gaatataac ttcctgtac aagccggga aatgtgaac 
cactcctta ccttttgtt gcaccatac tctcccagg 
ttggactgg cagatgttc tgggcggct tacaacact 
tacgacaag cagccttgg attttgagt ttaactcac 
cgattattg acggggaaa gccgaagtt ttggctctt 
ttggacaga caccattca ccgttcaac caaaaaccg 
ccaaaatac atccgagga attctctat aaatacaag 
tattcgtcg tggagtcaa aggtcgcag ccctcgtgg 
tgggttcgc caaaaagtg ggtgaatat ttccccgcc 
tacacaaaa gagtctcca gctttggtg gattactta 
aaggctagg aacctcttg cctacgtct tcgaaacag 
actgtcaac cccatttgg aagcagatt ttggatggg 
gtgaggtat attacaggg catttagaa gctactttg 
cttttgtgg tcagttttt acggctggt tgtgccatt 
attacaact tctgccaag aaataagaa ctgaatttg 
agtcactag tttttattt tctcattga aaagtttca 
gttaaggat ctttatggt gtgattttt tttattttt 
atatgtgca cacactaat ttatcgagt aatttcacc 
cctccattt agatcagaa tatgtcata cgatattgt 
tatcaggtt tgtcccgtg tgaagtttt taaatgtaa 
tgtttttgt tagtaaagt gcaaatata tcatttatt 
taaaa

      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