Status
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Gene information
General information
TC004675 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_007416.3: 150161..153696
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
    		TC004675
    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.
      {{ unavailableText }}

    * : mandatory fields
    For help on how to submit larger datasets or non experimental data please contact us.
    iBeetle screen iB_00750

    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: 0.0% (includes death as pupa, adult)

    adult nutritional state bad (cachectic) - Number of animals showing the phenotype: 2 (11 dpi)
    Days post injection

    Fertility
    mature egg not present - Number of animals showing the phenotype: 2
    vitellarium size increased - Number of animals showing the phenotype: 2

    vitellarium degenerated - Number of animals showing the phenotype: 2
    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
    • >TC004675 RA
      MGDTKEENP KKEEKPTEE DKNELSEED KQLQEELNL 
CVETLQEND ENLYLPALQ ALGNHIRAS TTSMTSVPK 
PLKFMKPHY GTMKNVYEK IRDPNVKSV CADVISVLA 
MTMGEGREC LKYRLSSKL DGIGEWGHE YVRHLAGEI 
AAEWAETDV CEDKDKDVL IELAKQIVP YNMSHNAEA 
EACDLLMEI ERLDLLEVY VDENTYPRV CLYLISCVP 
YVADPENTT LLQTALLLF RNFEQYPQA LRLAMQLND 
HNLIEEIFT SCPDSTVQK QLAFMLGRQ QIYIEIPES 
TPEYEDLVE IMANCHLNN HFLNLAREL DIMEPKTPE 
DVYKSHLEN TRPQFGSNQ VDSARQNLA ASFVNGFVN 
AAFGQDKLL MEDGNKWLY KNKEHGMLS ATASLGLVL 
LWDVDGGLT PIDKYLYSS EDHIKSGAL LACGIVNCG 
VRNECDPAL ALLSDYVLH NTNTMRIGA IVGLGLAYV 
GSNREAVLS LLTPVFSDS KSNMEVIGM AALACGMIA 
VGSGNSQIT TAIMQTLME KSEADLKDT YARFLPLGL 
GLCHLGKQE GIETIIAAL EVIPEPFKS MAVTMVDIC 
AYAGTGNVL KVQHLLHIC SEHYEPADK DESRDKNKD 
KSKEKEDKE KDLSARQAV AVLGIALIS MGEDIGSDM 
AFRTFGHLL RYCEPVIRR AVPLALGLI SVSNPKLSI 
LDTLSKFSH DSDAEVAHN AIFAMGLVG AGTNNARLA 
AMLRQLAQF HAKDPNNLF MVRIAQGLT HLGKGTLTL 
SPYHSDRQL MSPVAVAGL MATLVGFLD VKNIILGKS 
HYLLYTLAA AMQPRMLVT FDEDLNPLP VPVRVGLAV 
DVVGQAGKP KTITGFQTH TTPVLLAHG ERAELATEE 
YIALTPIME GFVILRKNP DFYPS
    CDS sequence
    • >TC004675 RA
      atgggtgat acgaaagaa gaaaacccg aaaaaagaa 
gaaaaaccc accgaagaa gataaaaat gagctgtcc 
gaagaagac aagcaactg caggaggaa ttgaatttg 
tgcgtcgag actttacag gaaaatgac gagaatctg 
tacctccca gcgctccag gccctcggt aaccacatc 
cgggcctcc accacatcc atgacctcg gtccccaaa 
cccctcaaa tttatgaaa ccccactac ggcaccatg 
aaaaacgtc tacgagaaa atccgtgac cctaacgtg 
aaaagcgtt tgtgctgac gttatctcc gtcctggcc 
atgacaatg ggcgaaggg cgcgagtgt ctcaaatac 
cgcctctcg tcgaagctg gacggtatc ggcgaatgg 
gggcacgaa tacgtgcgt catctcgct ggggaaatc 
gccgcagaa tgggcagag accgacgtt tgcgaggac 
aaagacaag gacgttttg atcgagttg gccaaacag 
atcgtcccg tacaacatg tcgcacaat gcagaggcc 
gaggcctgc gatttgttg atggaaatt gagagacta 
gacttgttg gaggtctac gttgacgaa aatacttat 
ccgagggtt tgcttgtat ttgatcagt tgtgtcccg 
tatgttgcc gatcctgag aacacgact ttgctacaa 
acggcgctg cttttgttc cgcaacttc gaacagtat 
ccgcaagct ctgagactc gcaatgcaa ctcaacgat 
cacaattta atcgaagaa attttcacg tcatgtcct 
gactctacg gttcagaaa caactagct ttcatgctc 
ggccggcaa cagatttac atcgagatt cccgagagc 
acacccgaa tacgaggat ttggtcgaa ataatggcc 
aattgtcac ttaaacaac cacttttta aatttggct 
cgagagctc gatatcatg gagcctaaa acaccggaa 
gatgtttac aaatcgcat ttggaaaac acacgacct 
cagtttggc tcaaatcag gtcgattca gcccgacag 
aatctcgcc gctagtttc gtcaatggt ttcgtcaac 
gctgccttc ggccaagat aaactccta atggaagat 
ggaaataag tggttgtac aagaacaaa gagcacggc 
atgttgagc gccaccgcg tcccttggg ttggtgcta 
ctgtgggac gtggacggg gggttaacc cccattgac 
aagtacttg tactcgtct gaggaccac attaaatcc 
ggggcttta ctcgcttgt gggattgtt aattgtggg 
gttcggaat gagtgtgat cctgcatta gcactatta 
tcggactat gtactacat aacactaat accatgagg 
attggggct atagtgggg cttgggtta gcatatgtg 
ggctcaaac cgcgaggct gttttgagt ctgctaacc 
ccagttttc tccgactcg aaatccaac atggaggtt 
ataggcatg gcggctttg gcatgcggt atgatcgct 
gtaggttca ggcaatagt caaataacc acagctata 
atgcaaaca ctgatggag aagtcggag gccgatttg 
aaagacacc tacgctagg tttttgccc ctggggctc 
ggcctgtgc catttgggc aaacaggag ggtattgag 
accataatt gcagccttg gaggtgatc ccagaaccg 
ttcaaatcc atggctgtg accatggtc gacatctgc 
gcctatgcc gggaccgga aacgtgctc aaagtccag 
catttgctc cacatctgc tccgagcac tacgaaccg 
gccgataaa gacgaaagt cgcgataaa aataaagac 
aagagtaag gaaaaagaa gacaaggag aaagaccta 
tcggcgaga caagccgtg gccgtgctg ggcatagcc 
ctgattagc atgggtgag gacattggg agtgacatg 
gcgttccga accttcggc cacttgtta cgctactgc 
gagcccgtg attcggcgc gcggtgcct ttggctctt 
gggcttata tctgtatca aaccccaaa ctgagtatt 
ctagacacc ttgagcaaa ttctcacac gatagtgac 
gccgaagtc gcccataac gccatcttc gcgatgggc 
ctagtcggc gctggaacc aacaacgca cggttggcg 
gcaatgctg cgccagttg gcgcaattc cacgccaaa 
gaccccaac aatctattc atggtgcga attgcacaa 
gggttgact catttaggc aagggaacg ttgacgttg 
agtccgtac cacagcgac cgacagttg atgagtcca 
gtggccgtc gccggtctg atggcgaca ctggttggt 
ttccttgat gtgaaaaac atcattctc ggcaaatct 
cactatctg ttgtacacc cttgccgcg gcgatgcag 
ccccgcatg ttggtaaca tttgatgag gatcttaac 
ccgcttccg gtgcccgtg cgagtgggt cttgccgtt 
gatgttgtg ggacaggcc gggaaaccc aaaactatc 
accgggttc caaacgcat acaacgccc gtgttgtta 
gcgcacggt gaaagggca gagttggca accgaggag 
tatatcgcg cttacgccc atcatggaa ggatttgtg 
attcttagg aaaaatccc gatttttac ccctcttaa
    mRNA sequence
    • >TC004675 RA
      caatttatt tgaaaattt tgaaactta taattagct 
acgttggcg aacctgacg tcacgtgac ccaaagtgt 
aatgactgg cacaatacg ttatatttc ggctatttt 
cttgaatta gtgttttta gtgaattac actcagtat 
ttagcagcg gtttaactt aaagttttt acgatgggt 
gatacgaaa gaagaaaac ccgaaaaaa gaagaaaaa 
cccaccgaa gaagataaa aatgagctg tccgaagaa 
gacaagcaa ctgcaggag gaattgaat ttgtgcgtc 
gagacttta caggaaaat gacgagaat ctgtacctc 
ccagcgctc caggccctc ggtaaccac atccgggcc 
tccaccaca tccatgacc tcggtcccc aaacccctc 
aaatttatg aaaccccac tacggcacc atgaaaaac 
gtctacgag aaaatccgt gaccctaac gtgaaaagc 
gtttgtgct gacgttatc tccgtcctg gccatgaca 
atgggcgaa gggcgcgag tgtctcaaa taccgcctc 
tcgtcgaag ctggacggt atcggcgaa tgggggcac 
gaatacgtg cgtcatctc gctggggaa atcgccgca 
gaatgggca gagaccgac gtttgcgag gacaaagac 
aaggacgtt ttgatcgag ttggccaaa cagatcgtc 
ccgtacaac atgtcgcac aatgcagag gccgaggcc 
tgcgatttg ttgatggaa attgagaga ctagacttg 
ttggaggtc tacgttgac gaaaatact tatccgagg 
gtttgcttg tatttgatc agttgtgtc ccgtatgtt 
gccgatcct gagaacacg actttgcta caaacggcg 
ctgcttttg ttccgcaac ttcgaacag tatccgcaa 
gctctgaga ctcgcaatg caactcaac gatcacaat 
ttaatcgaa gaaattttc acgtcatgt cctgactct 
acggttcag aaacaacta gctttcatg ctcggccgg 
caacagatt tacatcgag attcccgag agcacaccc 
gaatacgag gatttggtc gaaataatg gccaattgt 
cacttaaac aaccacttt ttaaatttg gctcgagag 
ctcgatatc atggagcct aaaacaccg gaagatgtt 
tacaaatcg catttggaa aacacacga cctcagttt 
ggctcaaat caggtcgat tcagcccga cagaatctc 
gccgctagt ttcgtcaat ggtttcgtc aacgctgcc 
ttcggccaa gataaactc ctaatggaa gatggaaat 
aagtggttg tacaagaac aaagagcac ggcatgttg 
agcgccacc gcgtccctt gggttggtg ctactgtgg 
gacgtggac ggggggtta acccccatt gacaagtac 
ttgtactcg tctgaggac cacattaaa tccggggct 
ttactcgct tgtgggatt gttaattgt ggggttcgg 
aatgagtgt gatcctgca ttagcacta ttatcggac 
tatgtacta cataacact aataccatg aggattggg 
gctatagtg gggcttggg ttagcatat gtgggctca 
aaccgcgag gctgttttg agtctgcta accccagtt 
ttctccgac tcgaaatcc aacatggag gttataggc 
atggcggct ttggcatgc ggtatgatc gctgtaggt 
tcaggcaat agtcaaata accacagct ataatgcaa 
acactgatg gagaagtcg gaggccgat ttgaaagac 
acctacgct aggtttttg cccctgggg ctcggcctg 
tgccatttg ggcaaacag gagggtatt gagaccata 
attgcagcc ttggaggtg atcccagaa ccgttcaaa 
tccatggct gtgaccatg gtcgacatc tgcgcctat 
gccgggacc ggaaacgtg ctcaaagtc cagcatttg 
ctccacatc tgctccgag cactacgaa ccggccgat 
aaagacgaa agtcgcgat aaaaataaa gacaagagt 
aaggaaaaa gaagacaag gagaaagac ctatcggcg 
agacaagcc gtggccgtg ctgggcata gccctgatt 
agcatgggt gaggacatt gggagtgac atggcgttc 
cgaaccttc ggccacttg ttacgctac tgcgagccc 
gtgattcgg cgcgcggtg cctttggct cttgggctt 
atatctgta tcaaacccc aaactgagt attctagac 
accttgagc aaattctca cacgatagt gacgccgaa 
gtcgcccat aacgccatc ttcgcgatg ggcctagtc 
ggcgctgga accaacaac gcacggttg gcggcaatg 
ctgcgccag ttggcgcaa ttccacgcc aaagacccc 
aacaatcta ttcatggtg cgaattgca caagggttg 
actcattta ggcaaggga acgttgacg ttgagtccg 
taccacagc gaccgacag ttgatgagt ccagtggcc 
gtcgccggt ctgatggcg acactggtt ggtttcctt 
gatgtgaaa aacatcatt ctcggcaaa tctcactat 
ctgttgtac acccttgcc gcggcgatg cagccccgc 
atgttggta acatttgat gaggatctt aacccgctt 
ccggtgccc gtgcgagtg ggtcttgcc gttgatgtt 
gtgggacag gccgggaaa cccaaaact atcaccggg 
ttccaaacg catacaacg cccgtgttg ttagcgcac 
ggtgaaagg gcagagttg gcaaccgag gagtatatc 
gcgcttacg cccatcatg gaaggattt gtgattctt 
aggaaaaat cccgatttt tacccctct taaatattt 
agctattta acagttttg tctatgttt tgtatccag 
ttcatttaa gttaataaa aaattatgt tctac

    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