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Protein trachealess

 TRH_DROME               Reviewed;        1022 AA.
Q24119; A8JNH0; A8WHG8; Q0E8K2; Q24165; Q8SX13; Q9W0Q7;
01-NOV-1997, integrated into UniProtKB/Swiss-Prot.
13-JUN-2012, sequence version 4.
30-AUG-2017, entry version 170.
RecName: Full=Protein trachealess;
Name=trh; ORFNames=CG6883;
Drosophila melanogaster (Fruit fly).
Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta;
Pterygota; Neoptera; Holometabola; Diptera; Brachycera; Muscomorpha;
Ephydroidea; Drosophilidae; Drosophila; Sophophora.
NCBI_TaxID=7227;
[1]
NUCLEOTIDE SEQUENCE [MRNA] (ISOFORMS A; B AND E), FUNCTION, TISSUE
SPECIFICITY, AND DEVELOPMENTAL STAGE.
TISSUE=Embryo;
PubMed=8557198; DOI=10.1101/gad.10.1.93;
Wilk R., Weizman I., Shilo B.-Z.;
"Trachealess encodes a bHLH-PAS protein that is an inducer of tracheal
cell fates in Drosophila.";
Genes Dev. 10:93-102(1996).
[2]
NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM A), FUNCTION, TISSUE SPECIFICITY,
AND DISRUPTION PHENOTYPE.
TISSUE=Embryo;
PubMed=8557189; DOI=10.1101/gad.10.1.103;
Isaac D.D., Andrew D.J.;
"Tubulogenesis in Drosophila: a requirement for the trachealess gene
product.";
Genes Dev. 10:103-117(1996).
[3]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=Berkeley;
PubMed=10731132; DOI=10.1126/science.287.5461.2185;
Adams M.D., Celniker S.E., Holt R.A., Evans C.A., Gocayne J.D.,
Amanatides P.G., Scherer S.E., Li P.W., Hoskins R.A., Galle R.F.,
George R.A., Lewis S.E., Richards S., Ashburner M., Henderson S.N.,
Sutton G.G., Wortman J.R., Yandell M.D., Zhang Q., Chen L.X.,
Brandon R.C., Rogers Y.-H.C., Blazej R.G., Champe M., Pfeiffer B.D.,
Wan K.H., Doyle C., Baxter E.G., Helt G., Nelson C.R., Miklos G.L.G.,
Abril J.F., Agbayani A., An H.-J., Andrews-Pfannkoch C., Baldwin D.,
Ballew R.M., Basu A., Baxendale J., Bayraktaroglu L., Beasley E.M.,
Beeson K.Y., Benos P.V., Berman B.P., Bhandari D., Bolshakov S.,
Borkova D., Botchan M.R., Bouck J., Brokstein P., Brottier P.,
Burtis K.C., Busam D.A., Butler H., Cadieu E., Center A., Chandra I.,
Cherry J.M., Cawley S., Dahlke C., Davenport L.B., Davies P.,
de Pablos B., Delcher A., Deng Z., Mays A.D., Dew I., Dietz S.M.,
Dodson K., Doup L.E., Downes M., Dugan-Rocha S., Dunkov B.C., Dunn P.,
Durbin K.J., Evangelista C.C., Ferraz C., Ferriera S., Fleischmann W.,
Fosler C., Gabrielian A.E., Garg N.S., Gelbart W.M., Glasser K.,
Glodek A., Gong F., Gorrell J.H., Gu Z., Guan P., Harris M.,
Harris N.L., Harvey D.A., Heiman T.J., Hernandez J.R., Houck J.,
Hostin D., Houston K.A., Howland T.J., Wei M.-H., Ibegwam C.,
Jalali M., Kalush F., Karpen G.H., Ke Z., Kennison J.A., Ketchum K.A.,
Kimmel B.E., Kodira C.D., Kraft C.L., Kravitz S., Kulp D., Lai Z.,
Lasko P., Lei Y., Levitsky A.A., Li J.H., Li Z., Liang Y., Lin X.,
Liu X., Mattei B., McIntosh T.C., McLeod M.P., McPherson D.,
Merkulov G., Milshina N.V., Mobarry C., Morris J., Moshrefi A.,
Mount S.M., Moy M., Murphy B., Murphy L., Muzny D.M., Nelson D.L.,
Nelson D.R., Nelson K.A., Nixon K., Nusskern D.R., Pacleb J.M.,
Palazzolo M., Pittman G.S., Pan S., Pollard J., Puri V., Reese M.G.,
Reinert K., Remington K., Saunders R.D.C., Scheeler F., Shen H.,
Shue B.C., Siden-Kiamos I., Simpson M., Skupski M.P., Smith T.J.,
Spier E., Spradling A.C., Stapleton M., Strong R., Sun E.,
Svirskas R., Tector C., Turner R., Venter E., Wang A.H., Wang X.,
Wang Z.-Y., Wassarman D.A., Weinstock G.M., Weissenbach J.,
Williams S.M., Woodage T., Worley K.C., Wu D., Yang S., Yao Q.A.,
Ye J., Yeh R.-F., Zaveri J.S., Zhan M., Zhang G., Zhao Q., Zheng L.,
Zheng X.H., Zhong F.N., Zhong W., Zhou X., Zhu S.C., Zhu X.,
Smith H.O., Gibbs R.A., Myers E.W., Rubin G.M., Venter J.C.;
"The genome sequence of Drosophila melanogaster.";
Science 287:2185-2195(2000).
[4]
GENOME REANNOTATION, AND ALTERNATIVE SPLICING.
STRAIN=Berkeley;
PubMed=12537572; DOI=10.1186/gb-2002-3-12-research0083;
Misra S., Crosby M.A., Mungall C.J., Matthews B.B., Campbell K.S.,
Hradecky P., Huang Y., Kaminker J.S., Millburn G.H., Prochnik S.E.,
Smith C.D., Tupy J.L., Whitfield E.J., Bayraktaroglu L., Berman B.P.,
Bettencourt B.R., Celniker S.E., de Grey A.D.N.J., Drysdale R.A.,
Harris N.L., Richter J., Russo S., Schroeder A.J., Shu S.Q.,
Stapleton M., Yamada C., Ashburner M., Gelbart W.M., Rubin G.M.,
Lewis S.E.;
"Annotation of the Drosophila melanogaster euchromatic genome: a
systematic review.";
Genome Biol. 3:RESEARCH0083.1-RESEARCH0083.22(2002).
[5]
NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM B).
STRAIN=Berkeley;
Stapleton M., Carlson J.W., Frise E., Kapadia B., Park S., Wan K.H.,
Yu C., Celniker S.E.;
Submitted (NOV-2007) to the EMBL/GenBank/DDBJ databases.
[6]
NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 17-1022 (ISOFORM B).
STRAIN=Berkeley; TISSUE=Head;
PubMed=12537569; DOI=10.1186/gb-2002-3-12-research0080;
Stapleton M., Carlson J.W., Brokstein P., Yu C., Champe M.,
George R.A., Guarin H., Kronmiller B., Pacleb J.M., Park S., Wan K.H.,
Rubin G.M., Celniker S.E.;
"A Drosophila full-length cDNA resource.";
Genome Biol. 3:RESEARCH0080.1-RESEARCH0080.8(2002).
[7]
PHOSPHORYLATION AT SER-673, MUTAGENESIS OF SER-579 AND SER-673, AND
SUBCELLULAR LOCATION.
PubMed=11740943; DOI=10.1016/S1534-5807(01)00090-9;
Jin J., Anthopoulos N., Wetsch B., Binari R.C., Isaac D.D.,
Andrew D.J., Woodgett J.R., Manoukian A.S.;
"Regulation of Drosophila tracheal system development by protein
kinase B.";
Dev. Cell 1:817-827(2001).
[8]
READTHROUGH OF STOP CODON.
PubMed=21994247; DOI=10.1101/gr.119974.110;
Jungreis I., Lin M.F., Spokony R., Chan C.S., Negre N., Victorsen A.,
White K.P., Kellis M.;
"Evidence of abundant stop codon readthrough in Drosophila and other
metazoa.";
Genome Res. 21:2096-2113(2011).
-!- FUNCTION: Transcription factor, master regulator of tracheal cell
fates in the embryo, necessary for the development of the salivary
gland duct and the posterior spiracles. It may induce a general
fate of branched tubular structures of epithelial origin.
Heterodimers of tgo/trh are involved in the control of breathless
expression. {ECO:0000269|PubMed:8557189,
ECO:0000269|PubMed:8557198}.
-!- SUBUNIT: Efficient DNA binding requires dimerization with another
bHLH protein. Heterodimer with tgo.
-!- SUBCELLULAR LOCATION: Nucleus {ECO:0000255|PROSITE-
ProRule:PRU00981, ECO:0000269|PubMed:11740943}.
-!- ALTERNATIVE PRODUCTS:
Event=Alternative splicing; Named isoforms=5;
Name=D;
IsoId=Q24119-5; Sequence=Displayed;
Note=No experimental confirmation available.;
Name=A;
IsoId=Q24119-1; Sequence=VSP_043934;
Name=B;
IsoId=Q24119-3; Sequence=VSP_043933, VSP_043934;
Name=C;
IsoId=Q24119-6; Sequence=VSP_043931, VSP_043933, VSP_043934;
Note=No experimental confirmation available.;
Name=E;
IsoId=Q24119-2; Sequence=VSP_043932, VSP_043934;
-!- TISSUE SPECIFICITY: Trachea, salivary gland ducts, posterior
spiracles (Filzkoeper primordia) and a subset of cells in the CNS.
{ECO:0000269|PubMed:8557189, ECO:0000269|PubMed:8557198}.
-!- DEVELOPMENTAL STAGE: During embryogenesis, first detected in the
tracheal placodes at stage 8, and expression continues throughout
embryonic and larval development. In the developing salivary
gland, expression is observed in the entire gland at stage 9 and
by stage 12, expression is confined to the salivary ducts.
{ECO:0000269|PubMed:8557198}.
-!- PTM: Ser-673 phosphorylation by PKB/Akt1 is required for nuclear
targeting and transcriptional activity.
{ECO:0000269|PubMed:11740943}.
-!- DISRUPTION PHENOTYPE: Tube-forming cells of the salivary gland,
trachea, and filzkorper fail to invaginate to form tubes and
remain on the embryo surface. {ECO:0000269|PubMed:8557189}.
-!- MISCELLANEOUS: Readthrough of the terminator UGA may occur between
the codons for 958-Ser and 960-Val.
-!- SEQUENCE CAUTION:
Sequence=AAA96257.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305};
Sequence=AAA96754.1; Type=Frameshift; Positions=22, 35; Evidence={ECO:0000305};
Sequence=AAM11264.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305};
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EMBL; U33427; AAA96257.1; ALT_INIT; mRNA.
EMBL; U42699; AAA96754.1; ALT_FRAME; mRNA.
EMBL; AE014296; AAF47386.1; -; Genomic_DNA.
EMBL; AE014296; ABI31226.1; -; Genomic_DNA.
EMBL; BT031114; ABX00736.1; -; mRNA.
EMBL; AY094911; AAM11264.1; ALT_INIT; mRNA.
RefSeq; NP_001036575.1; NM_001043110.2. [Q24119-3]
RefSeq; NP_001097461.2; NM_001103991.2. [Q24119-6]
RefSeq; NP_001261207.1; NM_001274278.1. [Q24119-5]
RefSeq; NP_523872.2; NM_079148.3. [Q24119-1]
UniGene; Dm.7330; -.
ProteinModelPortal; Q24119; -.
BioGrid; 63620; 3.
STRING; 7227.FBpp0303179; -.
iPTMnet; Q24119; -.
PaxDb; Q24119; -.
PRIDE; Q24119; -.
EnsemblMetazoa; FBtr0304120; FBpp0293063; FBgn0262139. [Q24119-1]
EnsemblMetazoa; FBtr0304121; FBpp0293064; FBgn0262139. [Q24119-3]
EnsemblMetazoa; FBtr0304122; FBpp0293065; FBgn0262139. [Q24119-6]
EnsemblMetazoa; FBtr0330146; FBpp0303179; FBgn0262139. [Q24119-5]
EnsemblMetazoa; FBtr0330147; FBpp0303180; FBgn0262139. [Q24119-2]
GeneID; 38065; -.
KEGG; dme:Dmel_CG42865; -.
UCSC; CG6883-RB; d. melanogaster.
CTD; 7200; -.
FlyBase; FBgn0262139; trh.
eggNOG; KOG3558; Eukaryota.
eggNOG; ENOG410YK57; LUCA.
GeneTree; ENSGT00760000118788; -.
InParanoid; Q24119; -.
KO; K09098; -.
OrthoDB; EOG091G02J4; -.
GenomeRNAi; 38065; -.
PRO; PR:Q24119; -.
Proteomes; UP000000803; Chromosome 3L.
Bgee; FBgn0262139; -.
ExpressionAtlas; Q24119; differential.
Genevisible; Q24119; DM.
GO; GO:0005634; C:nucleus; IDA:FlyBase.
GO; GO:0046982; F:protein heterodimerization activity; IPI:FlyBase.
GO; GO:0000981; F:RNA polymerase II transcription factor activity, sequence-specific DNA binding; ISS:FlyBase.
GO; GO:0043565; F:sequence-specific DNA binding; IDA:FlyBase.
GO; GO:0003700; F:transcription factor activity, sequence-specific DNA binding; TAS:FlyBase.
GO; GO:0048813; P:dendrite morphogenesis; IMP:FlyBase.
GO; GO:0007425; P:epithelial cell fate determination, open tracheal system; IMP:FlyBase.
GO; GO:0072175; P:epithelial tube formation; IMP:FlyBase.
GO; GO:0046331; P:lateral inhibition; IMP:FlyBase.
GO; GO:0060173; P:limb development; IMP:FlyBase.
GO; GO:0007443; P:Malpighian tubule morphogenesis; IMP:FlyBase.
GO; GO:0007424; P:open tracheal system development; IMP:UniProtKB.
GO; GO:0045944; P:positive regulation of transcription from RNA polymerase II promoter; IMP:FlyBase.
GO; GO:0007431; P:salivary gland development; IMP:UniProtKB.
GO; GO:0007435; P:salivary gland morphogenesis; IMP:FlyBase.
GO; GO:0035277; P:spiracle morphogenesis, open tracheal system; IMP:FlyBase.
GO; GO:0006366; P:transcription from RNA polymerase II promoter; IEA:GOC.
CDD; cd00083; HLH; 1.
CDD; cd00130; PAS; 2.
Gene3D; 4.10.280.10; -; 1.
InterPro; IPR011598; bHLH_dom.
InterPro; IPR001610; PAC.
InterPro; IPR000014; PAS.
InterPro; IPR013767; PAS_fold.
InterPro; IPR013655; PAS_fold_3.
Pfam; PF00989; PAS; 1.
Pfam; PF08447; PAS_3; 1.
SMART; SM00353; HLH; 1.
SMART; SM00086; PAC; 1.
SMART; SM00091; PAS; 2.
SUPFAM; SSF47459; SSF47459; 1.
SUPFAM; SSF55785; SSF55785; 2.
PROSITE; PS50888; BHLH; 1.
PROSITE; PS50112; PAS; 2.
1: Evidence at protein level;
Alternative splicing; Complete proteome; Developmental protein;
DNA-binding; Nucleus; Phosphoprotein; Reference proteome; Repeat;
Transcription; Transcription regulation.
CHAIN 1 1022 Protein trachealess.
/FTId=PRO_0000127476.
DOMAIN 86 139 bHLH. {ECO:0000255|PROSITE-
ProRule:PRU00981}.
DOMAIN 174 244 PAS 1. {ECO:0000255|PROSITE-
ProRule:PRU00140}.
DOMAIN 391 461 PAS 2. {ECO:0000255|PROSITE-
ProRule:PRU00140}.
DOMAIN 465 508 PAC.
MOTIF 629 636 Nuclear localization signal.
{ECO:0000255}.
COMPBIAS 244 281 Gly-rich.
COMPBIAS 976 984 His-rich.
MOD_RES 673 673 Phosphoserine; by PKB/Akt1.
{ECO:0000269|PubMed:11740943}.
VAR_SEQ 2 82 LPYQAAVAMDYAGYQRQPTPGHPGSHMATMGSLGMPAVPFT
HSWMVPTQDLCAMPPYNKMTGHQQPPGAGMHAQQQPLEPG
-> EHHGSGFVASPWAAVLGHHSMASDAGFAAAAAAAHVQN
HSMHHPIHSHHHHHSHSHPHPHPHSHPHHHPHLGTAGGMPM
DLHVPQGFPYYRYREDALCWGDRKSMEEIGAAQSSVNAR
(in isoform C). {ECO:0000305}.
/FTId=VSP_043931.
VAR_SEQ 281 286 Missing (in isoform E).
{ECO:0000303|PubMed:8557198}.
/FTId=VSP_043932.
VAR_SEQ 328 356 Missing (in isoform B and isoform C).
{ECO:0000303|PubMed:12537569,
ECO:0000303|PubMed:8557198,
ECO:0000303|Ref.5}.
/FTId=VSP_043933.
VAR_SEQ 959 1022 Missing (in isoform A, isoform B, isoform
C and isoform E).
{ECO:0000303|PubMed:12537569,
ECO:0000303|PubMed:8557189,
ECO:0000303|PubMed:8557198,
ECO:0000303|Ref.5}.
/FTId=VSP_043934.
MUTAGEN 579 579 S->A: No effect on phosphorylation by
Akt1; no effect on transcriptional
activity. {ECO:0000269|PubMed:11740943}.
MUTAGEN 673 673 S->A: Abolishes phosphorylation by Akt1,
nuclear localization, and transcriptional
activity. {ECO:0000269|PubMed:11740943}.
MUTAGEN 673 673 S->D: Slightly increases transcriptional
activity. {ECO:0000269|PubMed:11740943}.
CONFLICT 78 78 P -> A (in Ref. 1; AAA96257).
{ECO:0000305}.
CONFLICT 250 250 G -> GG (in Ref. 2; AAA96754).
{ECO:0000305}.
CONFLICT 627 627 S -> P (in Ref. 5; ABX00736).
{ECO:0000305}.
CONFLICT 703 703 A -> T (in Ref. 1; AAA96257).
{ECO:0000305}.
CONFLICT 708 708 A -> P (in Ref. 1; AAA96257).
{ECO:0000305}.
CONFLICT 829 829 A -> V (in Ref. 1; AAA96257).
{ECO:0000305}.
SEQUENCE 1022 AA; 109260 MW; CDF4C8CE3FB38E37 CRC64;
MLPYQAAVAM DYAGYQRQPT PGHPGSHMAT MGSLGMPAVP FTHSWMVPTQ DLCAMPPYNK
MTGHQQPPGA GMHAQQQPLE PGILELRKEK SRDAARSRRG KENYEFYELA KMLPLPAAIT
SQLDKASIIR LTISYLKLRD FSGHGDPPWT REASSSSKLK SAAIRRSPAV DLFEQHQGTH
ILQSLDGFAL AVAADGRFLY ISETVSIYLG LSQVEMTGSS IFDYIHQADH SEIADQLGLS
LTSGGGGGGG SSSSGGGGGG AGGGMASPTS GASDDGSGTH GTNNPDVAAS MTQASTSGYK
GYDRSFCVRM KSTLTKRGCH FKSSGYRASD ATSNCNNGNN ASNNAKNVKN PGSNYSVVLL
LCKLRPQYTF SHSRKSQPPL LGMVALAIAL PPPSVHEIRL ECDMFVTRVN FDLRVAHCEP
RVSDLLDYSP EDLVNKSLYS LCHAEDANRL RKSHSDLIEK GQVLTGYYRL MNKSGGYTWL
QTCATVVCST KNADEQNIIC VNYVISNREN ENMILDCCQL EPSPDSIKHE EGLGNDKSSG
SPGGDASGEG NSHLSAGDMK LNSPKTDSEG HSHRGRGRSA AASHGSSMNS LTMIKDSPTP
LGVEIDSGVL PTTVATPVPA ATPPVQSTKR KRKTKASQHA EDQGQEQVIS EQPLPKLPTM
EQRDQQPRSR LPSIVDEQPS SAADSAVKDL EQAMSKHLPS PAAVVSVAPP NTDFSADSLL
KQQQQQQQLD PNEKSSTIQW IGTPYQQPPA PMPATALLRQ LYANRESVIR ATARQTPTGV
GPGVFYGDQQ TGPLPTPPGS ESSYENQYLQ LHSAASGGHP GGQKTSADAF TNLVSTYGGY
HSSIDYHNAM TPPSSVSPRD SNQPGKAAPV LASNGGYDYA PDPLRGQYAT SSGDVVPATL
PLKPQASYTA TMHPSGSTTT EGGVTYSNLD QPQYFAPHSS FHLYHKGSPA SGWYSTPSXV
VDDQGQVPPS CQDQYHHHHH HHHHQDGSAG SSASQASERW DFVGALGKVA RMFFSARKGN
PG


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