PlantTFDB
PlantRegMap/PlantTFDB v5.0
Plant Transcription Factor Database
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(e.g., LFY)
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID Neem_11905_f_1
Organism
Azadirachta indica
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Sapindales; Meliaceae; Azadirachta
Family bHLH
Protein Properties Length: 1206aa    MW: 137387 Da    PI: 8.6776
Description bHLH family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Neem_11905_f_1genomeNGDView Nucleic Acid
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1HLH18.14.9e-0610531102155
                      CHHHHHHHHHHHHHHHHHHHHHHHCTSCCC...TTS-STCHHHHHHHHHHHHHHH CS
             HLH    1 rrrahnerErrRRdriNsafeeLrellPkaskapskKlsKaeiLekAveYIksLq 55  
                      r+  h+++Er RR++ ++ +  L ++lP+      +K +K +i + A + I++Lq
  Neem_11905_f_1 1053 RCHRHKINERMRREKEKQNYLALHSMLPPG-----TKGDKNAIIKTAAKRIQELQ 1102
                      5678************************97.....8*****************99 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PROSITE profilePS5129519.638245341IPR001890RNA-binding, CRM domain
Gene3DG3DSA:3.30.110.609.7E-22246335IPR001890RNA-binding, CRM domain
SuperFamilySSF754712.62E-21246335IPR001890RNA-binding, CRM domain
SMARTSM011031.0E-19247330IPR001890RNA-binding, CRM domain
PfamPF019852.1E-35247330IPR001890RNA-binding, CRM domain
PROSITE profilePS5129515.306470567IPR001890RNA-binding, CRM domain
Gene3DG3DSA:3.30.110.601.0E-26471563IPR001890RNA-binding, CRM domain
SuperFamilySSF754711.96E-16471561IPR001890RNA-binding, CRM domain
SMARTSM011033.5E-10472556IPR001890RNA-binding, CRM domain
PfamPF019851.4E-15473556IPR001890RNA-binding, CRM domain
PROSITE profilePS5129515.459681783IPR001890RNA-binding, CRM domain
SMARTSM011031.1E-14695772IPR001890RNA-binding, CRM domain
SuperFamilySSF754712.09E-17695781IPR001890RNA-binding, CRM domain
Gene3DG3DSA:3.30.110.608.4E-17705782IPR001890RNA-binding, CRM domain
PfamPF019851.6E-15705772IPR001890RNA-binding, CRM domain
SuperFamilySSF474591.44E-910501118IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
CDDcd000839.22E-610501102No hitNo description
PROSITE profilePS5088811.4910521101IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
Gene3DG3DSA:4.10.280.102.8E-610561119IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
SMARTSM003536.0E-410581107IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0000373Biological ProcessGroup II intron splicing
GO:0048316Biological Processseed development
GO:0009507Cellular Componentchloroplast
GO:0003723Molecular FunctionRNA binding
GO:0046983Molecular Functionprotein dimerization activity
Sequence ? help Back to Top
Protein Sequence    Length: 1206 aa     Download sequence    Send to blast
MALVPSRQFY PTTTIFDSFQ SSFSRFHGTH LPLFRYGHSI PLKNRFFYLN FSSDAASEQN  60
PPKKITSLST GKHVSQHDKD DNLNLSSSSS WLDKWNKHNK HNRPKPPRAV VNYRKNNNVD  120
LSSLGFARSS SDGGAVDEGG NSTMGKIVEK LKNFGYIDGG DDNERRQKEP ERMIEKGSIE  180
DIFYVEEGML PNTGGGFSKD SQLGLGEEIG SDGEVKFPWE KPKEKEEKGK WSAKQRTSRT  240
SLAELTLPES ELRRLRNLTF QTKSKTKIGG AGVTQAIVDT IHEKWKTSEI VRLKIEGAPA  300
LNMKRMHEIL ERKTGGLVIW RSGTAVSLYR GVSYEIPSVQ LSKRIFRRNE LPRSSLPQAT  360
DKQIYKRIDI CSNSLSTATD KTVHSHLEFG SYNNVHAPQA NLETTAEEQE TESTSEVKYE  420
DEVNKLLDGL GPRYTDWPGC DPLPVDADML PGIVSGYEPP FRVLPYGVRS TLARKEATNL  480
QRLARVLPPH FALGRSRQLQ GLAVAVIKLW EKSSIAKIAL KRGVQLTTSE RMAEDIKKLT  540
GGMLISRSKD FLVFYRGKDF LSSDVTEALL ERERLAKSLQ DEEEQARLRA SGFVLPSVET  600
TDQSGIAGAR GETSGTAGTL GETLDANARW GKRLDNSHKQ NLMREAEIMR HANLVRKLER  660
KLAIAERKLM KAERALLKVE EFLKPAERQA DPESITDEER FMFRKLGRRG VFDGTVENMH  720
LHWKYRELVK IIVKVKTFDQ VKKIALALEA ESGGVLVSVD KISKGYAIIV YRGKDYQRPS  780
TLRPRNLLTK RKALSRSIEL QRQEAILKHI ATVETRVGKL RYEIEQMNSV KDTGNEELYD  840
KLDSAYATED EDSESEGDEA YLETYDVGND SENENDDSIH NLPMETDFPY HTQDQESENE  900
PLDSEAKAHC SQDTLHQHQE KGEEQKHFSS SARLDWKMIM GSIAKRYAHH ENVHCIGWNQ  960
KSKFLWEKIR SMDEFFAEQF HGDSDGDSFW FNYEALPVKQ SAFVPYENRP RIELESRNAN  1020
DGPNSRNTNK KMMEFLRRIR SATMEDRVPN SERCHRHKIN ERMRREKEKQ NYLALHSMLP  1080
PGTKGDKNAI IKTAAKRIQE LQCCKGELER KNYELEERLG KNVNGGKKIR IRVANPTSGI  1140
DSMLEVIKCL KKIDSRTRSI QSKFSDHELT ATLDIETQMG AGEVEEAVQR TLHQVEQELL  1200
HRYQEG
Functional Description ? help Back to Top
Source Description
UniProtBinds specific group II introns in chloroplasts and facilitates their splicing. Acts on subgroup IIB introns. The substrates of the subgroup IIB also require the CRM domain proteins CAF1 or CAF2, with a simultaneous binding of CFM3A and CAF1 or CAF2. Required for seed development. May influence the biogenesis of the mitochondrial small ribosomal subunit. {ECO:0000269|PubMed:18799595}.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_006489518.10.0CRM-domain containing factor CFM3A, chloroplastic/mitochondrial-like
SwissprotF4J2U90.0CFM3A_ARATH; CRM-domain containing factor CFM3A, chloroplastic/mitochondrial
TrEMBLA0A067E3P70.0A0A067E3P7_CITSI; Uncharacterized protein
STRINGXP_006489518.10.0(Citrus sinensis)
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT5G43650.13e-36bHLH family protein
Publications ? help Back to Top
  1. Asakura Y,Bayraktar OA,Barkan A
    Two CRM protein subfamilies cooperate in the splicing of group IIB introns in chloroplasts.
    RNA, 2008. 14(11): p. 2319-32
    [PMID:18799595]