ZIM Genomic sequences

Minimum number of tobacco ZIM genes: 9

Count of tobacco ZIM sequences: 9

Pfam accession: Zim

SHOULD possess Zim domain but SHOULD NOT possess GATA domain

This short motif is found in a variety of plant transcription factors that contain GATA domains as well as other motifs. The most conserved amino acids form the pattern TIFF/YXG. This domain may be involved in binding DNA. The ZIM family gene is that contains ZIM motif but no belong to GATA family.

The deduced protein has a modular structure with a putative single C2-C2 zinc-finger motif distantly related to a GATA-1-type finger, a basic region with a sequence resembling a nuclear localization signal, and an acidic region. The gene seemed to have been formed by the exon-shuffling during its molecular evolution, since individual domains are encoded by discrete exons. RNA gel blot analysis showed its expression in shoot apex and flowers in the reproductive phase. The gene was named ZIM for Zinc-finger protein expressed in Inflorescence Meristem. The nuclear localization of ZIM was detected using GFP as a reporter. These results suggest that ZIM is a putative transcription factor involved in inflorescence and flower development.

By differential screening of an arrayed normalized cDNA library from the inflorescence apex in Arabidopsis, a cDNA clone having a deduced amino acid sequence with a motif for a zinc finger was isolated as one of the genes expressed specifically in the reproductive phase. The deduced protein has a modular structure with a putative single C2-C2 zinc-finger motif distantly related to a GATA-1-type finger, a basic region with a sequence resembling a nuclear localization signal, and an acidic region. The gene seemed to have been formed by the exon-shuffling during its molecular evolution, since individual domains are encoded by discrete exons. RNA gel blot analysis showed its expression in shoot apex and flowers in the reproductive phase. The gene was named ZIM for Zinc-finger protein expressed in Inflorescence Meristem. The nuclear localization of ZIM was detected using GFP as a reporter. These results suggest that ZIM is a putative transcription factor involved in inflorescence and flower development.

Papers

Nishii, A; Takemura, M; Fujita, H; Shikata, M; Yokota, A; Kohchi, T. Characterization of a novel gene encoding a putative single zinc-finger protein, ZIM, expressed during the reproductive phase in Arabidopsis thaliana. Biosci. Biotechnol. Biochem. 2000. 64(7):1402-9 PMID: 10945256



The ZIM domain is short.

Number of contigs: 6

Number of singlets: 3

Total minimum number – 9




Search sequences and info


Transcription factor sequences
Locus
Description
NCBI
ZIM_2 [comment=Complete ZIM domain PKTPAGPAQLTIFYVGSVCVYDNVSLEKVNALDL (Similar to Old gene 7)] [gss=CHO_OF440xp24f1.ab1, CHO_OF3160xk08f1.ab1] ET046469
ET043478
ZIM_7 [comment=Complete ZIM domain KEPKAAQLTMFYDGKVIVFDDFPANKARAEML (Old ZIM1)] [gss=CHO_OF4891xa04r1.ab1, CHO_OF4747xa10f1.ab1] ET048917
ET048123
ZIM_14 [comment=Last 12 aa ZIM domain. QMQAKAIIYLASR Divergent like AT1G30135.1] [gss=CHO_OF3131xm04f1.ab1, CHO_OF4422xc08f1.ab1, CHO_OF5011xj14f1.ab1] ET043397
ET046510
ET049851
ZIM_15 [comment=Complete ZIM dom. KSEPEKAQMTIFYGGQVIVFDDFPADKANEIMKLAT (Old gene 2)] [gss=CHO_OF4198xe20f1.ab1, CHO_OF5047xj06r1.ab1, CHO_OF4679xl09r1.ab1] ET045691
ET050141
ET047793
ZIM_16 [comment=Last 12 aa ZIM domain. Divergent like AT1G30135.1 MQAKAIIYLASR] [gss=CHO_OF4920xb08r1.ab1, CHO_OF3488xh23f1.ab1, CHO_OF3104xh02r1.ab1] ET049088
ET044245
ET043320
ZIM_18 [comment=Missing first 9aa ZIM domain.MFYDGKVIVFDDFPADKARAVMLLASK (Old gene 9)] [gss=CHO_OF573xm03r1.ab1, CHO_OF4426xc06f1.ab1, CHO_OF5092xk11r1.ab1] ET050911
ET046537
ET050423
ZIM_29 [comment=Full ZIM. Complete gene. SEPEKAQMTIFYGGQVIVFNDFPADKAKEIMLMAS (Old gene 4)] [gss=CHO_OF4673xd05r1.ab1, CHO_OF4673xd05f1.ab1, CHO_OF402xb16f2.ab1, CHO_OF402xb16r1.ab1] ET047769
ET047768
ET045083
ET045084
ZIM_37 [comment=GEANLNQLTLSFRGQVFVFDGVTTHKVSTL missing last 9 aa (up to KV), otherwise full] [gss=CHO_OF4303xf19f1.ab1, CHO_OF5079xe09f1.ab1, CHO_OF4773xi11r1.ab1, CHO_OF5008xg22f1.ab1, CHO_OF4720xp23r1.ab1] ET046189
ET050350
ET048296
ET049834
ET048004
ZIM_43 [comment=VDTSAGQMTIFYSGKVNVYDDVPADKV missing last 6-9 aa (up to KV), otherwise full (Old gene 5)] [gss=CHO_OF4967xn15r1.ab1, CHO_OF367xg21r5.ab1, CHO_OF367xg21r1.ab1, CHO_OF5070xk13f1.ab1, CHO_OF441xd17f2.ab1] ET049493
ET044615
ET044614
ET050296
ET046505
ZIM_51 [comment=EKSESEQLTIFYAGIVHVYDNLPVEKVQ missing last 8 aa (up to KV), otherwise full (Old gene 3)] [gss=CHO_OF3685xi16f1.ab1, CHO_OF4991xh05r1.ab1, CHO_OF3685xi16r1.ab1, CHO_OF4990xn20r1.ab1, CHO_OF4206xm23r1.ab1, CHO_OF360xj12f1.ab1, CHO_OF4569xa10f1.ab1] ET044643
ET049693
ET044644
ET049691
ET045754
ET044431
ET047129
ZIM_54 [comment=Complete ZIM gene SEPEKAQMTIFYGGQVIVFNDFPADKAKEIMLMASC (Old gene 6)] [gss=CHO_OF267xe10f1.ab1, CHO_OF164xj09f2.ab1, CHO_OF164xj09f1.ab1, CHO_OF291xj03r1.ab1, CHO_OF158xg03r1.ab1, CHO_OF4726xc20f1.ab1, CHO_OF3252xc22f1.ab1, CHO_OF009xb22r1.ab1, CHO_OF328xb24r1.ab1, CHO_OF3255xa03r1.ab1, CHO_OF4925xk14r1.ab1, CHO_OF291xj03f1.ab1] ET042896
ET042352
ET042351
ET042983
ET042328
ET048027
ET043728
ET041695
ET043858
ET043745
ET049136
ET042982
ZIM_58 [comment=Full ZIM domain KELKAAQLSIFYGGKVIMFDDFPADKARAMMLLASK (Old gene 8)] [gss=CHO_OF4920xo24f1.ab1] ET049099
ZIM_63 [comment=GSGASDQLTLSFQGEVYVFDAVSPEKV Full except last 9 aa] [gss=CHO_OF633xl11r1.ab1] ET051056
ZIM_66 [comment=Last 8 aa] [gss=CHO_OF4621xl01r1.ab1] ET047517


Tobacco published genes related to transcription factor family ZIM
Family Genbank ID Name
Authors of this site:

Paul J Rushton
Marta T. Bokowiec
Xianfeng (Jeff) Chen
Thomas (Tom) W Laudeman
Jennifer F. Brannock
Michael P. Timko

Contact:

pr8y@virginia.edu