PHD Genomic sequences

Minimum number of tobacco PHD genes: 59

Count of tobacco PHD sequences: 68

Pfam accession: PHD

SHOULD possess PHD domain but SHOULD NOT possess DDT Homeobox JmjC JmjN domains

PHD proteins seem to be found universally in the nucleus, and their functions tend to lie in the control of chromatin or transcription. Increasing evidence indicates that PHD fingers bind to specific nuclear protein partners, for which they apparently use their loop 2 surface. Perhaps each PHD finger has its own cognate nuclear ligand, much like RING fingers have their cognate E2 ligases. No doubt the list of specific PHD finger ligands will grow, and the set of these ligands is likely to reveal whether PHD fingers have a common function in the nucleus.

The homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in chromatin-mediated transcriptional regulation. The PHD finger motif is reminiscent of, but distinct from the C3HC4 type RING finger.

The function of this domain is not yet known but in analogy with the LIM domain it could be involved in protein-protein interaction and be important for the assembly or activity of multicomponent complexes involved in transcriptional activation or repression. Alternatively, the interactions could be intra-molecular and be important in maintaining the structural integrity of the protein. In similarity to the RING finger and the LIM domain, the PHD finger is thought to bind two zinc ions.

Papers

Bienz, M. The PHD finger, a nuclear protein-interaction domain. Trends Biochem. Sci. 2006. 31(1):35-40 PMID: 16297627



Number of contigs: 57

Number of singlets: 31

Number of N terminal – 19

Number of C terminal – 9

Number of full – 40

Total minimum number – 59




Search sequences and info


Transcription factor sequences
Locus
Description
NCBI
PHD_4 [comment=full] ET045008
ET051747
PHD_5 [comment=full] ET042254
ET048263
PHD_6 [comment=N terminal] ET047761
ET050772
PHD_7 [comment=C terminal] ET043543
ET043542
PHD_10 [comment=full] ET047637
ET047638
PHD_11 [comment=N terminal] ET042021
ET049485
PHD_12 [comment=full] ET042703
ET042702
PHD_13 [comment=full] ET048360
ET045284
PHD_14 [comment=N terminal] ET047643
ET043496
PHD_16 [comment=N terminal] ET046866
ET046867
PHD_17 [comment=full] ET043536
ET043537
PHD_19 [comment=N terminal] ET044056
ET051891
PHD_20 [comment=full] ET047470
ET044800
PHD_21 [comment=full] ET042815
ET048403
PHD_22 [comment=full] ET051401
ET043365
ET051402
PHD_24 [comment=full] ET043576
ET048929
ET048930
PHD_26 [comment=N terminal] ET045312
ET046019
ET050941
PHD_28 [comment=full ] ET042688
ET048906
ET043011
PHD_29 [comment=N terminal] ET050196
ET049388
ET042237
PHD_30 [comment=N terminal] ET046767
ET048763
ET043687
PHD_31 [comment=N terminal] ET042520
ET049730
ET044872
PHD_32 [comment=full] ET044698
ET050287
ET050199
PHD_33 [comment=full] ET049363
ET051073
ET051460
PHD_34 [comment=C terminal] ET042024
ET042025
ET044510
PHD_35 [comment=C terminal] ET051200
ET051201
ET048178
PHD_36 [comment=full] ET042771
ET048097
ET042770
PHD_38 [comment=N terminal] ET051641
ET050963
ET045449
ET047953
PHD_39 [comment=full] ET046381
ET047377
ET043599
ET049852
PHD_40 [comment=N terminal] ET047901
ET051368
ET048333
ET041761
PHD_41 [comment=full] ET050950
ET051862
ET045328
ET050949
PHD_42 [comment=C terminal] ET042209
ET046645
ET049643
ET042208
PHD_43 [comment=full] ET049586
ET044486
ET047507
ET042381
PHD_44 [comment=full] ET048666
ET046132
ET041705
ET051508
PHD_46 [comment=full] ET048747
ET050932
ET049963
ET050933
ET045242
PHD_47 [comment=N terminal] ET042139
ET044806
ET042138
ET050286
ET047870
ET051303
PHD_48 [comment=full] ET044270
ET044642
ET042436
ET050768
ET046694
ET043618
PHD_49 [comment=N terminal] ET049631
ET041859
ET041858
ET044763
ET049002
ET043524
PHD_50 [comment=full] ET041981
ET042282
ET044630
ET043469
ET046091
ET046092
PHD_51 [comment=full] ET041745
ET041950
ET041746
ET044794
ET041861
ET041862
PHD_52 [comment=N terminal] ET046206
ET046980
ET049811
ET045979
ET047290
ET049502
PHD_53 [comment=full] ET043822
ET045819
ET050723
ET050992
ET046054
ET045823
ET049442
PHD_54 [comment=N terminal] ET048017
ET044442
ET044500
ET049792
ET043986
ET048203
ET044211
ET043571
ET045563
PHD_56 [comment=N terminal] ET046039
ET046040
ET046049
ET046551
ET050602
ET045675
ET050601
ET045938
ET042528
ET050532
PHD_57 [comment=full] ET046928
ET044371
ET047155
ET050974
ET048737
ET049067
ET047077
ET045598
ET045868
ET044361
ET051615
PHD_58 [comment=full] ET043868
PHD_59 [comment=full] ET047359
PHD_60 [comment=C terminal] ET050506
PHD_61 [comment=full] ET047121
PHD_62 [comment=full ] ET051223
PHD_63 [comment=C terminal] ET044421
PHD_64 [comment=full ] ET048494
PHD_65 [comment=full ] ET046833
PHD_66 [comment=C terminal] ET051545
PHD_67 [comment=N terminal] ET047248
PHD_68 [comment=C terminal] ET051222
PHD_69 [comment=full] ET049182
PHD_70 [comment=full ] ET046936
PHD_71 [comment=full] ET042490
PHD_72 [comment=full] ET047709
PHD_73 [comment=full ] ET044262
PHD_74 [comment=full] ET045574
PHD_75 [comment=full] ET042987
PHD_76 [comment=full] ET045975
PHD_77 [comment=N terminal] ET041931
PHD_78 [comment=full] ET049893
PHD_79 [comment=N terminal ] ET043910
PHD_80 [comment=full] ET051464
PHD_81 [comment=C terminal] ET051783


Tobacco published genes related to transcription factor family PHD
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