ref-2 (Caenorhabditis elegans)
C2H2 ZF

TF Information

Pfam ID Interpro ID Gene ID CIS-BP ID Sequence source Animal TF db
PF00096 (zf-C2H2) IPR007087 WBGene00004335 T131569_2.00 Ensembl (2018-Dec-8) Link out
NCBI Gene Info:
Enables RNA polymerase II transcription regulatory region sequence-specific DNA binding activity and RNA polymerase II-specific DNA-binding transcription factor binding activity. Involved in neuron fate specification and positive regulation of transcription by RNA polymerase II. Acts upstream of or within with a positive effect on nematode larval development. Located in nucleus. Is expressed in several structures, including IL1 neuron; P3.p hermaphrodite; neuroblasts; rectal epithelial cell; and ventral nerve cord. Human ortholog(s) of this gene implicated in Dandy-Walker syndrome; X-linked VACTERL association; craniosynostosis; holoprosencephaly (multiple); and visceral heterotaxy (multiple). Orthologous to several human genes including ZIC1 (Zic family member 1); ZIC2 (Zic family member 2); and ZIC3 (Zic family member 3). [provided by Alliance of Genome Resources, Apr 2022]

Directly determined binding motifs

Name/Motif ID Species Forward Reverse Type/Study/Study ID SR
Score		 DBD
Identity
ref-2
M00621_2.00		 Caenorhabditis elegans
CMYRSNGNBH
DVNCNSYRKG		 PBM
Narasimhan et al.(2015)
pTH9089		 (Direct) (Direct)

Motifs from related TFs

Name/Motif ID Species Forward Reverse Type/Study/Study ID SR
Score		 DBD
Identity
opa
M03668_2.00 		Drosophila melanogaster
BVCCCCCCRYNGHB
VDCNRYGGGGGGBV		 SELEX
Nitta et al.(2015)
opa_1 		0.757 0.739
opa
M05861_2.00 		Drosophila melanogaster
VCCCCCCRYNGNK
MNCNRYGGGGGGB		 SMiLE-seq
Isakova et al.(2017)
Opa 		0.757 0.739
opa
M06468_2.00 		Drosophila melanogaster
GMCCCCCCGCDG
CHGCGGGGGGKC		 B1H
Mathelier et al.(2014)
MA0456.1 		0.757 0.739
opa
M06062_2.00 		Drosophila melanogaster
GMCCCCCCRCDG
CHGYGGGGGGKC		 B1H
Zhu et al.(2011)
opa_NAR_FBgn0003002 		0.757 0.739
opa
M06063_2.00 		Drosophila melanogaster
MKVMMCCCCMCYR
YRGKGGGGKKBMK		 B1H
Zhu et al.(2011)
Opa_SANGER_5_FBgn0003002 		0.757 0.739
For this family, TFs with SR scores > 0.755 will likely have a similar motif

Experimental Constructs

Motif ID Domain From To Sequence
M00621_2.00 C2H2 ZF 51 78
M00621_2.00 C2H2 ZF 84 106
M00621_2.00 C2H2 ZF 112 136
M00621_2.00 C2H2 ZF 142 166

DNA Binding Domains

Protein ID Domain From To Sequence
C47C12.3a.1 C2H2 ZF 106 133
C47C12.3a.1 C2H2 ZF 139 161
C47C12.3a.1 C2H2 ZF 167 191
C47C12.3a.1 C2H2 ZF 197 221
C47C12.3a.2 C2H2 ZF 106 133
C47C12.3a.2 C2H2 ZF 139 161
C47C12.3a.2 C2H2 ZF 167 191
C47C12.3a.2 C2H2 ZF 197 221
C47C12.3b C2H2 ZF 119 146
C47C12.3b C2H2 ZF 152 174
C47C12.3b C2H2 ZF 180 204
C47C12.3b C2H2 ZF 210 234

Links

Other C2H2 ZF family TFs
Other Caenorhabditis elegans TFs

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35 Related TFs

Name Species Gene ID Motif Evidence SR
Score		 Action