REF-1

WormBase ID: WBGene00004334

WormBase description: Is predicted to have protein dimerization activity. Is involved in several processes, including epidermal cell fate specification; negative regulation of transcription by RNA polymerase II; and nematode male tail tip morphogenesis. Localizes to nucleus. Is expressed in several structures, including E lineage cell; embryonic cell; intestine; mc3V; and pharyngeal cell.

KI information: mNeonGreen knockin at N-terminus

sgRNA1: GTACTGATGAGGACCATTTC

sgRNA2: TCATAACAGAAAAACATCAC

5'HR: GCATGCATCTTCTTCTCATTTTTTTGTTTGTTTTTTAGTTCCAGTATTTACTTTAGCTGTTTTGAGATTTTGAGAAGTGTATTTAGTATACATTCCTAATTATTTTTTGCCCTAAATTCTTTAGAGTCTTACAGTAGCAAATCTACAGTAGTCTATAGCTATGGTTAAGAGTTTCAGCTACAGTAGCAACATAGTTCTACCTCACCAGAAATAGTATTGCTACTGTAGCGCTTCCAATTTCTAGTTTTCCTTAAATTAACCAATTCTCACTTCATTTTAACATTCTTCCCCCGAATTCTCTATGTCTCACCTCACTATCAGTCTTCCAAATTTTCACCTCAAGTACAGTACATCTGAAACTCTAACACCTCCCCATGCATTTTACTGCCTGTAGATCCCTCTTGTTTACCAACTTCTTTCATGTTCTTCCGGTCTGCCGTTTCACTTCCTTTTCTCACCTTGTCGGACCCCTAGCTCTCCATTAAAGGATTAGTACCGCCTGAGCATCCGCCCGGCTCTTCACAGTGTCGCCTCTCACCAGGGGTTATCAAACCAATATGGTCAAGAGTTGTGGGAAACTGTGTCATGACTCAAGTGCTTTTTTCCCATGCACACTTATCAAATGATTCCCACACTGATAACTCGGCACGTCTTTTGTGGTTGATAGTGATGGGAACCATTGGGATATAATTTTTTTTGGCGAAACGACACAAAAAGTGGGTTTTTAGGGTTTAAGGCAATTAAATTTCTACGAATAAGATTCTAATCTAGAAAAAGAAGGCGTGCTGTAGAAGTGAGGGGTACTGTAAATCGCCACGCTCCCTCTTCCGAATGGTTTATGACTTTTCTCTATATCTCCTTCTCTTTCTCTATATTTCTCAAATTCCGCAACATTTCTCCCTTCTTGATTTTGTTCATTTACAAATCGAGCTATAAAAATCAATAAAAACTTAATTTTTTTTCCAGAAGGTACC

3'HR: CTGCAGATGGTCCTCATCAGTACCCCACCACCAGCTTACGCTCATAACAGAAAAACTTCACAAGAGAAGAAACGACGAGATGAGATTAATGCAAAGATCAAGGAGCTTCAACTATTGATTCAAAATGAATCGGATAATGAGAAAATGACGTGAGTTTTCTATTCGTTTAGTGTTATCTTCATTCAAATCTTACTAATTTTCAGCCAAGGTGATGTCTTAAACCGTGCAGTCGAAGTGGTCAGTCGCATGGAAACCGAATCACCTGGACCATCATCAAATCCAAATCGCAAAGGATTCTTTGACGGATTCCGATCAATCGAGTCGCTCACTTATTCCTTCATCAAATCCCTGGGCGTCAATTCAGATGTCTGTCAGGATTTTGTGCAACGTGCCAAGCAGTTTTTCGATCGAGAACGTTCATCTTTGCTGAGCACTGTATCTGGAAAATCAAAGAGAAGATCTGAGTCGGAAATTCTCCACTCTTCAATGAGCTATAGATCCCAGTCAAGCTCTCCATCGACATCGGAATCTGGAATCACAATTGATAGAAAGGAAGTGAAAAAGAATAGAGAGCAAGATAGAAGAGATCGTCAGGGAGAAGCTTTTGATGCTTTGAAGAACTTTATCATTGAGAACAAGCTCATGACATCTCATCAAGTGTAAGCTTAAATTTTCCCAATACCATAAATTAAACTTTTCCTTTTTTCAGCGAAAAAATGCAACGCTTGAACACCCTGGATATCATAATTGCCTACATTCAAAACAAGAAGCACAATTTTGTTAGTCGAAGCGACCAGGAGCAGTCACTCTATGCACATGCAATTGCAGAGGGAAAGAAGACTGCAAAAAACATTGCCTTCCAATTTTTCAAGGTGAGTTGTCAGGAACTTCGAGAAGATTTTTTTAAATGTTATCAATATATTTTCAGAGCGACCGTCACCTCGTTGTCCGATGCGCAGACCTTACTAGT

KI verification primers: REF-1-NKIF: 5'-ATTAGTCAACAAGTGGGGGCTATC-3' REF-1-NKIR: 5'-AGTGAATATGATGGAGACTGTTGAGAT-3'

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Strain name: SYS499

KI background: JIM113

Strain genotype: ujIs113 (pie-1p::mCherry::H2B; nhr-2p::mCherry::his-24::let858 3'UTR; unc-119(+)) II; ref-1 (devKi138 [mNeonGreen::ref-1]) II

Expression pattern: Lineage-specific, Skin-specific, Transient-expression

Lineage expression pattern

350 stage

600 stage

3D expression pattern

4-cells

8-cells

15-cells

28-cells

~50-cells

~100-cells

~200-cells

~350-cells

~500-cells

~600-cells

600-cells

bean-stage

Inferred TF relationships

Based on expression similarity (strong, medium, weak): LSL-1, RNT-1, CEH-16, HND-1, NOB-1, NHR-12, NHR-23, GMEB-1, LIN-26, ELT-1, HAM-2, NHR-25, CEH-39, HBL-1, TBX-11, NFI-1, CEH-74


Based on ChIP-seq (directly from ModERN database, targets from L1 stage ChIP-seq data are underlined)

Targeting: no-data

Targeted by: ELT-1, CEH-83, ELT-2, HLH-1, TBX-8, UNC-55, DSC-1

Based on reannotated ChIP-seq (peaks are assigned to a target if it is located within 2 kb relative to the transcription start site; targets from L1 stage ChIP-seq data are underlined)

Targeting: no-data

Targeted by: CEH-83, ELT-2