Supplemental Table 2. Summary of 194 Computationally Predicted CArG Element-Containing Genes
Gene Symbol/Alias-Chromosome No / RefSeq / Conserved CArG/flanking seq / From TSS / Expression / Gene OntologyCytoskeletal/Contractile Targets
Vcl/vinculin -14 / NM_009502 / CCTTATAAGG / -256, prom / Muscle / Focal adhesion/cyoskeletal
Pfn1/Profilin 1 -11 / NM_011072 / GAACCTTTGACCAAATAAGGGCAAAGTTGC / 1288, intron1 / Wide / Actin-binding cytoskeletal
Tagln/SM22alpha -9 / NM_011526 / TGTCTTTCCCCAAATATGGAGCCTGTGTGG / -157, prom / Smooth muscle / Actin filament binding
Actg2/Smooth muscle gamma actin -6 / NM_009610 / CCGTCAGCTGGCCTTTTTAGGGACT / -77, prom / Smooth muscle / Contractile
Tnnc1/Cardiac-slow Troponin C -14 / NM_009393 / ACCCAGTGCCCATACAAGGCCTGGCGG / 1150, intron 1 / Sarcomeric muscle / Contractile
Acta2/Smooth muscle alpha actin -6 / NM_007392 / GTGCTGAGGTCCCTATATGGTTGTGTTAGA / -135, prom / Muscle / Contractile
Atp2a2/SERCA2* -5 / NM_009722 / TGTTGACCAAATTTGGTCACTGACCT / 1950, intron 2 / cardiac muscle / Contractile
Pcdh12/protocadherin12 -18 / NM_017378 / GCCCATATATAC NOT A CArG / exonic / vascular / Adhesion
Cfl1/Cofilin1 -19 (next to Mus81) / NM_007687 / CCTTATTAGG / -1400, prom / Wide / Actin-binding/cytoskeletal
Cfl2/Cofilin2 -12 (manual prediction) / NM_007688 / CCTTATGTGG / +600, intron 1 / Muscle / Actin-binding/cytoskeletal
Actr3/actin-related protein 3 -1 / NM_023735 / CCTTATAAGGTAGTTTTT / +630, intron1 / mesodermal.tumors / Actin-binding/cytoskeletal
Hspb7/heat shock protein 7 -4 / NM_013868 / TGGGCCTTATAAAGCG / +895, 5' UTR / Muscle / Cytoskeletal/Stress response
Cdh11/Cadherin 11 -8 / NM_009866 / GACCCTCATATGG, plus 1 other in intron 1 / +3020, intron1 / restricted mesoderm / Adhesion
Enh/enigma homologue -3 / NM_019808 / CCTTATTTGGCCAACA / +800, intron1 / Muscle (splice) / Actin filament binding/z-disk
Cnn1/Smooth muscle calponin -9 / NM_009922 / CGCCTTATAAGGCG, 3 others / +845, intron1 / SMC / Contractile
Itgb1bp2/integrin b1 binding protein 1 -X / NM_013712 / CCTTGCCCATGTTTGGAGGTG, +2 upstream / -120, prom / Muscle / Contractile
Krt2-4/Keratin complex 2, basic, 4 -15 / NM_008475 / GCATATAAGC, NOT A CArG / -33, prom / ? / Cytoskeletal
Fscn3/Fascin 3 -6 / NM_019569 / CCACATATGG, NOT CONSERVED / +2522, exonic / Testes / Actin filament binding/spermatid
Tgfb1i1/TGFb-induced transcript -7 / NM_009365 / GGGTCCCGGCTTCCATACATGGT / -1300, prom / Lung/spleen high / Adhesion
Itga5/Integrin alpha 5 -15 / NM_010577 / GAGGACTTATAAGGGCAGA, 1 more in prox / -1700, prom / wide / Adhesion
Coro1a/Coronin actin-binding 1A -7 / NM_009898 / TTACCTTAAAAGGGC / +2160, intron2 / hematopoietic / Actin-binding/cytoskeletal
Dtna/Dystrobrevin alpha -18 / NM_010087 / CTTTATATGGGGAAAATAA / +1100, intron1 / muscle, brain / Sarcolemma/cytoskeletal
Aoc3/Amine oxidase copper containing 3 -11 / NM_009675 / CCATGTAAGGTCTGTGGA / +100, 5' utr / EC/SMC / Adhesion/copper binding
Ilk/Integrin linked kinase -7 / NM_010562 / CCTTTTATGG, NOT CONSERVED / +2616, intron 2 / wide / Focal adhesion
Tln1/Talin 1 -4 / NM_011602 / CAGTCTGTTACCAAATTTGGCCTCT / +3500, intron1 / wide / Focal adhesion/cytoskeletal
Actb/Beta actin -5 / NM_007393 / CCTTTTATGG / -65, prom / wide / Cytoskeletal
Arhe/RhoE -2 / NM_028810 / GCTCCCAGGCTCCATAAAAGGGGAGGAGG / -100, prom / wide / Cytoskeletal/GTPase
Trip6/Thyroid hormone receptor interactor 6 -5 / NM_011639 / CCAAAATTGGGGAGGAAG, 1 tolerable bp mismatch / +2, 5'UTR / wide / Cytoskeleton/signaling
Capza3/Capping protein (actin filament) muscle Z-line, alpha 3 -6 / NM_007605 / TAACACCTTGAATGGG / +33, 5'UTR / wide / Actin binding/cytoskeletal
Tnnc2/Skeletal Troponin C -2 / NM_009394 / CCTTGGCTAAATTAGGTAATGGG / -161, prom / skeletal muscle / Contractile
Casq1/Calsequestrin 1 -1 / NM_009813 / CCTTTCTTAATATGGCGATGAGCTCTTAG / -300, prom / sarcomeric muscle / Contractile
Sdc4/Syndecan 4 -2 / NM_011521 / GGCCAATTAAAGGCAGCCTTGTTT` / +2600, intron1 / wide / Cytoskeletal binding
Chad/Chondroadgerin -11 / NM_007689 / CCCATTAAAGCGC / -520, prom / restricted / Adhesion
Cryab/Alpha crystallin B Chain -9 / NM_009964 / CCCTTTTTGGG / -2600, prom / skeletal muscle / Contractile/Z-disk
Fbln5/Fibulin 5 -12 / NM_011812 / GCTCTGCACTTTATAAGGTCAGAGC / +1650, intron1 / restricted / Adhesion/calcium binding
Efha1/EF hand domain 1 -14 / NM_028643 / CCTTATTTGG, 1 tolerable bp mismatch / -3320, prom / ? / Muscle Development/Motor activity
Chl1/Cell adhesion molecule -6 / NM_007697 / GCTTATTAGG, NOT CONSERVED / +3100, intron1 / ? / Axon guidance
Actn1/alpha actinin -12 (manual prediction) / NM_134156 / TCATGTCCAAAAATGGTAACATTCA / +1500, intron / Sarcomeric muscle / Cytoskeletal
Dstn/Destrin -2 (manual prediction) / NM_019771 / GCACCAAAGTAGGT / -640, prom / Wide / Cytoskeletal
Enah/Enabled homologue -1 (manual prediction) / NM_010135 / ACCAAATATGAACAAGAAG / -2941, prom / Wide / Cytoskeletal
Flna/Filamin A –X (manual prediction) / NM_207130 / TTCCTTATGAGGTCAA / -2354, prom / Wide / Cytoskeletal
Flnc/Filamin C -6 (manual prediction) / XM_284175 / CAGAAACCTAAAAAGGCACTGAGC / 992, intron / Wide / Cytoskeletal
DNA/RNA Binding Targets
Wwtr1/WW domain-containing transcription regulator 1 -3 / NM_133784 / CAGACCAAATATGGTCACAAG / -622 prom / wide/Heart-kidney / Transcription
Ring1/Ring finger protein 1 -17 / NM_009066 / GCCCACATAAGGACTGGCCACGGACTG / -848, prom / CNS-restricted / Transcription
Fos/c-fos proto-oncogene -12 / NM_010234 / CACAGGATGTCCATATTAGGACATCTGCGT / -311, prom / Wide / Transcription
HoxB5/Homeobox B5 -11 / NM_008268 / CCCCCCCCATATTTGGCCGCATACAT / -100, prom / CNS/EC / Transcription
Nrf4A1/Nurr77 -15 / NM_010444 / CCCCCCGCGCCCTTGTATGGCCAAAGCT / -104, prom / Wide / Transcription
Copeb/kruppel-like factor 6 -13 / NM_011803 / GGGTCCTTATTTGGCTGC (see upstream too) / 2146, intron 1 / Kidney / Transcription
Ldb2/LIM domain binding 2 -5 / NM_010698 / ACATACACCATACATGGTACAGCCAGAG / +205, exon1 / Wide / Transcription
Fhl1/Four and a half LIM domains -X / NM_010211 / TCTGTAACCATATATGG / +1900, intron1 / muscle-restricted / Transcription/muscle development
Fhl2/Four and a half LIM domains -1 / NM_010212 / TCCTTATATGGTCAAATGAC / -140, prom / muscle-restricted / Transcription
Elf3/E74-related factor 3 -1 / NM_007921 / CCATAGATGG, 1 intolerable bp mismatch / +2350, exonic / Wide / Transcription
Ankmy2/ankyrin repeat and MYDN domain 2 -12 / NM_146033 / CCATGGCCCAGATTTGGCAC / -2100, prom / ? / DNA binding
Arx/Aristaless-related Hox -X / NM_007492 / CCATAAATG / -3700, prom / ? / Transcription
Tcf2/Transcription factor 2 -11 / NM_009330 / ATTTGCATATCTTATATGGCCTAATGG / -25, prom / Liver-restricted / Transcription
Sox5 /SRY-box containing gene 5 -6 / NM_011444 / TCCCTTATTGGGGCGGG / -1378, prom / testes / Transcription
Etv1/Ets variant 1 -12 / NM_007960 / GTTCCATTTAAGG, 1 tolerable mismatch / -1179, prom / Wide / Transcription
Bcl6b/B-cell CLL/lymphoma 6 -11 / NM_007528 / GCTTATAAGG, NOT CONSERVED / +2800, exonic / liver, heart / Transcription
Elf5/Ets-like factor -2 / NM_010125 / TATAATTTGCCATAAAAGGAATTA, 1 more / +3400, intron1 / wide / Transcription
NFATc4/nuclear factor of activated T-cells, cytoplasmic, calcineurin-dependent 4 -14 / NM_023699 / TCCTTTTTAGGTC / +300, intron1 / wide / Transcription
Hoxd11/Homeobox D11 -2 / NM_008273 / TAGGAAACCAATTTAGGTGGGCTTAA / +950, intron1 / wide / Transcription
Polr2g/RNA pol II G -19 / NM_026329 / CCTTTAAAGG, 1 tolerable mismatch / +1200, exon2 / wide / Transcription
Nfyb/CCAAT-binding -10 / NM_010914 / AATTCCTTTAAAGGCAAAT, 1 tolerable mismatch / +950, intron1 / wide / Transcription
Rfn12/Ring finger protein 12 -X / NM_011276 / CCTTTAAAGG, NOT CONSERVED / +1740, intronic / ? / Transcription
Lef1/Lymphoid enhancer factor 1 -3 / NM_010703 / TTTTCCTTAAATGGCA / +1900, intron1 / hematopoietic / Transcription
Rec8l1/Meiotic cohesion rec8 -14 / NM_020002 / CCTTTTTTGG / +1400, exonic / ? / DNA binding/chromosome org
Klf5/Kruppel like factor 5 -14 / NM_009769 / CCTTTTTTGG, NOT CONSERVED / -2400, prom / ? / Transcription
Aip/aryl-hydrocarbon receptor-interacting protein -19 / NM_016666 / TCCCTTTTTTGGCTTCT, NOT CONSERVED / 5'UTR / ? / Transcription
Zcchc12/zinc finger, CCHC domain containing 12 –X / NM_028325 / CCTTTAATGG / +1500, exonic / ? / Transcription
D130064H19Rik -13 / NM_172593 / CCTGCCCTATAAGGGGCCG / -150, prom / restricted / Transcription
Pogz/PogoTransposable element -3 / NM_172683 / AGGTCCCTTTAAGGCGACGG / +100s, 5'UTR / wide / Transcription
Tcfap2b/Transcription factor AP2 beta -1 / NM_009334 / AATTTAGCACCATAATTGG / +3200, intronic / skin, eye, kidney / Transcription
HoxB7 -11 / NM_010460 / CCTAGAAAGG, NOT CONSERVED / +805, 5'UTR / wide / Transcription
HoxC6 -15 / NM_010465 / CCGTTTATGG, possible upstream as well / -1500, prom / wide, kidney / Transcription
Atbt1/ankyrin repeat and BTB (POZ) domain containing -6 / NM_030251 / CCTTTGATGG, NOT CONSERVED / +2100, exonic / ? / Transcription
HoxC4 -15 / NM_013553 / GCAATTAAGG, NOT CONSERVED / -2000, prom / wide / Transcription
Carf/4921511I16Rik -8 / NM_172407 / CCTAAAAAGG,1 tolerable mismatch / +2040, exon3 / ? / RNA binding
5730449L18Rik -1 / NM_025677 / AATCAGCCATAATAGGTGAGC, 1 tolerable mismatch / +3300, exon3 / ? / mRNA processing
Nol5a /Nucleolar protein 5A -2 / NM_024193 / CCTGACCTATACAGGCCTCTGCTAT / +2400, exonic / wide / Ribosome biogenesis
Eef1b2/Translation elongation factor 1 beta 2 -1 / NM_018796 / ACCTTACAAGGCCAAGAGACTGAAG / +850, intron2 / wide / Protein biosynthesis
Eif2b1/Translation initiation factor -5 / NM_145371 / CCATTTTAGG, NOT CONSERVED / +100, exon1 / ? / Protein biosynthesis
Rps11/Ribosomal protein S11 -7 / NM_013725 / CCATAAATGG, NOT CONSERVED / +1300, intronic / ? / Protein biosynthesis
Mrrf/mito ribosome recycling -2 / NM_026422 / CCATATTTGG / 2859, intron1 / ? / Protein Biosynthesis
Bat1/HLA-B associated -17 / NM_019693 / GGCCCAATTATGGCAGAGAA , 1 tolerable mismatch / +1400, exonic / Wide / ATP-dependent helicase
Xrcc1/X-ray repair cross complementing protein 1-7 / NM_009532 / GCCCTTATAAGA, NOT CONSERVED / -1173, prom / ? / DNA Repair
Fen1/LAP endonuclease -19 / NM_007999 / CTGCCATTTATGGA, 1 tolerable mismatch / -930, prom / wide / DNA repair
Apex/apurinic/apyrimidinic endonuclease 1 -14 / NM_009687 / CCAAATTTGG,1 tolerable mismatch / +3000, exonic / ? / DNA repair
Kist/kinase interacting -1 / NM_010633 / CTTTATATGG, NOT CONSERVED / +2870, intron1 / wide / Splicing
Hnrpab/CBFA/ribonucleoprotein A/B -11 / NM_010448 / TCCTCTTTTGGGA, plus exonic / -500, prom / wide / Splicing
Elavl2/HUB -4 / NM_010486 / CCTTAAATGG, NOT CONSERVED / -2200 promo / ? / Splicing
3100004P22Rik -7 / NM_133693 / CCTTTTGTGG, NOT CONSERVED / +2400, exonic / ? / Splicing
Cugbp2/CUG triplet repeat RNA BP2 -2 / NM_010160 / GCTTTTAAGG, cannot place human / 5'UTR / heart/sk muscle / Splicing
Signaling Targets
Gnb1/Guanine nucleotide binding prot -4 / NM_008142 / CTTTATGTGG, NOT A CArG / +3700, intron1 / ? / Signaling/GTPase activity
Prss25/Protease serine 25 -6 / NM_019752 / ACATATAAGG / +3200, exonic / ? / Signaling/GTPase activity
Gnao/Guanine nucleotide binding prot alpha 0-8 / NM_010308 / CCATATTTGC, NOT CONSERVED / +500, 5'utr / wide / Signaling/GTP binding
Gps2/G protein suppressor 2 -11 / NM_019726 / CCTTAAACGG, NOT CONSERVED / -3700 / ? / GTPase inhibitor/signaling
Rrad/Ras-related diabetes -8 / NM_019662 / CAAGGCCTTTTTAGG, 1 tolerable mismatch / -1540, prom / muscle / GTPase/signaling
Gtpbp3/GTP binding -8 / NM_032544 / CCATACAAGG, NOT CONSERVED / +700, UTR / wide / Signaling/GTPase activity
2610024E20Rik -18 / NM_146084 / GAGAATATAGCCAAAATTGGGCTGTTGGTG / +800, intron1 / wide / GTPase activator
Dok1/Docking protein 1 -6 / NM_010070 / CCATATTTGG / -2350, exonic / ? / Signal transduction
Adm/adrenomedullin -7 / NM_009627 / CCTTATAAGG / -730, prom / restricted mesoderm / Signaling/Hormone
Traf4/TNFR associated factor -11 / NM_009423 / CCATAAAAAG, NOT CONSERVED / +3200, intron1 / CNS / Receptor activity/apoptosis
Mrgprf/Mas-related G protein -7 / NM_145379 / ACCAAATAAGGC, see downstream one too / -1500, prom / Muscle+cerebellum / GPCR signaling
Wdr12/WD repeat domain 12 -1 / NM_021312 / CCAAAAATGG, 1 tolerable mismatch / +3200, exonic / ? / Notch signaling
Moap1/modulator of apoptosis -12 / NM_022323 / CAATATTTGG, NOT CONSERVED / +16000, exonic / ? / Apoptosis
Wnt2/Wingless-related MMTV integration site 2-6 / NM_023653 / CCAAATAAGG, NOT CONSERVED / +1400, exonic / Thalamus / Signaling
Agpt2/Angiopoietin 2 -8 / NM_007426 / TCATATAAGG / -25, prom / Vascular / Signaling/angiogenesis
Hhip/Hedgehog interacting protein -8 / NM_020259 / CCATAAAAGG, NOT CONSERVED / +3700, intron1 / ? / Signaling/Development
Ctgf/Connective tissue growth factor -10 / NM_010217 / CCTTAGAAGG / +1800, exonic / wide / Signaling/angiogenesis
Dvl2/Dishevelled 2 -11 / NM_007888 / CCTTTTAAGGAAAG, one more at -1190 / -2445, hypgene / wide / Signaling/development
Il13r/Interleukin 13 receptor -X / NM_133990 / AGACTCCTTAAAAGGCAGATG / -3000, prom / wide / Signaling
Agpt/Angiopoietin 1 -15 / NM_009640 / CCTATTAAGG NOT CONSERVED / -388, prom / EC/heart/brain / Signaling/angiogenesis
Epha4/Ephrin A4 -1 / NM_007936 / CCTTTTTAGG, NOT CONSERVED / +3100, intron1 / ? / Signaling/ATP binding
Pdgfra/PDGF receptor a -5 / NM_011058 / CCATTAAAGG, NOT CONSERVED / -600, prom / wide / Signaling
Hrh1/Histamine receptor 1 -6 / NM_008285 / CCATTAATGG, NOT CONSERVED / -2500, prom / ? / Signaling
Dusp6/Dual specificity phosphatase 6 -10 / NM_026268 / GGCCTTGTATGGCTGTTTCCT / +3400, 3'UTR / wide / Signaling
Acvr1b/Activin A receptor -15 / NM_007395 / CTCCCCTTTAAGGCGGGCGC / -200, prom / wide / Signaling/ATP binding
Igf2/Insulin-like growth factor 2 -7 / NM_010514 / TCCCCCAAATTTGGGCATTGT / +750, 5'UTR / wide / Signaling/cell proliferation
Il17rb/Interleukin 17 receptor b -14 / NM_019583 / TGCCTAATTTGG / +1850, intron1 / wide / Signaling/receptor activity
Ppp6c/Protein phosphatase 6 -2 / NM_024209 / CCTAAAATGG, 1 tolerable mismatch / +80, 5'UTR / ? / Signaling/phosphatase
sh3bp5/SH3-binding protein 5 -14 / NM_011894 / CCAATTATGG, NOT CONSERVED / +1116, intronic / ? / Signaling
Stambp/Stam-binding protein -6 / NM_024239 / CCCAAAAAGG, NOT CONSERVED / +2151, intron / ? / Signaling/apoptosis
Pdzk11/PDZ domain containing 11 -X / NM_028303 / CCATTTCAGG, NOT CONSERVED / +500,exonic / ? / Signaling
Fgf10/Fibroblast GF 10 -13 / NM_008002 / GTCACCTTTAAAGGGGA / +2000, intron1 / wide / Signaling
Apbb3/Amyloid beta precursor -18 / NM_146085 / CCATACATGG, NOT CONSERVED / -2900, exon / ? / Signaling/apoptosis
Ptpla/protein tyrosine phosphatase-like (proline instead of catalytic arginine), member a -2 / NM_013935 / GGCATTGCCTAATACGGTGCACGG / +700, intron1 / sarcomeric muscle / Signaling/phosphatase
Gpc4/Glypican 4 -X / NM_008150 / TCCGAACCATTCATGGAAGTG / +1700, intron1 / kidney, brain / Signaling/development
Dm15/Dystrophia myotonica kinase -7 / NM_032418 / GCTGCCTTAAAAGGGCTCAA, 1 just upstream / +1400, intron1 / muscle, CNS / Signaling/ATP Binding
Metabolism Targets
Mut/methylmalonyl-CoA mutase -17 / NM_008650 / CCTTATATGG / 2533, exon / Wide / Metabolism
Cyp39a1/Cytochrome P450 39a1 -17 / NM_018887 / CCCTATAAGG, 1 bp mismatch / -3231, prom / Liver-restricted / Metabolism
Car3/Carbonic Anhydrase 3 -3 / NM_007606 / CGCTGACCTAATAAGGYCATGC / -60, prom / Skel muscle / Metabolism, muscle
Atp6v1F/ATPase -6 / NM_025381 / GCAAATATGG, 1 bp mismatch / 3830, intergenic / ? / Metabolism/ATP Biosynthesis
Hsd11b1/hydroxysteroid dehydrogenase -1 / NM_008288 / GCTTATATGG, NOT CONSERVED / -590, prom / restricted / Metabolism
Hibadh/3-hydroxyisobutyrate dehydrogenase -6 / NM_145567 / CCTTTTAAGG, NOT CONSERVED / -1594, prom / ? / Metabolism