Welcome to Benchling!

You're looking at a DNA Sequence. Here are some things you can do with it:

Create an alignment

  1. Create alignments with both DNA and AA sequences.
  2. Bulk-align multiple sequences at once.
  3. Powerful visualization tool to inspect alignments in detail.

Design a primer

Create a translation

Design a CRISPR guide

Assemble and transform a sequence

Benchling is actively tested against the latest versions of Chrome, Firefox, Safari, and Edge. **It doesn't look like your current browser is supported** - for more information, [click here](/browsers).
Monospace normal
Monospace bold
working...
Advanced Settings
pGRN_H-pU6:pPIN1_gRNA_Target1-tU6
  • Sequence Map
Editing disabled on read-only sequence.
ctaatcggagtacgtgaaatcgctaataaggtcacgtgaaatcgctaatcaaaaaggcacgtgagaacgctaatagccctttcagatcaacagcttgcaaacacccctcgctccggcaagtagttacagcaagtagtatgttcaattagcttttcaattatgaatatatatatcagattagcctcatgcactttagcgattattccagtgcactttagcgattagtttttccgtgcactcttgcgattatcgggaaagtctagttgtcgaacgtttgtggggagcgaggccgttcatcaatgtcgttcatcatacaagttaatcgaaaagttaatacttatatatatagt20406080100120140160
attattggtcgcccttggcttgtggacaatgcgctacgcgcaccggctccgcccgtggacaaccgcaagcggttgcccaccgtcgagcgccagcgcctttgcccacaacccggcggccggccgcaacagatcgttttataaatttttttttttgaaaaagaaaaagcccgaaaggtaataaccagcgggaaccgaacacctgttacgcgatgcgcgtggccgaggcgggcacctgttggcgttcgccaacgggtggcagctcgcggtcgcggaaacgggtgttgggccgccggccggcgttgtctagcaaaatatttaaaaaaaaaaactttttctttttcgggctttccBglIFseINaeIPsiIStyINgoMIV180200220240260280300320340
cggcaacctctcgggcttctggatttccgatccccggaattagaagatcttggcaggatatattgtggtgtaacgttatcgatctggattttagtactggattttggttttaggaattagaaattttattgatagaagtattttacaaatacaaatacatactaagggtttcttagccgttggagagcccgaagacctaaaggctaggggccttaatcttctagaaccgtcctatataacaccacattgcaatagctagacctaaaatcatgacctaaaaccaaaatccttaatctttaaaataactatcttcataaaatgtttatgtttatgtatgattcccaaagaatAclIAvaIClaIScaIBsoBIBspDILB360380400420440460480500520
tatgctcaacacatgagcgaaaccctataagaaccctaatttcccttatcgggaaactactcacacattatttatggagaaaatagagagagatagatttgtagagagagactggtgatttcagcgtaccgaattaattctcccgcgaccagccgagcgagcttagcgaactgtgatacgagttgtgtactcgctttgggatattcttgggattaaagggaatagccctttgatgagtgtgtaataaatacctcttttatctctctctatctaaacatctctctctgaccactaaagtcgcatggcttaattaagagggcgctggtcggctcgctcgaatcgcttgacacBcgIBlpIXmnI540560580600620640660680700
gacgagaactgtgccaccaagcgtaaggccgttctctcgcatttgccttgctaggctcgcgcgagttgctggctgaggcgttctcgaaatcagctcttgttcggtcggcatctactctattcctttgccctcggacgagtgctggggcgtcggtttccactatcggcgagtacttctgctcttgacacggtggttcgcattccggcaagagagcgtaaacggaacgatccgagcgcgctcaacgaccgactccgcaagagctttagtcgagaacaagccagccgtagatgagataaggaaacgggagcctgctcacgaccccgcagccaaaggtgatagccgctcatgaaBplIBplIScaIBbvCIBsaHIBpu10INmeAIIIHgR720740760780800820840860
ctacacagccatcggtccagacggccgcgcttctgcgggcgatttgtgtacgcccgacagtcccggctccggatcggacgattgcgtcgcatcgaccctgcgcccaagctgcatcatcgaaattgccgtcaaccaagctctgatagagttggtcaagaccaatgcggagcatatagatgtgtcggtagccaggtctgccggcgcgaagacgcccgctaaacacatgcgggctgtcagggccgaggcctagcctgctaacgcagcgtagctgggacgcgggttcgacgtagtagctttaacggcagttggttcgagactatctcaaccagttctggttacgcctcgtatatHincIIHgR8809009209409609801,0001,0201,040
cgcccggaggcgtggcgatcctgcaagctccggatgcctccgctcgaagtagcgcgtctgctgctccatacaagccaaccacggcctccagaagaagatgttggcgacctcgtattgggaatccccgaacatcgcctcgctccagtcaatgaccgctgttatgcggccattgtccgcgggcctccgcaccgctaggacgttcgaggcctacggaggcgagcttcatcgcgcagacgacgaggtatgttcggttggtgccggaggtcttcttctacaaccgctggagcataacccttaggggcttgtagcggagcgaggtcagttactggcgacaatacgccggtaacaggBtgZIHgR1,0601,0801,1001,1201,1401,1601,1801,2001,220
gtcaggacattgttggagccgaaatccgcgtgcacgaggtgccggacttcggggcagtcctcggcccaaagcatcagctcatcgagagcctgcgcgacggacgcactgacggtgtcgtccatcacagtttgccagtgatacacatggggatcagcaatcgcgcatatgaaatcaccagtcctgtaacaacctcggctttaggcgcacgtgctccacggcctgaagccccgtcaggagccgggtttcgtagtcgagtagctctcggacgcgctgcctgcgtgactgccacagcaggtagtgtcaaacggtcactatgtgtacccctagtcgttagcgcgtatactttagtgNdeIPflFIBstAPINmeAIIITth111IHgR1,2401,2601,2801,3001,3201,3401,3601,3801,400
gccatgtagtgtattgaccgattccttgcggtccgaatgggccgaacccgctcgtctggctaagatcggccgcagcgatcgcatccatagcctccgcgaccggctgaagaacagcgggcagttcggtttcaggcaggtcttgcaacgtgacaccctgtgcacggcgggagatgcacggtacatcacataactggctaaggaacgccaggcttacccggcttgggcgagcagaccgattctagccggcgtcgctagcgtaggtatcggaggcgctggccgacttcttgtcgcccgtcaagccaaagtccgtccagaacgttgcactgtgggacacgtgccgccctctacgtAcuIAsiSIBfuAIBspMIRsrIIBstAPIHgR1,4201,4401,4601,4801,5001,5201,5401,560
ataggtcaggctctcgctgaactccccaatgtcaagcacttccggaatcgggagcgcggccgatgcaaagtgccgataaacataacgatctttgtagaaaccatcggcgcagctatttacccgcaggacatatccacgccctcctacatcgaagctgaaagcacgagattcttcgtatccagtccgagagcgacttgaggggttacagttcgtgaaggccttagccctcgcgccggctacgtttcacggctatttgtattgctagaaacatctttggtagccgcgtcgataaatgggcgtcctgtataggtgcgggaggatgtagcttcgactttcgtgctctaagaagcHgR1,5801,6001,6201,6401,6601,6801,7001,7201,740
ccctccgagagctgcatcaggtcggagacgctgtcgaacttttcgatcagaaacttctcgacagacgtcgcggtgagttcaggctttttcatagggatcagcttgggctgtcctctccaaatgaaatgaacttccttatatagaggaagggtcttgcgaaggatagtgggattgtgggaggctctcgacgtagtccagcctctgcgacagcttgaaaagctagtctttgaagagctgtctgcagcgccactcaagtccgaaaaagtatccctagtcgaacccgacaggagaggtttactttacttgaaggaatatatctccttcccagaacgcttcctatcaccctaacaZraIAatIIBsaHIBsmBIEsp3IPflFIPshAITth111IHgR35S1,7601,7801,8001,8201,8401,8601,8801,9001,920
gcgtcatcccttacgtcagtggagatgtcacatcaatccacttgctttgaagacgtggttggaacgtcttctttttccacgatgctcctcgtgggtgggggtccatctttgggaccactgtcggcagaggcatcttgaatgatagcctttcctttatcgcaatgatggcatttgtcgcagtagggaatgcagtcacctctacagtgtagttaggtgaacgaaacttctgcaccaaccttgcagaagaaaaaggtgctacgaggagcacccacccccaggtagaaaccctggtgacagccgtctccgtagaacttactatcggaaaggaaatagcgttactaccgtaaacaXmnIBmgBIBseRICspCIPshAI1,9401,9601,9802,0002,0202,0402,0602,0802,100
aggagccaccttccttttctactgtcctttcgatgaagtgacagatagctgggcaatggaatccgaggaggtttcccgaaattaccctttgttgaaaagtctcaatagccctttggtcttctgagactgtatctttgacatttttggagtaggggtacgataacattaacgtttatcctcggtggaaggaaaagatgacaggaaagctacttcactgtctatcgacccgttaccttaggctcctccaaagggctttaatgggaaacaacttttcagagttatcgggaaaccagaagactctgacatagaaactgtaaaaacctcatccccatgctattgtaattgcaaatAclIBseRI2,1202,1402,1602,1802,2002,2202,2402,260
caatttcgcgccattcgccattcaggctgcgcaactgttgggaagggcgatcggtgcgggcctcttcgctattacgccagctggcgaaagggggatgtgctgcaaggcgattaagttgggtaacgccagggttttcccagtcacgacgttgtaaaacgacggccagtgaattgtagttaaagcgcggtaagcggtaagtccgacgcgttgacaacccttcccgctagccacgcccggagaagcgataatgcggtcgaccgctttccccctacacgacgttccgctaattcaacccattgcggtcccaaaagggtcagtgctgcaacattttgctgccggtcacttaacatBglIBmrIFspIPvuIIM13F2,2802,3002,3202,3402,3602,3802,4002,4202,440
atacgactcactatagggcgaattgggtaccGGTCTCAccctTCGACGTAAAGCCTGTAGAAGAGGTTTCTAGCGAACGACACGAGTTTGAGCCTCATGAAGCTTCGTTGAACAACGGAAACTCGACTTGCCTTCCGCACAATACATCATTTCTTCTTAGCTTTTTTTCTTCTTCtatgctgagtgatatcccgcttaacccatggCCAGAGTgggaAGCTGCATTTCGGACATCTTCTCCAAAGATCGCTTGCTGTGCTCAAACTCGGAGTACTTCGAAGCAACTTGTTGCCTTTGAGCTGAACGGAAGGCGTGTTATGTAGTAAAGAAGAATCGAAAAAAAGAAGAAGAgeIBsaIKpnIAcc65IHindIIIUBQ6 promoter paperj5_0363_... AnnealPr...r2,4602,4802,5002,5202,5402,5602,5802,6002,620
TTCGTTCATACAGTTTTTTTTTGTTTATCAGCTTACATTTTCTTGAACCGTAGCTTTCGTTTTCTTCTTTTTAACTTTCCATTCGGAGTTTTTGTATCTTGTTTCATAGTTTGTCCCAGGATTAGAATGATTAGGCATCGAACCTTCAAGAATTTGATTGAATAAAACATCTTCAAAGCAAGTATGTCAAAAAAAAACAAATAGTCGAATGTAAAAGAACTTGGCATCGAAAGCAAAAGAAGAAAAATTGAAAGGTAAGCCTCAAAAACATAGAACAAAGTATCAAACAGGGTCCTAATCTTACTAATCCGTAGCTTGGAAGTTCTTAAACTAACTTATTTTGTAGAAGTUBQ6 promoter paper2,6402,6602,6802,7002,7202,7402,7602,7802,800
TTCTTAAGATATGAAGATAATCTTCAAAAGGCCCCTGGGAATCTGAAAGAAGAGAAGCAGGCCCATTTATATGGGAAAGAACAATAGTATTTCTTATATAGGCCCATTTAAGTTGAAAACAATCTTCAAAAGTCCCACATCGCTTAGATAAGAAAACGAAGCTGAGTTTATATACAAGAATTCTATACTTCTATTAGAAGTTTTCCGGGGACCCTTAGACTTTCTTCTCTTCGTCCGGGTAAATATACCCTTTCTTGTTATCATAAAGAATATATCCGGGTAAATTCAACTTTTGTTAGAAGTTTTCAGGGTGTAGCGAATCTATTCTTTTGCTTCGACTCAAATATATGMslIPasIAflIIBstXIBtgZIEcoO109IUBQ6 promoter paper2,8202,8402,8602,8802,9002,9202,9402,960
AGCTAGAGTCGAAGTAGTGATTCATCACACACACTATTATGTgttttagagctagaaatagcaagttaaaataaggctagtccgttatcaacttgaaaaagtggcaccgagtcggtgcttttTTTGCAAAATTTTCCAGATCGATTTCTTCTTCCTCTGTTCTTCGGCGTTCAATTCGATCTCAGCTTCATCACTAAGTAGTGTGTGTGATAATACAcaaaatctcgatctttatcgttcaattttattccgatcaggcaatagttgaactttttcaccgtggctcagccacgaaaaAAACGTTTTAAAAGGTCTAGCTAAAGAAGAAGGAGACAAGAAGCCGCAAGTTAClaIMslIBspDIgRNA HandleUBQ6 terminator paperUBQ6 pro...r paperpPIN1_Target1 2,9803,0003,0203,0403,0603,0803,1003,1203,140
TTCTGGGTTTTTCTCTTCGTTTTCTGTAACTGAAACCTAAAATTTGACCTAAAAAAAATCTCAAATAATATGATTCAGTGGTTTTGTACTTTTCAGTTAGTTGAGTTTTGCAGTTCCGATGAGATAAACCAATAACTTTGCTTAGATCTAATTCATTCCGTTACACCTCTGATGGAAGACCCAAAAAGAGAAGCAAAAGACATTGACTTTGGATTTTAAACTGGATTTTTTTTAGAGTTTATTATACTAAGTCACCAAAACATGAAAAGTCAATCAACTCAAAACGTCAAGGCTACTCTATTTGGTTATTGAAACGAATCTAGATTAAGTAAGGCAATGTGGAGACTACCUBQ6 terminator paper3,1603,1803,2003,2203,2403,2603,2803,3003,320
AGATGGAAGGTTCTTAATAATGATGCCATTTTTTGGGTAATAATTTTGAATTAGAATCAAGGGTATAAGATTCATAATTAACATCACTTAAGCAAAGTTCGTAATATACGACCACAGGATATAATTTTTGGTACgagaTGAGACCgagctccagcttttgttccctttagtgaggTCTACCTTCCAAGAATTATTACTACGGTAAAAAACCCATTATTAAAACTTAATCTTAGTTCCCATATTCTAAGTATTAATTGTAGTGAATTCGTTTCAAGCATTATATGCTGGTGTCCTATATTAAAAACCATGctctACTCTGGctcgaggtcgaaaacaagggaaatcactccBsaISacIAflIIBanIIPflMIEco53kIUBQ6 terminator paperj5_0362...AnnealPo...r3,3403,3603,3803,4003,4203,4403,4603,4803,500
gttaattccgagcttggcgtaatcatggtcatagctgtttcctgtgtgaaattgttatccgctcacaattccacacaacatacgagccggaagdcataaagtgtaaagcctggggtgcctaatgagtgagctaactcacattaattgcgttgcgctcactgcccgctttccagtccaattaaggctcgaaccgcattagtaccagtatcgacaaaggacacactttaacaataggcgagtgttaaggtgtgttgtatgctcggccttchgtatttcacatttcggaccccacggattactcactcgattgagtgtaattaacgcaacgcgagtgacgggcgaaaggtcagM13R3,5203,5403,5603,5803,6003,6203,6403,660
gggaaacctgtcgtgccagctgcattaatgaatcggccaacgcgcggggagaggcggtttgcgtattgggcgctcttccgcttcctcgctcactgactcgctgcgctcggtcgttcggctgcggcgagcggtatcagctcactcaaaggcggtaatacggttatccacagaatcaccctttggacagcacggtcgacgtaattacttagccggttgcgcgcccctctccgccaaacgcataacccgcgagaaggcgaaggagcgagtgactgagcgacgcgagccagcaagccgacgccgctcgccatagtcgagtgagtttccgccattatgccaataggtgtcttagtSapIBspQIPvuII3,6803,7003,7203,7403,7603,7803,8003,8203,840
ggggataacgcaggaaagaacatgaaggccttgacaggatatattggcgggtaaactaagtcgctgtatgtgtttgtttgagatctgatctcatgtgagcaaaaggccagcaaaaggccaggaaccgtaaaaaggccgcgttgctggcgtttttccataggctccgcccccctgacccctattgcgtcctttcttgtacttccggaactgtcctatataaccgcccatttgattcagcgacatacacaaacaaactctagactagagtacactcgttttccggtcgttttccggtccttggcatttttccggcgcaacgaccgcaaaaaggtatccgaggcggggggactStuIRB3,8603,8803,9003,9203,9403,9603,9804,0004,020
cgagcatcacaaaaatcgacgctcaagtcagaggtggcgaaacccgacaggactataaagataccaggcgtttccccctggaagctccctcgtgcgctctcctgttccgaccctgccgcttaccggatacctgtccgcctttctcccttcgggaagcgtggcgctttctcatagcgctcgtagtgtttttagctgcgagttcagtctccaccgctttgggctgtcctgatatttctatggtccgcaaagggggaccttcgagggagcacgcgagaggacaaggctgggacggcgaatggcctatggacaggcggaaagagggaagcccttcgcaccgcgaaagagtatcgBciVI4,0404,0604,0804,1004,1204,1404,1604,1804,200
tcacgctgtaggtatctcagttcggtgtaggtcgttcgctccaagctgggctgtgtgcacgaaccccccgttcagcccgaccgctgcgccttatccggtaactatcgtcttgagtccaacccggtaagacacgacttatcgccactggcagcagccactggtaacaggattagcaagtgcgacatccatagagtcaagccacatccagcaagcgaggttcgacccgacacacgtgcttggggggcaagtcgggctggcgacgcggaataggccattgatagcagaactcaggttgggccattctgtgctgaatagcggtgaccgtcgtcggtgaccattgtcctaatcgtAlwNI4,2204,2404,2604,2804,3004,3204,3404,360
gagcgaggtatgtaggcggtgctacagagttcttgaagtggtggcctaactacggctacactagaagaacagtatttggtatctgcgctctgctgaagccagttaccttcggaagaagagttggtagctcttgatccggcaaacaaaccaccgctggtagcggtggtttttttgtctcgctccatacatccgccacgatgtctcaagaacttcaccaccggattgatgccgatgtgatcttcttgtcataaaccatagacgcgagacgacttcggtcaatggaagccttcttctcaaccatcgagaactaggccgtttgtttggtggcgaccatcgccaccaaaaaaacaAcuI4,3804,4004,4204,4404,4604,4804,5004,5204,540
ttgcaagcagcagattacgcgcagaaaaaaaggatctcaagaagatcctttgatcttttctacggggtctgacgctcagtggaacgaaaactcacgttaagggattttggtcatgagattatcaaaaaggatcttcacctagatccttttaaattaaaaatgaagttttaaatcaaacgttcgtcgtctaatgcgcgtctttttttcctagagttcttctaggaaactagaaaagatgccccagactgcgagtcaccttgcttttgagtgcaattccctaaaaccagtactctaatagtttttcctagaagtggatctaggaaaatttaatttttacttcaaaatttagtDraIDraI4,5604,5804,6004,6204,6404,6604,6804,7004,720
atctaaagtatatatgtgtaacattggtctagtgattagaaaaactcatcgagcatcaaatgaaactgcaatttattcatatcaggattatcaataccatatttttgaaaaagccgtttctgtaatgaaggagaaaactcaccgaggcagttccataggatggcaagatcctggttagatttcatatatacacattgtaaccagatcactaatctttttgagtagctcgtagtttactttgacgttaaataagtatagtcctaatagttatggtataaaaactttttcggcaaagacattacttcctcttttgagtggctccgtcaaggtatcctaccgttctaggaccaPflMI4,7404,7604,7804,8004,8204,8404,8604,8804,900
atcggtctgcgattccgactcgtccaacatcaatacaacctattaatttcccctcgtcaaaaataaggttatcaagtgagaaatcaccatgagtgacgactgaatccggtgagaatggcaaaagtttatgcatttctttccagacttgttcaacaggccagccattacgctcgtctagccagacgctaaggctgagcaggttgtagttatgttggataattaaaggggagcagtttttattccaatagttcactctttagtggtactcactgctgacttaggccactcttaccgttttcaaatacgtaaagaaaggtctgaacaagttgtccggtcggtaatgcgagcagNsiI4,9204,9404,9604,9805,0005,0205,0405,060
atcaaaatcactcgcatcaaccaaaccgttattcattcgtgattgcgcctgagcgagacgaaatacgcgatcgctgttaaaaggacaattacaaacaggaatcgaatgcaaccggcgcaggaacactgccagcgcatcaacaatattttcacctgaatcaggatattcttctaattagttttagtgagcgtagttggtttggcaataagtaagcactaacgcggactcgctctgctttatgcgctagcgacaattttcctgttaatgtttgtccttagcttacgttggccgcgtccttgtgacggtcgcgtagttgttataaaagtggacttagtcctataagaagattaBsmISspIAsiSIBsmBIEcoNIEsp3IBpu10Isplit KAN F5,0805,1005,1205,1405,1605,1805,2005,2205,240
acctggaatgctgttttccctgggatcgcagtggtgagtaaccatgcatcatcaggagtacggataaaatgcttgatggtcggaagaggcataaattccgtcagccagtttagtctgaccatctcatctgtaacaacattggcaacgctacctttgccatgtttcagaaacaacttggaccttacgacaaaagggaccctagcgtcaccactcattggtacgtagtagtcctcatgcctattttacgaactaccagccttctccgtatttaaggcagtcggtcaaatcagactggtagagtagacattgttgtaaccgttgcgatggaaacggtacaaagtctttgttgaBsmINsiIPasI5,2605,2805,3005,3205,3405,3605,3805,4005,420
ctggcgcatcgggcttcccatacaatcggtagattgtcgcacctgattgcccgacattatcgcgagcccatttatacccatataaatcagcatccatgttggaatttaatcgcggccttgagcaagacgtttcccgttgaatatggctcataacaccccttgtattactgtttatgaccgcgtagcccgaagggtatgttagccatctaacagcgtggactaacgggctgtaatagcgctcgggtaaatatgggtatatttagtcgtaggtacaaccttaaattagcgccggaactcgttctgcaaagggcaacttataccgagtattgtggggaacataatgacaaataNruIBanII5,4405,4605,4805,5005,5205,5405,5605,5805,600
gtaagcagacagttttattgttcatgatgatatatttttatcttgtgcaatgtaacatcagagattttgagacacaacgtggctttgttgaataaatcgaacttttgctgagttgaaggatcagatcacgcatcttcccgacaacgcagaccgttccgtggcaaagcaaaagttccattcgtctgtcaaaataacaagtactactatataaaaatagaacacgttacattgtagtctctaaaactctgtgttgcaccgaaacaacttatttagcttgaaaacgactcaacttcctagtctagtgcgtagaagggctgttgcgtctggcaaggcaccgtttcgttttcaag5,6205,6405,6605,6805,7005,7205,7405,760
aaaatcaccaactggtccacctacaacaaagctctcatcaaccgtggctccctcactttctggctggatgatggggcgattcaggcgatccccatccaacagcccgccgtcgagcgggcttttttatccccggaagcctgtggatagagggtagttatccacgtgaaaccgctaattttagtggttgaccaggtggatgttgtttcgagagtagttggcaccgagggagtgaaagaccgacctactaccccgctaagtccgctaggggtaggttgtcgggcggcagctcgcccgaaaaaataggggccttcggacacctatctcccatcaataggtgcactttggcgattBsaBI5,7805,8005,8205,8405,8605,8805,9005,9205,940
tgccccgcaaagccttgattcacggggctttccggcccgctccaaaaactatccacgtgaaatcgctaatcagggtacgtgaaatcgacggggcgtttcggaactaagtgccccgaaaggccgggcgaggtttttgataggtgcactttagcgattagtcccatgcactttagc5,9605,9806,0006,020
  • Plasmid
Editing disabled on read-only sequence.
6037 bp45005000550050010001500HgRpUBQ6-pPIN1_Target1-r (DNA)pPIN1_Target1-f (DNA)pPIN1_Target1-gRNA_Handle-f (DNA)

Welcome to Benchling!

Sign in to view data.

New digest

Saved digests

Enzyme AatII
Enzyme lists
Cut sites visible on maps
Find enzyme
Name Cuts
Selected Color
Show enzymes that cut

Primers

History

Lineage

 Show Full History
Change User Timestamp

Sequence Alignments

Saved Alignments

Sequence Info

Tags

Name
Parent Version
Folder
Topology
Start Index
Locked
Created
--
Length
--
Export Data
Split Workspace
Bases
6037