AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene53270


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene53270.t1 MTR_3g011050 60.784 51 20 0 33 83 37 87 1.30e-13 63.9
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 53 sgRNAs with CRISPR-Local

Find 83 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CTTCCAATTTGGGAAGAAAT+TGG 0.111299 4.3:-13535007 MS.gene53270:CDS
GTGACTCTGCAATTGATTTC+TGG 0.157766 4.3:+13536135 None:intergenic
AAAGTTAGAAGAGGAGATAA+AGG 0.273945 4.3:-13535098 MS.gene53270:CDS
GACCCAATTTCTTCCCAAAT+TGG 0.274164 4.3:+13535004 None:intergenic
ATAAAGGGAAAGAAATTCTT+TGG 0.305857 4.3:-13535082 MS.gene53270:CDS
AAAGTTCCGGTTCTTGTTCA+TGG 0.322486 4.3:-13536158 MS.gene53270:CDS
AAAGATCTCAGGCTCGCTTT+TGG 0.326368 4.3:-13536046 MS.gene53270:CDS
AATGTCCTTCCATCTCTTCA+TGG 0.338522 4.3:-13534958 MS.gene53270:CDS
ACCGGAACTTTCTTATGAAT+CGG 0.380626 4.3:+13536170 None:intergenic
TTCCAATTTGGGAAGAAATT+GGG 0.398944 4.3:-13535006 MS.gene53270:CDS
CCCGATTCATAAGAAAGTTC+CGG 0.414826 4.3:-13536171 MS.gene53270:CDS
TTATTGCCACCGTCGCATAA+AGG 0.420018 4.3:-13534867 MS.gene53270:CDS
ACCTTGATCTTGCTCTTGGA+TGG 0.423990 4.3:-13535042 MS.gene53270:CDS
TAAAGAATCATTTCATCCCT+TGG 0.429286 4.3:+13534887 None:intergenic
CCGGAACTTTCTTATGAATC+GGG 0.433313 4.3:+13536171 None:intergenic
TTCTGGCCATGAACAAGAAC+CGG 0.434336 4.3:+13536152 None:intergenic
GGCTAAGTTATCTGATGAAA+AGG 0.437582 4.3:-13536024 MS.gene53270:intron
GGGTACCTTGATCTTGCTCT+TGG 0.453072 4.3:-13535046 MS.gene53270:CDS
TCTTTGGAGGGGACACTATC+GGG 0.454808 4.3:-13535066 MS.gene53270:CDS
TGATTAAGAAAGGTGATGAA+TGG 0.474122 4.3:-13535156 MS.gene53270:intron
AAAGGAGGCAAGAGAAATCA+TGG 0.475218 4.3:-13535122 MS.gene53270:CDS
TTCTTTGGAGGGGACACTAT+CGG 0.475345 4.3:-13535067 MS.gene53270:CDS
GATTAAGAAAGGTGATGAAT+GGG 0.480475 4.3:-13535155 MS.gene53270:intron
AAGTTAGAAGAGGAGATAAA+GGG 0.491500 4.3:-13535097 MS.gene53270:CDS
GAAAGGTGATGAATGGGAAA+AGG 0.495659 4.3:-13535149 MS.gene53270:CDS
TGAGATCTTTGATAAGGATC+AGG 0.498359 4.3:+13536059 None:intergenic
AGTTGGTCGTAGAGTTGAAT+GGG 0.508405 4.3:-13536273 MS.gene53270:CDS
CAGTTGGTCGTAGAGTTGAA+TGG 0.517051 4.3:-13536274 MS.gene53270:CDS
TGATCCTTATCAAAGATCTC+AGG 0.520135 4.3:-13536057 MS.gene53270:CDS
CGAGCCTGAGATCTTTGATA+AGG 0.520914 4.3:+13536053 None:intergenic
AAACACTCCTTGATGATGAT+AGG 0.524604 4.3:+13534914 None:intergenic
AATCATGGAAAAGTTAGAAG+AGG 0.531445 4.3:-13535107 MS.gene53270:CDS
AGGGAAAGAAATTCTTTGGA+GGG 0.536580 4.3:-13535078 MS.gene53270:CDS
ATTGATCTTCCATGAAGAGA+TGG 0.543546 4.3:+13534949 None:intergenic
TGAATGGGAAAAGGCTCTAA+AGG 0.545680 4.3:-13535140 MS.gene53270:CDS
TCCATCCAAGAGCAAGATCA+AGG 0.557485 4.3:+13535041 None:intergenic
TAAGGATCAGGAGGCAGCAA+TGG 0.562517 4.3:+13536071 None:intergenic
CAAGGAGTGTTTGCCACCAA+GGG 0.564625 4.3:-13534903 MS.gene53270:CDS
TGAATGGGCTCTAAAACTCA+AGG 0.568264 4.3:-13536258 MS.gene53270:CDS
TCAAGGAGTGTTTGCCACCA+AGG 0.571195 4.3:-13534904 MS.gene53270:CDS
ACTCCTTGATGATGATAGGA+TGG 0.572678 4.3:+13534918 None:intergenic
TTGAATACATTGATGAAACA+TGG 0.575829 4.3:-13536103 MS.gene53270:CDS
AAGGGAAAGAAATTCTTTGG+AGG 0.576725 4.3:-13535079 MS.gene53270:CDS
GAGCCATCCTATCATCATCA+AGG 0.581782 4.3:-13534921 MS.gene53270:CDS
AAGAATACTCCTTTATGCGA+CGG 0.595491 4.3:+13534858 None:intergenic
GGGAAAGAAATTCTTTGGAG+GGG 0.609810 4.3:-13535077 MS.gene53270:CDS
ATCTTCCATGAAGAGATGGA+AGG 0.621011 4.3:+13534953 None:intergenic
AGAATCATTTCATCCCTTGG+TGG 0.643379 4.3:+13534890 None:intergenic
GAATGGGCTCTAAAACTCAA+GGG 0.646090 4.3:-13536257 MS.gene53270:CDS
GATCTTTGATAAGGATCAGG+AGG 0.658191 4.3:+13536062 None:intergenic
ATGGGAAAAGGCTCTAAAGG+AGG 0.677413 4.3:-13535137 MS.gene53270:CDS
AATACTCCTTTATGCGACGG+TGG 0.688837 4.3:+13534861 None:intergenic
GAGTATTCTTCAACTCATCG+TGG 0.696267 4.3:-13534845 MS.gene53270:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TCAATATAAAACTATTTTAA+AGG + chr4.3:13535697-13535716 None:intergenic 10.0%
!! TAATTTACACATACAAAAAT+AGG + chr4.3:13535906-13535925 None:intergenic 15.0%
!!! AATAATTGTTTTATGAACTT+AGG - chr4.3:13535304-13535323 MS.gene53270:intron 15.0%
!! TATCTCTTGAATTTATTAGA+TGG + chr4.3:13535488-13535507 None:intergenic 20.0%
!! TATGTTGTTCAAATTTAACT+AGG - chr4.3:13535134-13535153 MS.gene53270:CDS 20.0%
!!! AAAATTATGTTTCCTTTTTG+AGG - chr4.3:13535203-13535222 MS.gene53270:intron 20.0%
! AAAATATTCTTGCCTCAAAA+AGG + chr4.3:13535218-13535237 None:intergenic 25.0%
! AAATACTACGTTTCTTTCAA+AGG - chr4.3:13535174-13535193 MS.gene53270:intron 25.0%
! ATAAAGGGAAAGAAATTCTT+TGG - chr4.3:13536030-13536049 MS.gene53270:CDS 25.0%
! ATTACTTGAGTACAATTGTT+TGG - chr4.3:13535359-13535378 MS.gene53270:intron 25.0%
! TTGAATACATTGATGAAACA+TGG - chr4.3:13535009-13535028 MS.gene53270:CDS 25.0%
!!! TTGAGGCAAGAATATTTTTT+TGG - chr4.3:13535220-13535239 MS.gene53270:intron 25.0%
!!! TTTTTTTGGTGTTAATCATC+CGG - chr4.3:13535234-13535253 MS.gene53270:intron 25.0%
AAAGTTAGAAGAGGAGATAA+AGG - chr4.3:13536014-13536033 MS.gene53270:intron 30.0%
AAGTTAGAAGAGGAGATAAA+GGG - chr4.3:13536015-13536034 MS.gene53270:intron 30.0%
AATCATGGAAAAGTTAGAAG+AGG - chr4.3:13536005-13536024 MS.gene53270:intron 30.0%
ACCGTTTCTATCAACATATT+AGG + chr4.3:13535756-13535775 None:intergenic 30.0%
ATTTAACTAGGCTTATTCTG+AGG - chr4.3:13535146-13535165 MS.gene53270:CDS 30.0%
CATGATCAATATGTGTTTAG+TGG - chr4.3:13535331-13535350 MS.gene53270:intron 30.0%
GATGTTAATTATTCCATTCC+AGG - chr4.3:13535577-13535596 MS.gene53270:intron 30.0%
GATTAAGAAAGGTGATGAAT+GGG - chr4.3:13535957-13535976 MS.gene53270:intron 30.0%
TAAAGAATCATTTCATCCCT+TGG + chr4.3:13536228-13536247 None:intergenic 30.0%
TGATTAAGAAAGGTGATGAA+TGG - chr4.3:13535956-13535975 MS.gene53270:intron 30.0%
TGTTAATCATCCGGTTAATA+GGG - chr4.3:13535243-13535262 MS.gene53270:intron 30.0%
TTCCAATTTGGGAAGAAATT+GGG - chr4.3:13536106-13536125 MS.gene53270:CDS 30.0%
! GCCTAATATGTTGATAGAAA+CGG - chr4.3:13535752-13535771 MS.gene53270:intron 30.0%
! TAAATTATTATAGCTTGCGC+TGG - chr4.3:13535919-13535938 MS.gene53270:intron 30.0%
!! AGATGGAAGGACATTTTAAT+GGG + chr4.3:13536149-13536168 None:intergenic 30.0%
!! CACTTGTTTTCTTCCAATTT+GGG - chr4.3:13536095-13536114 MS.gene53270:CDS 30.0%
!! TCACTTGTTTTCTTCCAATT+TGG - chr4.3:13536094-13536113 MS.gene53270:CDS 30.0%
!! TGGATTGCATTGATTAAGAA+AGG - chr4.3:13535946-13535965 MS.gene53270:intron 30.0%
AAGAATACTCCTTTATGCGA+CGG + chr4.3:13536257-13536276 None:intergenic 35.0%
AAGGGAAAGAAATTCTTTGG+AGG - chr4.3:13536033-13536052 MS.gene53270:CDS 35.0%
ACAATACTTGAATGTATGCC+TGG + chr4.3:13535598-13535617 None:intergenic 35.0%
ACCGGAACTTTCTTATGAAT+CGG + chr4.3:13534945-13534964 None:intergenic 35.0%
AGGGAAAGAAATTCTTTGGA+GGG - chr4.3:13536034-13536053 MS.gene53270:CDS 35.0%
ATTGATCTTCCATGAAGAGA+TGG + chr4.3:13536166-13536185 None:intergenic 35.0%
CTTCCAATTTGGGAAGAAAT+TGG - chr4.3:13536105-13536124 MS.gene53270:CDS 35.0%
GGCTAAGTTATCTGATGAAA+AGG - chr4.3:13535088-13535107 MS.gene53270:CDS 35.0%
GTGTTAATCATCCGGTTAAT+AGG - chr4.3:13535242-13535261 MS.gene53270:intron 35.0%
GTTAATCATCCGGTTAATAG+GGG - chr4.3:13535244-13535263 MS.gene53270:intron 35.0%
TGAGATCTTTGATAAGGATC+AGG + chr4.3:13535056-13535075 None:intergenic 35.0%
TGATCCTTATCAAAGATCTC+AGG - chr4.3:13535055-13535074 MS.gene53270:CDS 35.0%
! GAGATGGAAGGACATTTTAA+TGG + chr4.3:13536150-13536169 None:intergenic 35.0%
!! AAACACTCCTTGATGATGAT+AGG + chr4.3:13536201-13536220 None:intergenic 35.0%
AAAGGAGGCAAGAGAAATCA+TGG - chr4.3:13535990-13536009 MS.gene53270:intron 40.0%
AAAGTTCCGGTTCTTGTTCA+TGG - chr4.3:13534954-13534973 MS.gene53270:CDS 40.0%
AATGTCCTTCCATCTCTTCA+TGG - chr4.3:13536154-13536173 MS.gene53270:CDS 40.0%
ACTTGAATGTATGCCTGGAA+TGG + chr4.3:13535593-13535612 None:intergenic 40.0%
AGAATCATTTCATCCCTTGG+TGG + chr4.3:13536225-13536244 None:intergenic 40.0%
ATCTTCCATGAAGAGATGGA+AGG + chr4.3:13536162-13536181 None:intergenic 40.0%
CCCGATTCATAAGAAAGTTC+CGG - chr4.3:13534941-13534960 MS.gene53270:CDS 40.0%
CCGGAACTTTCTTATGAATC+GGG + chr4.3:13534944-13534963 None:intergenic 40.0%
GAAAGGTGATGAATGGGAAA+AGG - chr4.3:13535963-13535982 MS.gene53270:intron 40.0%
GACCCAATTTCTTCCCAAAT+TGG + chr4.3:13536111-13536130 None:intergenic 40.0%
GAGTATTCTTCAACTCATCG+TGG - chr4.3:13536267-13536286 MS.gene53270:CDS 40.0%
GATCTTTGATAAGGATCAGG+AGG + chr4.3:13535053-13535072 None:intergenic 40.0%
! GGGAAAGAAATTCTTTGGAG+GGG - chr4.3:13536035-13536054 MS.gene53270:CDS 40.0%
! GTGACTCTGCAATTGATTTC+TGG + chr4.3:13534980-13534999 None:intergenic 40.0%
! TGAATGGGAAAAGGCTCTAA+AGG - chr4.3:13535972-13535991 MS.gene53270:intron 40.0%
!! ACTCCTTGATGATGATAGGA+TGG + chr4.3:13536197-13536216 None:intergenic 40.0%
!! GAATGGGCTCTAAAACTCAA+GGG - chr4.3:13534855-13534874 MS.gene53270:CDS 40.0%
!! TGAATGGGCTCTAAAACTCA+AGG - chr4.3:13534854-13534873 MS.gene53270:CDS 40.0%
AATACTCCTTTATGCGACGG+TGG + chr4.3:13536254-13536273 None:intergenic 45.0%
ACCTTGATCTTGCTCTTGGA+TGG - chr4.3:13536070-13536089 MS.gene53270:CDS 45.0%
ACTCTCCTTCCCCTATTAAC+CGG + chr4.3:13535256-13535275 None:intergenic 45.0%
ATCATCCGGTTAATAGGGGA+AGG - chr4.3:13535248-13535267 MS.gene53270:intron 45.0%
CGAGCCTGAGATCTTTGATA+AGG + chr4.3:13535062-13535081 None:intergenic 45.0%
GAGCCATCCTATCATCATCA+AGG - chr4.3:13536191-13536210 MS.gene53270:CDS 45.0%
TCCATCCAAGAGCAAGATCA+AGG + chr4.3:13536074-13536093 None:intergenic 45.0%
TTATTGCCACCGTCGCATAA+AGG - chr4.3:13536245-13536264 MS.gene53270:CDS 45.0%
TTCTGGCCATGAACAAGAAC+CGG + chr4.3:13534963-13534982 None:intergenic 45.0%
! AAAGATCTCAGGCTCGCTTT+TGG - chr4.3:13535066-13535085 MS.gene53270:CDS 45.0%
! TTCTTTGGAGGGGACACTAT+CGG - chr4.3:13536045-13536064 MS.gene53270:CDS 45.0%
!! AAGATCTCAGGCTCGCTTTT+GGG - chr4.3:13535067-13535086 MS.gene53270:CDS 45.0%
!! ATGGGAAAAGGCTCTAAAGG+AGG - chr4.3:13535975-13535994 MS.gene53270:intron 45.0%
!! TTATAGCTTGCGCTGGTTCA+TGG - chr4.3:13535926-13535945 MS.gene53270:intron 45.0%
GGAAGGAGAGTTCTCTCGAA+AGG - chr4.3:13535265-13535284 MS.gene53270:intron 50.0%
GGGTACCTTGATCTTGCTCT+TGG - chr4.3:13536066-13536085 MS.gene53270:CDS 50.0%
TAAGGATCAGGAGGCAGCAA+TGG + chr4.3:13535044-13535063 None:intergenic 50.0%
! TCTTTGGAGGGGACACTATC+GGG - chr4.3:13536046-13536065 MS.gene53270:CDS 50.0%
!! CAAGGAGTGTTTGCCACCAA+GGG - chr4.3:13536209-13536228 MS.gene53270:CDS 50.0%
!! TCAAGGAGTGTTTGCCACCA+AGG - chr4.3:13536208-13536227 MS.gene53270:CDS 50.0%


Chromosome Type Strat End Strand Name
chr4.3 gene 13534841 13536293 13534841 ID=MS.gene53270
chr4.3 mRNA 13534841 13536293 13534841 ID=MS.gene53270.t1;Parent=MS.gene53270
chr4.3 exon 13536025 13536293 13536025 ID=MS.gene53270.t1.exon1;Parent=MS.gene53270.t1
chr4.3 CDS 13536025 13536293 13536025 ID=cds.MS.gene53270.t1;Parent=MS.gene53270.t1
chr4.3 exon 13534841 13535170 13534841 ID=MS.gene53270.t1.exon2;Parent=MS.gene53270.t1
chr4.3 CDS 13534841 13535170 13534841 ID=cds.MS.gene53270.t1;Parent=MS.gene53270.t1
Gene Sequence

>MS.gene53270

TTGGTCGTAGAGTTGAATGGGCTCTAAAACTCAAGGGTGTTGAGTATGATTATATAGAAGAAGATATCTTCAACAAAAGTAGTCTTCTTTTCGAATTGAACCCGATTCATAAGAAAGTTCCGGTTCTTGTTCATGGCCAGAAATCAATTGCAGAGTCACTAATTATTCTTGAATACATTGATGAAACATGGAAGCAATATCCATTGCTGCCTCCTGATCCTTATCAAAGATCTCAGGCTCGCTTTTGGGCTAAGTTATCTGATGAAAAGGTGATAGTTTATTTATTTTTTCTTTATGTTGTTCAAATTTAACTAGGCTTATTCTGAGGTTATAAAATACTACGTTTCTTTCAAAGGAAAAAAAAAATTATGTTTCCTTTTTGAGGCAAGAATATTTTTTTGGTGTTAATCATCCGGTTAATAGGGGAAGGAGAGTTCTCTCGAAAGGTAAGTAAATTCTAGTCAATAATTGTTTTATGAACTTAGGTTTTCATGATCAATATGTGTTTAGTGGAGCTCATTACTTGAGTACAATTGTTTGGTTAGAGACAAGAATATTTAATGTTACATAGAAGATATACACAAATTTTAATTTGAAGTTATATAATTCTATCAATTTTTTTAATAACATAACTTAAAAAACAGCCATCTAATAAATTCAAGAGATACTTTAATTATGAGAAAATATATTAAAAATAAAATATAAATATAGAAGATTTTAATTTTTGTATATTGTCGATGTTAATTATTCCATTCCAGGCATACATTCAAGTATTGTTACATTATTTAAAGAATATGACAAATTATATAGTTTTAAACACGATACGCAATGCAATGATATTCAATTGAATTTACCTTTAAAATAGTTTTATATTGACTATGCATACAAGTTAAACTCAATATAGAATAGTTGCCTAATATGTTGATAGAAACGGTACATTATTAAAATTGCATTGAAATGACTGTGCATGTTATTTCTTTTTTTAGTTTTGATTTGTACGAACTTTATTCGATTGAATGACATATAATTATTCAAATAATTCAATGACTTATATTTCAAAAGCCTATTTTTGTATGTGTAAATTATTATAGCTTGCGCTGGTTCATGGATTGCATTGATTAAGAAAGGTGATGAATGGGAAAAGGCTCTAAAGGAGGCAAGAGAAATCATGGAAAAGTTAGAAGAGGAGATAAAGGGAAAGAAATTCTTTGGAGGGGACACTATCGGGTACCTTGATCTTGCTCTTGGATGGATCACTTGTTTTCTTCCAATTTGGGAAGAAATTGGGTCAACGCAGATACTTGACCCATTAAAATGTCCTTCCATCTCTTCATGGAAGATCAATTTTCTGAGCCATCCTATCATCATCAAGGAGTGTTTGCCACCAAGGGATGAAATGATTCTTTATTGCCACCGTCGCATAAAGGAGTATTCTTCAACTCATCGTGGTTAA

Protein sequence

>MS.gene53270.t1

LVVELNGLUNSRVLSMIIUKKISSTKVVFFSNUTRFIRKFRFLFMARNQLQSHULFLNTLMKHGSNIHCCLLILIKDLRLAFGLSYLMKRKVMNGKRLURRQEKSWKSUKRRURERNSLEGTLSGTLILLLDGSLVFFQFGKKLGQRRYLTHUNVLPSLHGRSIFUAILSSSRSVCHQGMKUFFIATVAURSILQLIVV