AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene99291

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene99291.t1 MTR_1g048720 93.117 247 17 0 1 247 1 247 4.44e-168 464
MS.gene99291.t1 MTR_1g048720 92.713 247 17 1 1 247 1 246 1.20e-165 457
MS.gene99291.t1 MTR_1g048720 94.064 219 13 0 1 219 1 219 1.76e-150 418
MS.gene99291.t1 MTR_1g048720 93.607 219 13 1 1 219 1 218 5.94e-148 412
MS.gene99291.t1 MTR_1g048710 87.705 244 21 2 1 244 1 235 2.11e-143 401
MS.gene99291.t1 MTR_1g048750 84.862 218 25 1 1 218 1 210 2.71e-133 377
MS.gene99291.t1 MTR_7g090410 57.371 251 88 7 1 241 1 242 9.29e-65 202
MS.gene99291.t1 MTR_0007s0330 31.928 166 101 6 65 227 6 162 7.25e-12 62.4
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene99291.t1 AT3G56970 41.767 249 134 5 1 240 1 247 1.57e-55 179
MS.gene99291.t1 AT3G56980 39.560 273 115 6 1 242 1 254 1.67e-46 155
MS.gene99291.t1 AT2G41240 38.800 250 133 5 1 242 1 238 4.95e-46 154
MS.gene99291.t1 AT2G41240 38.400 250 133 6 1 242 1 237 1.48e-43 147
MS.gene99291.t1 AT5G04150 46.012 163 83 2 60 219 78 238 6.95e-37 130
MS.gene99291.t1 AT5G04150 44.262 183 94 4 60 237 78 257 2.09e-36 129

Find 38 sgRNAs with CRISPR-Local

Find 63 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TCAACTTGTTTCTGTAATTC+TGG 0.201065 1.3:+30977636 None:intergenic
TGTAACTATGCTTCTTCCTT+TGG 0.251062 1.3:+30977535 None:intergenic
CTTCTATAATTTGCATTTCC+AGG 0.265122 1.3:-30977343 MS.gene99291:intron
TTCTGAGATCTTGATATGTT+TGG 0.287728 1.3:-30977424 MS.gene99291:CDS
GTAACTATGCTTCTTCCTTT+GGG 0.307422 1.3:+30977536 None:intergenic
TGAGAAGCTCTTATCAATAA+TGG 0.319674 1.3:-30976739 MS.gene99291:CDS
CTTTCTTCATCTCAGACCTT+TGG 0.339976 1.3:-30977375 MS.gene99291:CDS
AGGACTCTTGAAATTGTTGC+TGG 0.367920 1.3:+30977669 None:intergenic
TCTTCATCTCAGACCTTTGG+AGG 0.399010 1.3:-30977372 MS.gene99291:CDS
AGTACCATTTGATCTGAAAC+AGG 0.414053 1.3:+30977908 None:intergenic
ATGAATTCTGATGATGGTTA+TGG 0.420513 1.3:+30978119 None:intergenic
TCTTCCTGTTTCAGATCAAA+TGG 0.439923 1.3:-30977912 MS.gene99291:intron
AACAATTGGATGGCCCTTTG+AGG 0.464251 1.3:-30978152 MS.gene99291:CDS
ACTTTCTCCTCAAGAAGAAA+AGG 0.466916 1.3:-30977577 MS.gene99291:CDS
TGAAGGACTAAGTAAGAGAA+AGG 0.469978 1.3:-30977616 MS.gene99291:CDS
CATATCAAGATCTCAGAAAG+TGG 0.493296 1.3:+30977429 None:intergenic
CATGCCAAGGTCACTGCTTG+TGG 0.499479 1.3:+30978015 None:intergenic
AAGAAAGATTAAGAAGCAAA+AGG 0.505181 1.3:+30977391 None:intergenic
TGTAGAATGAATTCTGATGA+TGG 0.522101 1.3:+30978113 None:intergenic
ACAAATTATTGATCTTCTTG+CGG 0.529574 1.3:+30977954 None:intergenic
TTGATATGTTTGGAAAATGA+TGG 0.537710 1.3:-30977414 MS.gene99291:CDS
CTTCATCTCAGACCTTTGGA+GGG 0.548412 1.3:-30977371 MS.gene99291:CDS
AAGAAGCATAGTTACAACTC+TGG 0.551749 1.3:-30977528 MS.gene99291:CDS
GCTCTTATCAATAATGGAGA+AGG 0.554810 1.3:-30976733 MS.gene99291:CDS
GAATTACAGAAACAAGTTGA+AGG 0.556198 1.3:-30977633 MS.gene99291:CDS
CATCCAATTGTTGAAAACAT+AGG 0.558093 1.3:+30978163 None:intergenic
TCTCAGAAAGTGGAATCTTG+TGG 0.569417 1.3:+30977439 None:intergenic
CAATCCACAAGCAGTGACCT+TGG 0.569748 1.3:-30978019 MS.gene99291:CDS
AGTGTAACATGATATCTGAA+TGG 0.570967 1.3:+30977464 None:intergenic
TTCTGCAGGTGGATAAAGCA+CGG 0.571707 1.3:-30976785 MS.gene99291:intron
CCAATTGTTGAAAACATAGG+AGG 0.582074 1.3:+30978166 None:intergenic
GTCACTGCTTGTGGATTGTG+AGG 0.591686 1.3:+30978024 None:intergenic
ATAGAAGACTCTCCCTCCAA+AGG 0.594272 1.3:+30977359 None:intergenic
CACAAGCAGTGACCTTGGCA+TGG 0.602895 1.3:-30978014 MS.gene99291:CDS
TTCTAAGCAAAGAATCCCAA+AGG 0.620328 1.3:-30977551 MS.gene99291:CDS
TTATCAATAATGGAGAAGGA+AGG 0.636620 1.3:-30976729 MS.gene99291:CDS
CAAGCTTCTTAACCATGCCA+AGG 0.655760 1.3:+30978002 None:intergenic
TCACTGCTTGTGGATTGTGA+GGG 0.698792 1.3:+30978025 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TTAAAAACATGTAAGAAATA+AGG - chr1.3:30977921-30977940 MS.gene99291:CDS 15.0%
!! TTACAAATAGTTGATTACTT+GGG - chr1.3:30977983-30978002 MS.gene99291:CDS 20.0%
!! TTTACAAATAGTTGATTACT+TGG - chr1.3:30977982-30978001 MS.gene99291:CDS 20.0%
! AAGAAAGATTAAGAAGCAAA+AGG + chr1.3:30977503-30977522 None:intergenic 25.0%
! ACAAATTATTGATCTTCTTG+CGG + chr1.3:30976940-30976959 None:intergenic 25.0%
! ACAATTAGAAACAGAAAGAA+GGG + chr1.3:30977017-30977036 None:intergenic 25.0%
! TCTAATTGTCAATAATGCTT+TGG - chr1.3:30977028-30977047 MS.gene99291:intron 25.0%
! TTGATATGTTTGGAAAATGA+TGG - chr1.3:30977477-30977496 MS.gene99291:CDS 25.0%
!! GTAATTCTGGTATGTATTTT+AGG + chr1.3:30977245-30977264 None:intergenic 25.0%
!!! TAATTTTCATGATCAAGTTG+AGG - chr1.3:30976823-30976842 MS.gene99291:intron 25.0%
AGTGTAACATGATATCTGAA+TGG + chr1.3:30977430-30977449 None:intergenic 30.0%
CATCCAATTGTTGAAAACAT+AGG + chr1.3:30976731-30976750 None:intergenic 30.0%
GAAAACACATAAGTGCTTTA+AGG + chr1.3:30978089-30978108 None:intergenic 30.0%
GACAATTAGAAACAGAAAGA+AGG + chr1.3:30977018-30977037 None:intergenic 30.0%
GATGTATAGACTCATATAAG+AGG - chr1.3:30978048-30978067 MS.gene99291:CDS 30.0%
TGAGAAGCTCTTATCAATAA+TGG - chr1.3:30978152-30978171 MS.gene99291:CDS 30.0%
TGTAGAATGAATTCTGATGA+TGG + chr1.3:30976781-30976800 None:intergenic 30.0%
! AGAATAACCTTTTCTTCTTG+AGG + chr1.3:30977324-30977343 None:intergenic 30.0%
! CTATGTTTTCAACAATTGGA+TGG - chr1.3:30976729-30976748 MS.gene99291:CDS 30.0%
! CTTCTATAATTTGCATTTCC+AGG - chr1.3:30977548-30977567 MS.gene99291:CDS 30.0%
! GAATTACAGAAACAAGTTGA+AGG - chr1.3:30977258-30977277 MS.gene99291:intron 30.0%
! TTATCAATAATGGAGAAGGA+AGG - chr1.3:30978162-30978181 MS.gene99291:CDS 30.0%
!! ATGAATTCTGATGATGGTTA+TGG + chr1.3:30976775-30976794 None:intergenic 30.0%
!! GTTTTGTAGTTTCAAGTAGT+AGG - chr1.3:30977385-30977404 MS.gene99291:CDS 30.0%
!! TCAACTTGTTTCTGTAATTC+TGG + chr1.3:30977258-30977277 None:intergenic 30.0%
!! TTCTGAGATCTTGATATGTT+TGG - chr1.3:30977467-30977486 MS.gene99291:CDS 30.0%
!!! TCTAATTGTGATGTCGTTTT+TGG - chr1.3:30977123-30977142 MS.gene99291:intron 30.0%
ACTTTCTCCTCAAGAAGAAA+AGG - chr1.3:30977314-30977333 MS.gene99291:intron 35.0%
CATATCAAGATCTCAGAAAG+TGG + chr1.3:30977465-30977484 None:intergenic 35.0%
CCAATTGTTGAAAACATAGG+AGG + chr1.3:30976728-30976747 None:intergenic 35.0%
GTAACTATGCTTCTTCCTTT+GGG + chr1.3:30977358-30977377 None:intergenic 35.0%
TCTTCCTGTTTCAGATCAAA+TGG - chr1.3:30976979-30976998 MS.gene99291:intron 35.0%
TGAAGGACTAAGTAAGAGAA+AGG - chr1.3:30977275-30977294 MS.gene99291:intron 35.0%
TGTAACTATGCTTCTTCCTT+TGG + chr1.3:30977359-30977378 None:intergenic 35.0%
TTCTAAGCAAAGAATCCCAA+AGG - chr1.3:30977340-30977359 MS.gene99291:intron 35.0%
! AAGAAGCATAGTTACAACTC+TGG - chr1.3:30977363-30977382 MS.gene99291:CDS 35.0%
! AGTACCATTTGATCTGAAAC+AGG + chr1.3:30976986-30977005 None:intergenic 35.0%
! CCTCCTATGTTTTCAACAAT+TGG - chr1.3:30976725-30976744 MS.gene99291:CDS 35.0%
! CTTGAAAACCTTGTGTTTTG+AGG - chr1.3:30977084-30977103 MS.gene99291:intron 35.0%
! GCTCTTATCAATAATGGAGA+AGG - chr1.3:30978158-30978177 MS.gene99291:CDS 35.0%
!!! TGATGATGGTTATGGCTTTT+TGG + chr1.3:30976767-30976786 None:intergenic 35.0%
ACCATACTCCTCAAAACACA+AGG + chr1.3:30977095-30977114 None:intergenic 40.0%
AGGACTCTTGAAATTGTTGC+TGG + chr1.3:30977225-30977244 None:intergenic 40.0%
CCAGGTGTGTTAATTTCACT+AGG - chr1.3:30977566-30977585 MS.gene99291:CDS 40.0%
CCTAGTGAAATTAACACACC+TGG + chr1.3:30977569-30977588 None:intergenic 40.0%
CTTTCTTCATCTCAGACCTT+TGG - chr1.3:30977516-30977535 MS.gene99291:CDS 40.0%
TCTCAGAAAGTGGAATCTTG+TGG + chr1.3:30977455-30977474 None:intergenic 40.0%
! ACTTATGTGTTTTCTGCAGG+TGG - chr1.3:30978095-30978114 MS.gene99291:CDS 40.0%
! AGCACTTATGTGTTTTCTGC+AGG - chr1.3:30978092-30978111 MS.gene99291:CDS 40.0%
!!! ACCTTGTGTTTTGAGGAGTA+TGG - chr1.3:30977091-30977110 MS.gene99291:intron 40.0%
AACAATTGGATGGCCCTTTG+AGG - chr1.3:30976739-30976758 MS.gene99291:CDS 45.0%
ATAGAAGACTCTCCCTCCAA+AGG + chr1.3:30977535-30977554 None:intergenic 45.0%
CAAGCTTCTTAACCATGCCA+AGG + chr1.3:30976892-30976911 None:intergenic 45.0%
CTTCATCTCAGACCTTTGGA+GGG - chr1.3:30977520-30977539 MS.gene99291:CDS 45.0%
TCTTCATCTCAGACCTTTGG+AGG - chr1.3:30977519-30977538 MS.gene99291:CDS 45.0%
TTCTGCAGGTGGATAAAGCA+CGG - chr1.3:30978106-30978125 MS.gene99291:CDS 45.0%
! TCACTGCTTGTGGATTGTGA+GGG + chr1.3:30976869-30976888 None:intergenic 45.0%
!!! ATGGCTTTTTGGCTCCTCAA+AGG + chr1.3:30976756-30976775 None:intergenic 45.0%
!!! TGGCTTTTTGGCTCCTCAAA+GGG + chr1.3:30976755-30976774 None:intergenic 45.0%
CAATCCACAAGCAGTGACCT+TGG - chr1.3:30976872-30976891 MS.gene99291:intron 50.0%
! GTCACTGCTTGTGGATTGTG+AGG + chr1.3:30976870-30976889 None:intergenic 50.0%
CACAAGCAGTGACCTTGGCA+TGG - chr1.3:30976877-30976896 MS.gene99291:intron 55.0%
CATGCCAAGGTCACTGCTTG+TGG + chr1.3:30976879-30976898 None:intergenic 55.0%


Chromosome Type Strat End Strand Name
chr1.3 gene 30976710 30978203 30976710 ID=MS.gene99291
chr1.3 mRNA 30976710 30978203 30976710 ID=MS.gene99291.t1;Parent=MS.gene99291
chr1.3 exon 30977913 30978203 30977913 ID=MS.gene99291.t1.exon1;Parent=MS.gene99291.t1
chr1.3 CDS 30977913 30978203 30977913 ID=cds.MS.gene99291.t1;Parent=MS.gene99291.t1
chr1.3 exon 30977344 30977706 30977344 ID=MS.gene99291.t1.exon2;Parent=MS.gene99291.t1
chr1.3 CDS 30977344 30977706 30977344 ID=cds.MS.gene99291.t1;Parent=MS.gene99291.t1
chr1.3 exon 30976710 30976799 30976710 ID=MS.gene99291.t1.exon3;Parent=MS.gene99291.t1
chr1.3 CDS 30976710 30976799 30976710 ID=cds.MS.gene99291.t1;Parent=MS.gene99291.t1
Gene Sequence

>MS.gene99291

ATGTTAGCGATATCTCCTCCTATGTTTTCAACAATTGGATGGCCCTTTGAGGAGCCAAAAAGCCATAACCATCATCAGAATTCATTCTACAAAGACACTGTTGATCAATTATTTAATTTTCATGATCAAGTTGAGGCAGAAATTAATTCAACAGATCCCTCACAATCCACAAGCAGTGACCTTGGCATGGTTAAGAAGCTTGTTCATAATGCTAGTGAACGCGATCGCCGCAAGAAGATCAATAATTTGTATTCATCACTTCGTTCACTTCTTCCTGTTTCAGATCAAATGGTACTTAATTAAACCCTTCTTTCTGTTTCTAATTGTCAATAATGCTTTGGTCATTTCTCTGTCTTTTTTTTTTTTTTTTTAATCTTGAAAACCTTGTGTTTTGAGGAGTATGGTTGCAATTGTCTAATTGTGATGTCGTTTTTGGAACTTGCATATCTCTTGTTAGAACTATTGTCTTAGTATTAATATATACATATATGTTGCAGAAGAAATTGAGCATTCCAGCAACAATTTCAAGAGTCCTAAAATACATACCAGAATTACAGAAACAAGTTGAAGGACTAAGTAAGAGAAAGGATGAGATCTTATTGAGACTTTCTCCTCAAGAAGAAAAGGTTATTCTAAGCAAAGAATCCCAAAGGAAGAAGCATAGTTACAACTCTGGTTTTGTAGTTTCAAGTAGTAGGCTCAATGATAGTGAAATTACCATTCAGATATCATGTTACACTGTCCACAAGATTCCACTTTCTGAGATCTTGATATGTTTGGAAAATGATGGCCTTTTGCTTCTTAATCTTTCTTCATCTCAGACCTTTGGAGGGAGAGTCTTCTATAATTTGCATTTCCAGGTGTGTTAATTTCACTAGGCTTGTTTACTTTTTAAATATTTTGTCATTTATTATCGAGTGAACTCTTTATTGAATATTTTTTTAAATTATAAATTATTGAGTGAACTCTTTATTGAATATTTTTTTAAATTATAAAATAAGCTTAATAACTATTTCATATATTTTTGAAAGAAAAAACTATTTTGATCATATATAATTATGATTTGTTTTTTTTGAAGCATCATACATAATTATGATGTTACTTTATTATATTTATTATAAAATTATTTTCACAAATATTAAATTTAGAAATACTCTTAGATGCATATTTAATTATTTTTTTTATCATTCAATTATTTTAAGAATATTATTTTAAAAACATGTAAGAAATAAGGAACTAAAAATATAAGAAATTATGAAAACTATATTTTATTTTACAAATAGTTGATTACTTGGGAAAAAATAAAAAAAAATAATTTAAAAGTTAACTTTTTCTCAAGATGTATAGACTCATATAAGAGGTACAACAAACATTTTCCTTAAAGCACTTATGTGTTTTCTGCAGGTGGATAAAGCACGGAGATTAGAATATCATATTCTAAATGAGAAGCTCTTATCAATAATGGAGAAGGAAGGAGAGTTTTTAAAACAATAA
Protein sequence

>MS.gene99291.t1

MLAISPPMFSTIGWPFEEPKSHNHHQNSFYKDTVDQLFNFHDQVEAEINSTDPSQSTSSDLGMVKKLVHNASERDRRKKINNLYSSLRSLLPVSDQMKKLSIPATISRVLKYIPELQKQVEGLSKRKDEILLRLSPQEEKVILSKESQRKKHSYNSGFVVSSSRLNDSEITIQISCYTVHKIPLSEILICLENDGLLLLNLSSSQTFGGRVFYNLHFQVDKARRLEYHILNEKLLSIMEKEGEFLKQ