AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene80405

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene80405.t1 MTR_1g115415 97.260 146 4 0 1 146 356 501 2.58e-99 294
MS.gene80405.t1 MTR_8g105560 74.306 144 15 1 1 144 303 424 7.46e-66 209
MS.gene80405.t1 MTR_8g105560 83.621 116 17 1 31 146 421 534 5.69e-51 170
MS.gene80405.t1 MTR_5g068860 47.826 115 58 1 1 113 388 502 3.47e-32 119
MS.gene80405.t1 MTR_5g041630 39.806 103 57 2 4 101 200 302 2.14e-14 68.9
MS.gene80405.t1 MTR_2g067230 32.500 120 78 2 4 120 207 326 7.84e-14 67.4
MS.gene80405.t1 MTR_6g003960 35.354 99 63 1 4 101 495 593 1.08e-13 67.4
MS.gene80405.t1 MTR_2g034600 39.806 103 57 3 1 100 448 548 6.22e-13 65.1
MS.gene80405.t1 MTR_4g070060 30.612 98 68 0 4 101 494 591 6.39e-13 65.1
MS.gene80405.t1 MTR_2g034600 39.806 103 57 3 1 100 452 552 6.99e-13 65.1
MS.gene80405.t1 MTR_2g034600 39.806 103 57 3 1 100 387 487 7.37e-13 65.1
MS.gene80405.t1 MTR_2g049780 37.805 82 50 1 20 100 228 309 7.20e-12 61.6
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene80405.t1 AT2G44020 70.748 147 42 1 1 146 361 507 2.51e-66 209
MS.gene80405.t1 AT4G02990 45.872 109 59 0 1 109 396 504 1.04e-26 104
MS.gene80405.t1 AT4G02990 45.872 109 59 0 1 109 396 504 1.04e-26 104
MS.gene80405.t1 AT1G78930 33.333 99 65 1 4 101 482 580 1.23e-14 70.1
MS.gene80405.t1 AT2G21710 30.928 97 67 0 4 100 501 597 8.37e-14 67.8
MS.gene80405.t1 AT2G03050 40.217 92 54 1 9 99 182 273 2.50e-12 62.8
MS.gene80405.t1 AT2G03050 40.217 92 54 1 9 99 181 272 2.51e-12 62.8
MS.gene80405.t1 AT2G34620 35.632 87 55 1 16 101 210 296 1.26e-11 61.2
MS.gene80405.t1 AT2G36000 35.227 88 56 1 17 103 228 315 1.31e-11 61.2
MS.gene80405.t1 AT2G36000 46.429 56 30 0 45 100 257 312 3.31e-11 60.1

Find 36 sgRNAs with CRISPR-Local

Find 40 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AGAATACTTCACCTATAGTT+TGG 0.284806 6.3:+28824803 MS.gene80405:CDS
AAACTATAGGTGAAGTATTC+TGG 0.305579 6.3:-28824801 None:intergenic
TCACCTATAGTTTGGAATCT+AGG 0.308236 6.3:+28824811 MS.gene80405:CDS
CTCTTAAGCCTCTGGTATCT+AGG 0.309752 6.3:-28824840 None:intergenic
GGATAAAGTGTTCATTGAAT+TGG 0.316271 6.3:+28824868 MS.gene80405:CDS
ATCTGAAACTATATCATTCC+CGG 0.367449 6.3:-28824997 None:intergenic
TCCCCTTGCTCTTAAGCCTC+TGG 0.375995 6.3:-28824848 None:intergenic
GAGATTTGAAGAGAGATTGC+AGG 0.401297 6.3:+28824911 MS.gene80405:CDS
ATCGCATGATGTGGCTAGTA+TGG 0.422295 6.3:+28824671 MS.gene80405:CDS
TAAAACAGTGATTATGAAAC+CGG 0.427491 6.3:+28824620 None:intergenic
GCAATCTCTCTTCAAATCTC+TGG 0.437449 6.3:-28824908 None:intergenic
AATCCTAGATTCCAAACTAT+AGG 0.441030 6.3:-28824814 None:intergenic
GAATGAAGGACCTATACTTT+CGG 0.441319 6.3:-28824949 None:intergenic
ATAGGTCCTTCATTCTGTAT+TGG 0.452739 6.3:+28824957 MS.gene80405:CDS
TATAGTTTCAGATGAGGAAG+AGG 0.454451 6.3:+28825007 MS.gene80405:CDS
TACTTCTTCAAAAGTGAGAT+GGG 0.459036 6.3:+28824750 MS.gene80405:CDS
GGTCCTTCATTCTGTATTGG+TGG 0.495994 6.3:+28824960 MS.gene80405:CDS
TACCAGAGGCTTAAGAGCAA+GGG 0.502139 6.3:+28824846 MS.gene80405:CDS
GGTGATCAAGTGTCCTCAAT+TGG 0.503619 6.3:+28824692 MS.gene80405:CDS
TTACTTCTTCAAAAGTGAGA+TGG 0.508844 6.3:+28824749 MS.gene80405:CDS
ACTCGCAGCGCAACCAATTG+AGG 0.528224 6.3:-28824705 None:intergenic
TATATCGAAACCGAAAGTAT+AGG 0.540273 6.3:+28824939 MS.gene80405:CDS
GTCCTTCATTCTGTATTGGT+GGG 0.540317 6.3:+28824961 MS.gene80405:CDS
AGATTTGAAGAGAGATTGCA+GGG 0.561148 6.3:+28824912 MS.gene80405:CDS
ATACCAGAGGCTTAAGAGCA+AGG 0.565715 6.3:+28824845 MS.gene80405:CDS
TTCCCACCAATACAGAATGA+AGG 0.566084 6.3:-28824963 None:intergenic
GAGACCTGTAAAAGAGCTTG+TGG 0.581965 6.3:+28824773 MS.gene80405:CDS
GGCAATACCATCGCATGATG+TGG 0.603609 6.3:+28824662 MS.gene80405:CDS
ACCAGAGGCTTAAGAGCAAG+GGG 0.605082 6.3:+28824847 MS.gene80405:CDS
TCTGAAACTATATCATTCCC+GGG 0.612098 6.3:-28824996 None:intergenic
GTGGGAAATTAGAGCTACCC+GGG 0.615038 6.3:+28824979 MS.gene80405:CDS
GGTGGGAAATTAGAGCTACC+CGG 0.623613 6.3:+28824978 MS.gene80405:CDS
ACTTCTTCAAAAGTGAGATG+GGG 0.645282 6.3:+28824751 MS.gene80405:CDS
GAATGATATAGTTTCAGATG+AGG 0.656227 6.3:+28825001 MS.gene80405:CDS
ATACTAGCCACATCATGCGA+TGG 0.674562 6.3:-28824669 None:intergenic
GGATTAAACCTAGATACCAG+AGG 0.689589 6.3:+28824832 MS.gene80405:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
AATCCTAGATTCCAAACTAT+AGG - chr6.3:28824817-28824836 None:intergenic 30.0%
AGAATACTTCACCTATAGTT+TGG + chr6.3:28824803-28824822 MS.gene80405:CDS 30.0%
GAATGATATAGTTTCAGATG+AGG + chr6.3:28825001-28825020 MS.gene80405:CDS 30.0%
TACTTCTTCAAAAGTGAGAT+GGG + chr6.3:28824750-28824769 MS.gene80405:CDS 30.0%
TTACTTCTTCAAAAGTGAGA+TGG + chr6.3:28824749-28824768 MS.gene80405:CDS 30.0%
! AAACTATAGGTGAAGTATTC+TGG - chr6.3:28824804-28824823 None:intergenic 30.0%
! ATCTGAAACTATATCATTCC+CGG - chr6.3:28825000-28825019 None:intergenic 30.0%
! GGATAAAGTGTTCATTGAAT+TGG + chr6.3:28824868-28824887 MS.gene80405:CDS 30.0%
! TATATCGAAACCGAAAGTAT+AGG + chr6.3:28824939-28824958 MS.gene80405:CDS 30.0%
ACTTCTTCAAAAGTGAGATG+GGG + chr6.3:28824751-28824770 MS.gene80405:CDS 35.0%
AGATTTGAAGAGAGATTGCA+GGG + chr6.3:28824912-28824931 MS.gene80405:CDS 35.0%
ATAGGTCCTTCATTCTGTAT+TGG + chr6.3:28824957-28824976 MS.gene80405:CDS 35.0%
CTACCAAGTAAAAACTCAAC+CGG - chr6.3:28824642-28824661 None:intergenic 35.0%
GAATGAAGGACCTATACTTT+CGG - chr6.3:28824952-28824971 None:intergenic 35.0%
TATAGTTTCAGATGAGGAAG+AGG + chr6.3:28825007-28825026 MS.gene80405:CDS 35.0%
! AAACCGGTTGAGTTTTTACT+TGG + chr6.3:28824636-28824655 MS.gene80405:CDS 35.0%
! GGTTGAGTTTTTACTTGGTA+GGG + chr6.3:28824641-28824660 MS.gene80405:CDS 35.0%
! TCACCTATAGTTTGGAATCT+AGG + chr6.3:28824811-28824830 MS.gene80405:CDS 35.0%
! TCTGAAACTATATCATTCCC+GGG - chr6.3:28824999-28825018 None:intergenic 35.0%
GAGATTTGAAGAGAGATTGC+AGG + chr6.3:28824911-28824930 MS.gene80405:CDS 40.0%
GCAATCTCTCTTCAAATCTC+TGG - chr6.3:28824911-28824930 None:intergenic 40.0%
GGATTAAACCTAGATACCAG+AGG + chr6.3:28824832-28824851 MS.gene80405:CDS 40.0%
TTCCCACCAATACAGAATGA+AGG - chr6.3:28824966-28824985 None:intergenic 40.0%
! AACTCCACAAGCTCTTTTAC+AGG - chr6.3:28824780-28824799 None:intergenic 40.0%
! CGGTTGAGTTTTTACTTGGT+AGG + chr6.3:28824640-28824659 MS.gene80405:CDS 40.0%
! GTCCTTCATTCTGTATTGGT+GGG + chr6.3:28824961-28824980 MS.gene80405:CDS 40.0%
ATACCAGAGGCTTAAGAGCA+AGG + chr6.3:28824845-28824864 MS.gene80405:CDS 45.0%
ATACTAGCCACATCATGCGA+TGG - chr6.3:28824672-28824691 None:intergenic 45.0%
ATCGCATGATGTGGCTAGTA+TGG + chr6.3:28824671-28824690 MS.gene80405:CDS 45.0%
CTCTTAAGCCTCTGGTATCT+AGG - chr6.3:28824843-28824862 None:intergenic 45.0%
GAGACCTGTAAAAGAGCTTG+TGG + chr6.3:28824773-28824792 MS.gene80405:CDS 45.0%
GGTCCTTCATTCTGTATTGG+TGG + chr6.3:28824960-28824979 MS.gene80405:CDS 45.0%
GGTGATCAAGTGTCCTCAAT+TGG + chr6.3:28824692-28824711 MS.gene80405:CDS 45.0%
TACCAGAGGCTTAAGAGCAA+GGG + chr6.3:28824846-28824865 MS.gene80405:CDS 45.0%
ACCAGAGGCTTAAGAGCAAG+GGG + chr6.3:28824847-28824866 MS.gene80405:CDS 50.0%
GGCAATACCATCGCATGATG+TGG + chr6.3:28824662-28824681 MS.gene80405:CDS 50.0%
GGTGGGAAATTAGAGCTACC+CGG + chr6.3:28824978-28824997 MS.gene80405:CDS 50.0%
GTGGGAAATTAGAGCTACCC+GGG + chr6.3:28824979-28824998 MS.gene80405:CDS 50.0%
ACTCGCAGCGCAACCAATTG+AGG - chr6.3:28824708-28824727 None:intergenic 55.0%
TCCCCTTGCTCTTAAGCCTC+TGG - chr6.3:28824851-28824870 None:intergenic 55.0%


Chromosome Type Strat End Strand Name
chr6.3 gene 28824633 28825073 28824633 ID=MS.gene80405
chr6.3 mRNA 28824633 28825073 28824633 ID=MS.gene80405.t1;Parent=MS.gene80405
chr6.3 exon 28824633 28825073 28824633 ID=MS.gene80405.t1.exon1;Parent=MS.gene80405.t1
chr6.3 CDS 28824633 28825073 28824633 ID=cds.MS.gene80405.t1;Parent=MS.gene80405.t1
Gene Sequence

>MS.gene80405

ATGAAACCGGTTGAGTTTTTACTTGGTAGGGCAATACCATCGCATGATGTGGCTAGTATGGTGATCAAGTGTCCTCAATTGGTTGCGCTGCGAGTTGAGCTCATGAAGAACAGTTATTACTTCTTCAAAAGTGAGATGGGGAGACCTGTAAAAGAGCTTGTGGAGTTTCCAGAATACTTCACCTATAGTTTGGAATCTAGGATTAAACCTAGATACCAGAGGCTTAAGAGCAAGGGGATAAAGTGTTCATTGAATTGGATGCTCAATTGTCGTGACCAGAGATTTGAAGAGAGATTGCAGGGCAATTATATCGAAACCGAAAGTATAGGTCCTTCATTCTGTATTGGTGGGAAATTAGAGCTACCCGGGAATGATATAGTTTCAGATGAGGAAGAGGAGAGTGATGATGAAATGCTAAACAGAAGAACTGTTTCTCTTTAG
Protein sequence

>MS.gene80405.t1

MKPVEFLLGRAIPSHDVASMVIKCPQLVALRVELMKNSYYFFKSEMGRPVKELVEFPEYFTYSLESRIKPRYQRLKSKGIKCSLNWMLNCRDQRFEERLQGNYIETESIGPSFCIGGKLELPGNDIVSDEEEESDDEMLNRRTVSL