AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene065140

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene065140.t1 MTR_1g110710 100.000 27 0 0 23 49 146 172 4.07e-15 67.0
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene065140.t1 AT1G68480 65.909 44 15 0 6 49 32 75 8.84e-16 68.2
MS.gene065140.t1 AT1G13400 90.000 30 3 0 20 49 45 74 4.59e-14 62.8

Find 15 sgRNAs with CRISPR-Local

Find 67 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TACAACAGTTACAGGTTATA+AGG 0.239483 1.2:+81981856 MS.gene065140:intron
TCTGCAAGTCTCAGGCTCTT+GGG 0.377536 1.2:+81981951 MS.gene065140:CDS
TTCTGCAAGTCTCAGGCTCT+TGG 0.381581 1.2:+81981950 MS.gene065140:CDS
CCTGAGACTTGCAGAATTTG+AGG 0.395585 1.2:-81981943 None:intergenic
CCTCAAATTCTGCAAGTCTC+AGG 0.440903 1.2:+81981943 MS.gene065140:CDS
CTGCAAGTCTCAGGCTCTTG+GGG 0.469661 1.2:+81981952 MS.gene065140:CDS
AGTTACAGGTTATAAGGAAA+AGG 0.489629 1.2:+81981862 MS.gene065140:intron
CTGAGACTTGCAGAATTTGA+GGG 0.491629 1.2:-81981942 None:intergenic
GTAGAGGAAGTAGCTAGCCT+TGG 0.533084 1.2:-81981994 None:intergenic
GGTTATAAGGAAAAGGAAAA+CGG 0.534242 1.2:+81981869 MS.gene065140:CDS
GTAGCTAGCCTTGGCGATGA+CGG 0.551166 1.2:-81981985 None:intergenic
TGATGATAGAAAAGACGAGA+AGG 0.615488 1.2:+81981898 MS.gene065140:CDS
CACATGAACCGTCATCGCCA+AGG 0.619007 1.2:+81981977 MS.gene065140:CDS
TGCAAGTCTCAGGCTCTTGG+GGG 0.639905 1.2:+81981953 MS.gene065140:CDS
GTGTGTGTGATGAAGAAGGG+AGG 0.708784 1.2:+81981059 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAATAAATTAATGAATTACC+AGG - chr1.2:81981455-81981474 None:intergenic 15.0%
!!! ACTTTATTTAATTAAGGTAA+AGG + chr1.2:81981795-81981814 MS.gene065140:intron 15.0%
!!! TATATATTATTTTCACAATG+CGG + chr1.2:81981543-81981562 MS.gene065140:intron 15.0%
!!! TGGTATACTTTATTTAATTA+AGG + chr1.2:81981789-81981808 MS.gene065140:intron 15.0%
!! AGAAAAAAATGAAATGAAAG+GGG + chr1.2:81981692-81981711 MS.gene065140:intron 20.0%
!! ATTTAATTAAGGTAAAGGAA+GGG + chr1.2:81981800-81981819 MS.gene065140:intron 20.0%
!! GAGAAAAAAATGAAATGAAA+GGG + chr1.2:81981691-81981710 MS.gene065140:intron 20.0%
!! TATTTAATTAAGGTAAAGGA+AGG + chr1.2:81981799-81981818 MS.gene065140:intron 20.0%
! AAAAAGAGTAGAAGTTGAAA+AGG - chr1.2:81981260-81981279 None:intergenic 25.0%
! ATAAAATGAAAGACTAAGCT+AGG + chr1.2:81981576-81981595 MS.gene065140:intron 25.0%
! GAAAGAAAAAGATATTGTAG+AGG - chr1.2:81981165-81981184 None:intergenic 25.0%
! GGAGAAAAAAATGAAATGAA+AGG + chr1.2:81981690-81981709 MS.gene065140:intron 25.0%
! TAAATTAATGAATTACCAGG+TGG - chr1.2:81981452-81981471 None:intergenic 25.0%
!! TATTTTGTTACAACAGTTAC+AGG + chr1.2:81981848-81981867 MS.gene065140:intron 25.0%
!!! AGTCTTTCATTTTATTTCCA+TGG - chr1.2:81981571-81981590 None:intergenic 25.0%
!!! TGCTTCCTTTTAATTATTAC+AGG + chr1.2:81981327-81981346 MS.gene065140:intron 25.0%
AGAAAAAGGGTAATGTATCA+TGG - chr1.2:81981617-81981636 None:intergenic 30.0%
AGAGACGATAAAGAAGAAAA+AGG - chr1.2:81981631-81981650 None:intergenic 30.0%
AGTTACAGGTTATAAGGAAA+AGG + chr1.2:81981862-81981881 MS.gene065140:intron 30.0%
CTCATCAAAGTTGCTTAAAT+TGG + chr1.2:81981824-81981843 MS.gene065140:intron 30.0%
CTTGTTTGTAAGCATATACT+AGG + chr1.2:81981669-81981688 MS.gene065140:intron 30.0%
GAGACGATAAAGAAGAAAAA+GGG - chr1.2:81981630-81981649 None:intergenic 30.0%
GGTCTCCTGTAATAATTAAA+AGG - chr1.2:81981335-81981354 None:intergenic 30.0%
GGTTATAAGGAAAAGGAAAA+CGG + chr1.2:81981869-81981888 MS.gene065140:CDS 30.0%
TACAACAGTTACAGGTTATA+AGG + chr1.2:81981856-81981875 MS.gene065140:intron 30.0%
TCATATTACAATCACCATGT+AGG + chr1.2:81981206-81981225 MS.gene065140:intron 30.0%
TGATTATGTGTGATCACTAA+TGG - chr1.2:81981496-81981515 None:intergenic 30.0%
!!! AATGATGGTTTTGGGTTATT+GGG + chr1.2:81981758-81981777 MS.gene065140:intron 30.0%
AAAAGGAGAAGATGATCAAG+TGG - chr1.2:81981243-81981262 None:intergenic 35.0%
AAAGGAGAAGATGATCAAGT+GGG - chr1.2:81981242-81981261 None:intergenic 35.0%
AATGAAATGAAAGGGGTAGT+TGG + chr1.2:81981699-81981718 MS.gene065140:intron 35.0%
AATGCAATGCAATGCAATGA+TGG + chr1.2:81981743-81981762 MS.gene065140:intron 35.0%
AATTATTACAGGAGACCAGA+TGG + chr1.2:81981338-81981357 MS.gene065140:intron 35.0%
ATTAATGAATTACCAGGTGG+AGG - chr1.2:81981449-81981468 None:intergenic 35.0%
TGATGATAGAAAAGACGAGA+AGG + chr1.2:81981898-81981917 MS.gene065140:CDS 35.0%
TTAATGAATTACCAGGTGGA+GGG - chr1.2:81981448-81981467 None:intergenic 35.0%
! ATGCAATGCAATGATGGTTT+TGG + chr1.2:81981749-81981768 MS.gene065140:intron 35.0%
! TGCAATGCAATGATGGTTTT+GGG + chr1.2:81981750-81981769 MS.gene065140:intron 35.0%
!!! CAATGATGGTTTTGGGTTAT+TGG + chr1.2:81981757-81981776 MS.gene065140:intron 35.0%
AAGGAGAAGATGATCAAGTG+GGG - chr1.2:81981241-81981260 None:intergenic 40.0%
AGGTCTAAAGGATTTCCATC+TGG - chr1.2:81981356-81981375 None:intergenic 40.0%
CAGGAAGAAGTTGTTTAGCA+TGG - chr1.2:81981415-81981434 None:intergenic 40.0%
CTGAGACTTGCAGAATTTGA+GGG - chr1.2:81981945-81981964 None:intergenic 40.0%
GGCAGATTGTTAAGGTCTAA+AGG - chr1.2:81981368-81981387 None:intergenic 40.0%
GTGTGATCACTAATGGAAGA+AGG - chr1.2:81981489-81981508 None:intergenic 40.0%
TAATGAATTACCAGGTGGAG+GGG - chr1.2:81981447-81981466 None:intergenic 40.0%
TAGAGGCTATAGTTGAGTGA+TGG - chr1.2:81981148-81981167 None:intergenic 40.0%
TGAAAGACTAAGCTAGGTCA+TGG + chr1.2:81981582-81981601 MS.gene065140:intron 40.0%
TGGGTTATTGGGAATGAAGT+TGG + chr1.2:81981769-81981788 MS.gene065140:intron 40.0%
TGTCATCAGGCAGATTGTTA+AGG - chr1.2:81981376-81981395 None:intergenic 40.0%
! ATTTTCACAATGCGGTACCA+TGG + chr1.2:81981551-81981570 MS.gene065140:intron 40.0%
ACAAACAAGTGCACAACGCT+AGG - chr1.2:81981658-81981677 None:intergenic 45.0%
AGGAGAAGATGATCAAGTGG+GGG - chr1.2:81981240-81981259 None:intergenic 45.0%
CCTCAAATTCTGCAAGTCTC+AGG + chr1.2:81981943-81981962 MS.gene065140:CDS 45.0%
CCTGAGACTTGCAGAATTTG+AGG - chr1.2:81981946-81981965 None:intergenic 45.0%
TCTCTGCTAGAGTTGTCATC+AGG - chr1.2:81981389-81981408 None:intergenic 45.0%
GAAGATGATCAAGTGGGGGA+CGG - chr1.2:81981236-81981255 None:intergenic 50.0%
TCTGCAAGTCTCAGGCTCTT+GGG + chr1.2:81981951-81981970 MS.gene065140:CDS 50.0%
TTCTGCAAGTCTCAGGCTCT+TGG + chr1.2:81981950-81981969 MS.gene065140:CDS 50.0%
CACATGAACCGTCATCGCCA+AGG + chr1.2:81981977-81981996 MS.gene065140:CDS 55.0%
CTGCAAGTCTCAGGCTCTTG+GGG + chr1.2:81981952-81981971 MS.gene065140:CDS 55.0%
TGAATTACCAGGTGGAGGGG+AGG - chr1.2:81981444-81981463 None:intergenic 55.0%
TGCAAGTCTCAGGCTCTTGG+GGG + chr1.2:81981953-81981972 MS.gene065140:CDS 55.0%
ATTACCAGGTGGAGGGGAGG+TGG - chr1.2:81981441-81981460 None:intergenic 60.0%
TGGGGGACGGAAGACCTACA+TGG - chr1.2:81981223-81981242 None:intergenic 60.0%
GACACCACCTCCCCTCCACC+TGG + chr1.2:81981434-81981453 MS.gene065140:intron 70.0%
GGTGGAGGGGAGGTGGTGTC+AGG - chr1.2:81981434-81981453 None:intergenic 70.0%


Chromosome Type Strat End Strand Name
chr1.2 gene 81981068 81982003 81981068 ID=MS.gene065140
chr1.2 mRNA 81981068 81982003 81981068 ID=MS.gene065140.t1;Parent=MS.gene065140
chr1.2 exon 81981068 81981080 81981068 ID=MS.gene065140.t1.exon1;Parent=MS.gene065140.t1
chr1.2 CDS 81981068 81981080 81981068 ID=cds.MS.gene065140.t1;Parent=MS.gene065140.t1
chr1.2 exon 81981864 81982003 81981864 ID=MS.gene065140.t1.exon2;Parent=MS.gene065140.t1
chr1.2 CDS 81981864 81982003 81981864 ID=cds.MS.gene065140.t1;Parent=MS.gene065140.t1
Gene Sequence

>MS.gene065140

ATGAAGAAGGGAGGTAAGTGAGAGAGAGAGTGTAGCAGAAGAACTGATAGAGAACTTTCAAAGCTCTTTATCTTCTACCATCACTCAACTATAGCCTCTACAATATCTTTTTCTTTCTGTAGTCTCTTTCTGCTTGTATCATATTACAATCACCATGTAGGTCTTCCGTCCCCCACTTGATCATCTTCTCCTTTTCAACTTCTACTCTTTTTTCTTCTTTTTTTATCTCTTTCTTTCTCTCTCTTATGATTTTGTTAATTGCTTCCTTTTAATTATTACAGGAGACCAGATGGAAATCCTTTAGACCTTAACAATCTGCCTGATGACAACTCTAGCAGAGATCACCATGCTAAACAACTTCTTCCTGACACCACCTCCCCTCCACCTGGTAATTCATTAATTTATTTAATTAATTAAACCTTCTTCCATTAGTGATCACACATAATCAAAACAACATAAAAATTGATTATTTTTTTATATATTATTTTCACAATGCGGTACCATGGAAATAAAATGAAAGACTAAGCTAGGTCATGGTTTTTTTCACCATGATACATTACCCTTTTTCTTCTTTATCGTCTCTTAGACCTAGCGTTGTGCACTTGTTTGTAAGCATATACTAGGAGAAAAAAATGAAATGAAAGGGGTAGTTGGTAAAGTGATAAGAAATGAATAAATGCAATGCAATGCAATGATGGTTTTGGGTTATTGGGAATGAAGTTGGTATACTTTATTTAATTAAGGTAAAGGAAGGGTCTCATCAAAGTTGCTTAAATTGGATATTTTGTTACAACAGTTACAGGTTATAAGGAAAAGGAAAACGGCGAAGATGATGATAGAAAAGACGAGAAGGTCTATGAATGTAGATTTTGTTCCCTCAAATTCTGCAAGTCTCAGGCTCTTGGGGGACACATGAACCGTCATCGCCAAGGCTAG
Protein sequence

>MS.gene065140.t1

MKKGVTGYKEKENGEDDDRKDEKVYECRFCSLKFCKSQALGGHMNRHRQG