AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene06173

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene06173.t1 MTR_8g101900 96.596 235 8 0 1 235 1 235 1.14e-169 467
MS.gene06173.t1 MTR_8g021225 72.926 229 61 1 6 233 5 233 1.40e-120 343
MS.gene06173.t1 MTR_6g091680 70.996 231 67 0 5 235 8 238 4.08e-110 316
MS.gene06173.t1 MTR_4g085590 58.929 224 91 1 12 234 23 246 6.73e-97 283
MS.gene06173.t1 MTR_4g094925 54.626 227 102 1 9 234 16 242 5.46e-90 265
MS.gene06173.t1 MTR_4g094815 53.509 228 105 1 8 234 20 247 1.70e-89 264
MS.gene06173.t1 MTR_4g094898 54.825 228 102 1 8 234 20 247 1.12e-83 249
MS.gene06173.t1 MTR_4g094812 55.804 224 98 1 12 234 22 245 1.14e-80 242
MS.gene06173.t1 MTR_4g094368 52.232 224 103 3 12 232 5 227 1.63e-78 236
MS.gene06173.t1 MTR_4g094925 53.646 192 87 2 45 234 20 211 2.87e-75 227
MS.gene06173.t1 MTR_4g094898 55.914 186 81 1 50 234 1 186 9.75e-68 207
MS.gene06173.t1 MTR_2g070410 41.204 216 118 4 18 233 91 297 4.02e-48 160
MS.gene06173.t1 MTR_2g070410 41.860 172 96 2 18 189 91 258 4.77e-38 134
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene06173.t1 AT4G26220 65.022 223 78 0 12 234 9 231 6.58e-108 310
MS.gene06173.t1 AT4G34050 59.111 225 91 1 12 235 35 259 8.75e-97 283
MS.gene06173.t1 AT4G34050 59.111 225 91 1 12 235 62 286 1.07e-96 284
MS.gene06173.t1 AT1G67980 56.637 226 93 2 12 235 10 232 4.35e-88 260
MS.gene06173.t1 AT1G24735 55.947 227 95 3 12 235 16 240 6.95e-83 247
MS.gene06173.t1 AT1G67990 53.097 226 102 2 12 235 10 233 1.40e-79 239
MS.gene06173.t1 AT1G24735 45.848 277 94 4 12 234 16 290 1.30e-74 228
MS.gene06173.t1 AT1G24735 58.011 181 73 2 55 234 16 194 4.46e-71 216
MS.gene06173.t1 AT1G67980 50.909 165 78 1 70 234 2 163 3.69e-54 172
MS.gene06173.t1 AT3G61990 42.647 204 108 4 30 233 95 289 6.73e-48 160
MS.gene06173.t1 AT3G62000 40.000 205 115 4 30 233 80 277 4.68e-46 154
MS.gene06173.t1 AT4G34050 54.472 123 55 1 113 234 25 147 6.42e-45 147
MS.gene06173.t1 AT3G62000 37.383 214 123 5 11 223 64 267 4.44e-38 135

Find 40 sgRNAs with CRISPR-Local

Find 88 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GTTTCTGAAACTACCGTTTC+TGG 0.209949 4.2:+3287654 None:intergenic
CCATGAGAGGCTTATCAAAT+TGG 0.230744 4.2:-3287736 MS.gene06173:CDS
GTAATTCTTCAGTGGCTTCA+TGG 0.334176 4.2:-3288575 MS.gene06173:intron
TCAAAAGTACCTTCATTTGC+AGG 0.353092 4.2:+3287801 None:intergenic
TGCCTACGATAACACCCTTT+GGG 0.369512 4.2:-3287694 MS.gene06173:CDS
TCTAAAAGTTTATCAAGAAC+TGG 0.389451 4.2:+3287916 None:intergenic
ACCTGATGCGGGTCAGCTAA+TGG 0.395308 4.2:-3288545 MS.gene06173:CDS
ATACAAACCTTTCCATCATA+TGG 0.399941 4.2:+3288433 None:intergenic
TTGCCTACGATAACACCCTT+TGG 0.417902 4.2:-3287695 MS.gene06173:CDS
TTTCAGAAACAAAGAGAGAA+TGG 0.425659 4.2:-3287641 MS.gene06173:CDS
GACAGAAAAGCTTATGAGAT+AGG 0.427880 4.2:-3288003 MS.gene06173:CDS
TTATCAAGAACTGGCAAAGC+TGG 0.435178 4.2:+3287925 None:intergenic
GCCATTAGCTGACCCGCATC+AGG 0.436416 4.2:+3288544 None:intergenic
ATCAAATTGGTTAAGATCGG+TGG 0.482512 4.2:-3287723 MS.gene06173:CDS
GCACTTAACATTCCATATGA+TGG 0.489413 4.2:-3288445 MS.gene06173:CDS
AACTGTTGCCTTGCCAGAAA+CGG 0.495235 4.2:-3287667 MS.gene06173:CDS
CATGGTCACTTCACCTGATG+CGG 0.504087 4.2:-3288557 MS.gene06173:CDS
CTTATCAAATTGGTTAAGAT+CGG 0.511198 4.2:-3287726 MS.gene06173:CDS
TTGAGAGTCTCTGCTTCTCG+TGG 0.514299 4.2:+3288837 None:intergenic
TTTCAATGAAGCAGTTTCAA+AGG 0.518882 4.2:-3287601 MS.gene06173:CDS
TGAAACTACCGTTTCTGGCA+AGG 0.521241 4.2:+3287659 None:intergenic
ATGGTCACTTCACCTGATGC+GGG 0.527395 4.2:-3288556 MS.gene06173:CDS
CTGCAAAATAACTGCATTGG+TGG 0.528279 4.2:+3288986 None:intergenic
CCAATTTGATAAGCCTCTCA+TGG 0.530119 4.2:+3287736 None:intergenic
TAACATTCCATATGATGGAA+AGG 0.530971 4.2:-3288440 MS.gene06173:intron
GCAGAGCGAGGGCTTACTCA+AGG 0.558409 4.2:-3288967 MS.gene06173:intron
TGCTTCTCGTGGGTAAACAC+TGG 0.559815 4.2:+3288848 None:intergenic
GGCAACAGTTCCTCCCCAAA+GGG 0.563275 4.2:+3287680 None:intergenic
AGGCAACAGTTCCTCCCCAA+AGG 0.565907 4.2:+3287679 None:intergenic
TCAAATTGGTTAAGATCGGT+GGG 0.567728 4.2:-3287722 MS.gene06173:CDS
TGAGAGTCTCTGCTTCTCGT+GGG 0.576132 4.2:+3288838 None:intergenic
GCTCTGCAAAATAACTGCAT+TGG 0.577755 4.2:+3288983 None:intergenic
GCGACGGACTCACTATCTGC+AGG 0.587918 4.2:-3287545 MS.gene06173:CDS
ACTATTGGAATTACCATGAG+AGG 0.588635 4.2:-3287749 MS.gene06173:CDS
TTGATGCAGCCTGCAAATGA+AGG 0.599302 4.2:-3287810 MS.gene06173:intron
GCCTACGATAACACCCTTTG+GGG 0.620350 4.2:-3287693 MS.gene06173:CDS
TACGATAACACCCTTTGGGG+AGG 0.624507 4.2:-3287690 MS.gene06173:CDS
AGTTTCAAAGGATCCTCGTA+TGG 0.625984 4.2:-3287589 MS.gene06173:CDS
TCCCCAAAGGGTGTTATCGT+AGG 0.628321 4.2:+3287692 None:intergenic
ACAAAAGCAAGTTCCATACG+AGG 0.723375 4.2:+3287576 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! AAATTTTAGATTAATTAAGT+AGG + chr4.2:3287649-3287668 None:intergenic 10.0%
!!! TTAATTAATCTAAAATTTTG+TGG - chr4.2:3287651-3287670 MS.gene06173:CDS 10.0%
!! AAATAACTTCTATGATTTAT+AGG + chr4.2:3287796-3287815 None:intergenic 15.0%
!! AAAATTTGATTATGCATACA+AGG - chr4.2:3287824-3287843 MS.gene06173:intron 20.0%
!! ACAATGTTAAATGAATATGT+TGG - chr4.2:3288341-3288360 MS.gene06173:intron 20.0%
!!! AAAGTATCACATATAGTTTA+TGG - chr4.2:3288165-3288184 MS.gene06173:intron 20.0%
! AACTTCTATGATTTATAGGT+TGG + chr4.2:3287792-3287811 None:intergenic 25.0%
! AAGGAAAAGAAAAACCATTA+TGG + chr4.2:3288704-3288723 None:intergenic 25.0%
! AGGAAAAGAAAAACCATTAT+GGG + chr4.2:3288703-3288722 None:intergenic 25.0%
! AGTCTTAAGAATAATTACAG+AGG + chr4.2:3287755-3287774 None:intergenic 25.0%
! ATGCTGACAAAAATAACTAT+TGG - chr4.2:3288774-3288793 MS.gene06173:intron 25.0%
! CTTATCAAATTGGTTAAGAT+CGG - chr4.2:3288812-3288831 MS.gene06173:CDS 25.0%
! TCTAAAAGTTTATCAAGAAC+TGG + chr4.2:3288625-3288644 None:intergenic 25.0%
!! TAGTTCAAAAGACTTTTACT+TGG + chr4.2:3288198-3288217 None:intergenic 25.0%
AGGACTTCCATTCATAAAAA+AGG - chr4.2:3288555-3288574 MS.gene06173:CDS 30.0%
ATACAAACCTTTCCATCATA+TGG + chr4.2:3288108-3288127 None:intergenic 30.0%
CTAAACAGTTACAACAAACA+TGG + chr4.2:3287616-3287635 None:intergenic 30.0%
GCTAAAAAGACAATTGAAGT+AGG - chr4.2:3288039-3288058 MS.gene06173:intron 30.0%
TAAATGTATGCAAAGAGAGA+GGG + chr4.2:3288429-3288448 None:intergenic 30.0%
TTTCAATGAAGCAGTTTCAA+AGG - chr4.2:3288937-3288956 MS.gene06173:intron 30.0%
TTTCAGAAACAAAGAGAGAA+TGG - chr4.2:3288897-3288916 MS.gene06173:intron 30.0%
! ATTTTTGTCAGCATCAACAA+AGG + chr4.2:3288768-3288787 None:intergenic 30.0%
! CTTTTGAACTAGAACAATGA+TGG - chr4.2:3288207-3288226 MS.gene06173:intron 30.0%
! GTGTTATTGTAATTCTTCAG+TGG - chr4.2:3287955-3287974 MS.gene06173:CDS 30.0%
! TAACATTCCATATGATGGAA+AGG - chr4.2:3288098-3288117 MS.gene06173:intron 30.0%
!! GAACTTGCTTTTGTTTCAAT+AGG - chr4.2:3288971-3288990 MS.gene06173:CDS 30.0%
ACTATTGGAATTACCATGAG+AGG - chr4.2:3288789-3288808 MS.gene06173:intron 35.0%
ATCAAATTGGTTAAGATCGG+TGG - chr4.2:3288815-3288834 MS.gene06173:CDS 35.0%
ATCTCCACATATATCTTTCC+AGG - chr4.2:3288667-3288686 MS.gene06173:intron 35.0%
CTAAATGTATGCAAAGAGAG+AGG + chr4.2:3288430-3288449 None:intergenic 35.0%
CTTCCATTCATAAAAAAGGC+TGG - chr4.2:3288559-3288578 MS.gene06173:CDS 35.0%
CTTCTTCTCTACCAAATTGA+CGG + chr4.2:3288302-3288321 None:intergenic 35.0%
GACAGAAAAGCTTATGAGAT+AGG - chr4.2:3288535-3288554 MS.gene06173:CDS 35.0%
GCACTTAACATTCCATATGA+TGG - chr4.2:3288093-3288112 MS.gene06173:intron 35.0%
TCAAATTGGTTAAGATCGGT+GGG - chr4.2:3288816-3288835 MS.gene06173:CDS 35.0%
! ATCTCATAAGCTTTTCTGTC+TGG + chr4.2:3288535-3288554 None:intergenic 35.0%
! ATTGAAGTAGGAGTTTTCAC+TGG - chr4.2:3288051-3288070 MS.gene06173:intron 35.0%
!! TCAAAAGTACCTTCATTTGC+AGG + chr4.2:3288740-3288759 None:intergenic 35.0%
!!! ACACCAGCCTTTTTTATGAA+TGG + chr4.2:3288565-3288584 None:intergenic 35.0%
AAACCATTATGGGTCTGACT+TGG + chr4.2:3288693-3288712 None:intergenic 40.0%
ACAAAAGCAAGTTCCATACG+AGG + chr4.2:3288965-3288984 None:intergenic 40.0%
AGTTTCAAAGGATCCTCGTA+TGG - chr4.2:3288949-3288968 MS.gene06173:intron 40.0%
CCAATTTGATAAGCCTCTCA+TGG + chr4.2:3288805-3288824 None:intergenic 40.0%
CCATGAGAGGCTTATCAAAT+TGG - chr4.2:3288802-3288821 MS.gene06173:intron 40.0%
CGTCAATTTGGTAGAGAAGA+AGG - chr4.2:3288300-3288319 MS.gene06173:intron 40.0%
CTGCAAAATAACTGCATTGG+TGG + chr4.2:3287555-3287574 None:intergenic 40.0%
CTGTAGAAGCCAGTATGTAT+AGG + chr4.2:3288141-3288160 None:intergenic 40.0%
GAATCCAATCACCGTCAATT+TGG - chr4.2:3288288-3288307 MS.gene06173:intron 40.0%
GCTCTGCAAAATAACTGCAT+TGG + chr4.2:3287558-3287577 None:intergenic 40.0%
GTAATTCTTCAGTGGCTTCA+TGG - chr4.2:3287963-3287982 MS.gene06173:CDS 40.0%
TAGAAGCCAGTATGTATAGG+AGG + chr4.2:3288138-3288157 None:intergenic 40.0%
TCTACCAAATTGACGGTGAT+TGG + chr4.2:3288295-3288314 None:intergenic 40.0%
TGCTTTCCTCCTATACATAC+TGG - chr4.2:3288129-3288148 MS.gene06173:intron 40.0%
TTATCAAGAACTGGCAAAGC+TGG + chr4.2:3288616-3288635 None:intergenic 40.0%
TTGGCCTGGAAAGATATATG+TGG + chr4.2:3288674-3288693 None:intergenic 40.0%
! AGCTTTTCTGTCTGGATCTA+CGG + chr4.2:3288527-3288546 None:intergenic 40.0%
!! ATACATACTGGCTTCTACAG+TGG - chr4.2:3288141-3288160 MS.gene06173:intron 40.0%
!! GCTTTTGTTTCAATAGGCGA+CGG - chr4.2:3288977-3288996 MS.gene06173:CDS 40.0%
!! GTTTCTGAAACTACCGTTTC+TGG + chr4.2:3288887-3288906 None:intergenic 40.0%
AACTGTTGCCTTGCCAGAAA+CGG - chr4.2:3288871-3288890 MS.gene06173:intron 45.0%
ATCTACAGCAGGCAGACAAA+TGG + chr4.2:3288499-3288518 None:intergenic 45.0%
TCTACAGCAGGCAGACAAAT+GGG + chr4.2:3288498-3288517 None:intergenic 45.0%
TGACTTCTTCAGTCAGCATC+AGG - chr4.2:3287915-3287934 MS.gene06173:CDS 45.0%
TGCCTACGATAACACCCTTT+GGG - chr4.2:3288844-3288863 MS.gene06173:CDS 45.0%
TTGATGCAGCCTGCAAATGA+AGG - chr4.2:3288728-3288747 MS.gene06173:intron 45.0%
TTGCCTACGATAACACCCTT+TGG - chr4.2:3288843-3288862 MS.gene06173:CDS 45.0%
!! GCAGTTATTTTGCAGAGCGA+GGG - chr4.2:3287560-3287579 MS.gene06173:CDS 45.0%
!! TGAAACTACCGTTTCTGGCA+AGG + chr4.2:3288882-3288901 None:intergenic 45.0%
!! TGCAGTTATTTTGCAGAGCG+AGG - chr4.2:3287559-3287578 MS.gene06173:CDS 45.0%
AGGCCAAGTCAGACCCATAA+TGG - chr4.2:3288687-3288706 MS.gene06173:intron 50.0%
ATGGTCACTTCACCTGATGC+GGG - chr4.2:3287982-3288001 MS.gene06173:CDS 50.0%
CATGGTCACTTCACCTGATG+CGG - chr4.2:3287981-3288000 MS.gene06173:CDS 50.0%
CTACAGCAGGCAGACAAATG+GGG + chr4.2:3288497-3288516 None:intergenic 50.0%
CTACGGCTGTAATCTACAGC+AGG + chr4.2:3288510-3288529 None:intergenic 50.0%
GCCTACGATAACACCCTTTG+GGG - chr4.2:3288845-3288864 MS.gene06173:CDS 50.0%
TGAGAGTCTCTGCTTCTCGT+GGG + chr4.2:3287703-3287722 None:intergenic 50.0%
TGCAGGCTGCATCAAGACAA+AGG + chr4.2:3288723-3288742 None:intergenic 50.0%
TGCTTCTCGTGGGTAAACAC+TGG + chr4.2:3287693-3287712 None:intergenic 50.0%
TTGAGAGTCTCTGCTTCTCG+TGG + chr4.2:3287704-3287723 None:intergenic 50.0%
! TACGATAACACCCTTTGGGG+AGG - chr4.2:3288848-3288867 MS.gene06173:CDS 50.0%
!! ATTATGGGTCTGACTTGGCC+TGG + chr4.2:3288688-3288707 None:intergenic 50.0%
!! TCCCCAAAGGGTGTTATCGT+AGG + chr4.2:3288849-3288868 None:intergenic 50.0%
ACCTGATGCGGGTCAGCTAA+TGG - chr4.2:3287993-3288012 MS.gene06173:CDS 55.0%
AGGCAACAGTTCCTCCCCAA+AGG + chr4.2:3288862-3288881 None:intergenic 55.0%
GGCAACAGTTCCTCCCCAAA+GGG + chr4.2:3288861-3288880 None:intergenic 55.0%
GCAGAGCGAGGGCTTACTCA+AGG - chr4.2:3287571-3287590 MS.gene06173:CDS 60.0%
GCCATTAGCTGACCCGCATC+AGG + chr4.2:3287997-3288016 None:intergenic 60.0%
! GCGACGGACTCACTATCTGC+AGG - chr4.2:3288993-3289012 MS.gene06173:CDS 60.0%


Chromosome Type Strat End Strand Name
chr4.2 gene 3287533 3289027 3287533 ID=MS.gene06173
chr4.2 mRNA 3287533 3289027 3287533 ID=MS.gene06173.t1;Parent=MS.gene06173
chr4.2 exon 3288968 3289027 3288968 ID=MS.gene06173.t1.exon1;Parent=MS.gene06173.t1
chr4.2 CDS 3288968 3289027 3288968 ID=cds.MS.gene06173.t1;Parent=MS.gene06173.t1
chr4.2 exon 3288804 3288883 3288804 ID=MS.gene06173.t1.exon2;Parent=MS.gene06173.t1
chr4.2 CDS 3288804 3288883 3288804 ID=cds.MS.gene06173.t1;Parent=MS.gene06173.t1
chr4.2 exon 3288441 3288585 3288441 ID=MS.gene06173.t1.exon3;Parent=MS.gene06173.t1
chr4.2 CDS 3288441 3288585 3288441 ID=cds.MS.gene06173.t1;Parent=MS.gene06173.t1
chr4.2 exon 3287912 3288043 3287912 ID=MS.gene06173.t1.exon4;Parent=MS.gene06173.t1
chr4.2 CDS 3287912 3288043 3287912 ID=cds.MS.gene06173.t1;Parent=MS.gene06173.t1
chr4.2 exon 3287533 3287823 3287533 ID=MS.gene06173.t1.exon5;Parent=MS.gene06173.t1
chr4.2 CDS 3287533 3287823 3287533 ID=cds.MS.gene06173.t1;Parent=MS.gene06173.t1
Gene Sequence

>MS.gene06173

ATGGACAAAATATCAGCTTCCACCAATGCAGTTATTTTGCAGAGCGAGGGCTTACTCAAGGTTTACATACACATCTCTTGCCATGTTTGTTGTAACTGTTTAGATTGATTTTTCCTACTTAATTAATCTAAAATTTTGTGGCAGTATATACTAGAAACCAGTGTTTACCCACGAGAAGCAGAGACTCTCAAAGAGCTGAGAAATGCAACAGCAAATCATCCTCTGTAATTATTCTTAAGACTGCTATACTATACATCCAACCTATAAATCATAGAAGTTATTTAACATAACAAAATTTGATTATGCATACAAGGATTTTTCAAACAAAAATAGTATGATATTATTATTATTATTATTATTATTATTTTATTCTTGTTGAACTTGACTTCTTCAGTCAGCATCAGGAAACTTTTTCTTATGTAGTGTTATTGTAATTCTTCAGTGGCTTCATGGTCACTTCACCTGATGCGGGTCAGCTAATGGCTTTGCTCTTGAAACTTCTAAATGCTAAAAAGACAATTGAAGTAGGAGTTTTCACTGGATACTCTCTTCTACTCACAGCACTTAACATTCCATATGATGGAAAGGTTTGTATCTGCTTTCCTCCTATACATACTGGCTTCTACAGTGGAAAAGTATCACATATAGTTTATGGTAGATCACCAAGTAAAAGTCTTTTGAACTAGAACAATGATGGATGTTGCTCTTCGTAAGTAGAAGCTCATGATATTATGCATTCTCAAGACTGAGACGATGAATCCAATCACCGTCAATTTGGTAGAGAAGAAGGAACAAAAAAACTATTTGAACAATGTTAAATGAATATGTTGGTCATCGTAAGAGTTTTGAACAATTTCAATGCATAAGATGCTTAATTCTCACGCTAGCAATCACCCTCTCTCTTTGCATACATTTAGATAATAACGTCGCAAGTATGTGTCTATTATTTTTATGTTACTAGCCCCATTTGTCTGCCTGCTGTAGATTACAGCCGTAGATCCAGACAGAAAAGCTTATGAGATAGGACTTCCATTCATAAAAAAGGCTGGTGTCTTACACAAGATTGACTACATAGAGTCTCCAGCTTTGCCAGTTCTTGATAAACTTTTAGAAGATGTAAGCAACTTACTTAACATCTCCACATATATCTTTCCAGGCCAAGTCAGACCCATAATGGTTTTTCTTTTCCTTTGTCTTGATGCAGCCTGCAAATGAAGGTACTTTTGACTTTGCCTTTGTTGATGCTGACAAAAATAACTATTGGAATTACCATGAGAGGCTTATCAAATTGGTTAAGATCGGTGGGATTGTTGCCTACGATAACACCCTTTGGGGAGGAACTGTTGCCTTGCCAGAAACGGTAGTTTCAGAAACAAAGAGAGAATGGAGAAGATGTACACTTGATTTCAATGAAGCAGTTTCAAAGGATCCTCGTATGGAACTTGCTTTTGTTTCAATAGGCGACGGACTCACTATCTGCAGGCGCATTTGCTGA
Protein sequence

>MS.gene06173.t1

MDKISASTNAVILQSEGLLKYILETSVYPREAETLKELRNATANHPLGFMVTSPDAGQLMALLLKLLNAKKTIEVGVFTGYSLLLTALNIPYDGKITAVDPDRKAYEIGLPFIKKAGVLHKIDYIESPALPVLDKLLEDPANEGTFDFAFVDADKNNYWNYHERLIKLVKIGGIVAYDNTLWGGTVALPETVVSETKREWRRCTLDFNEAVSKDPRMELAFVSIGDGLTICRRIC