AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene55237

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene55237.t1 MTR_5g041040 93.421 228 15 0 1 228 1 228 7.23e-151 419
MS.gene55237.t1 MTR_5g041010 71.491 228 64 1 1 228 1 227 4.56e-123 348
MS.gene55237.t1 MTR_5g041080 73.362 229 60 1 1 228 1 229 7.65e-121 343
MS.gene55237.t1 MTR_5g041095 71.179 229 64 2 1 228 1 228 3.72e-110 316
MS.gene55237.t1 MTR_5g040940 60.294 204 81 0 25 228 25 228 2.71e-95 278
MS.gene55237.t1 MTR_5g040960 58.667 225 90 3 7 228 6 230 6.57e-93 272
MS.gene55237.t1 MTR_3g030660 35.266 207 120 10 25 226 76 273 2.20e-28 108
MS.gene55237.t1 MTR_3g030640 36.275 204 116 10 28 226 74 268 3.33e-28 107
MS.gene55237.t1 MTR_8g028080 38.021 192 95 6 26 194 41 231 8.88e-26 102
MS.gene55237.t1 MTR_0129s0080 30.374 214 137 7 6 212 3 211 5.54e-23 93.2
MS.gene55237.t1 MTR_6g071425 33.333 207 125 8 28 225 78 280 3.64e-22 92.0
MS.gene55237.t1 MTR_5g086410 29.279 222 145 9 9 226 1 214 4.15e-21 87.8
MS.gene55237.t1 MTR_2g021750 33.333 180 109 7 34 212 163 332 1.06e-20 89.4
MS.gene55237.t1 MTR_2g021830 30.244 205 125 8 23 225 1 189 1.35e-19 83.2
MS.gene55237.t1 MTR_6g071505 33.971 209 119 10 27 225 70 269 2.97e-19 84.0
MS.gene55237.t1 MTR_4g057825 30.348 201 120 9 28 226 21 203 8.92e-19 81.6
MS.gene55237.t1 MTR_5g086770 31.847 157 96 4 57 211 60 207 1.32e-17 78.6
MS.gene55237.t1 MTR_6g090200 26.991 226 142 9 3 225 1 206 1.93e-17 78.2
MS.gene55237.t1 MTR_2g104370 33.824 136 79 4 86 211 52 186 3.46e-17 77.0
MS.gene55237.t1 MTR_0002s1200 29.902 204 130 8 28 226 104 299 6.16e-15 72.8
MS.gene55237.t1 MTR_5g022810 25.490 204 135 9 35 226 31 229 1.40e-12 65.1
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene55237.t1 AT1G26820 59.641 223 89 1 6 228 1 222 4.65e-104 300
MS.gene55237.t1 AT1G14220 57.399 223 94 1 6 228 7 228 1.51e-98 286
MS.gene55237.t1 AT2G02990 53.982 226 104 0 3 228 5 230 1.95e-92 271
MS.gene55237.t1 AT1G14210 48.430 223 110 3 8 226 5 226 1.97e-71 218
MS.gene55237.t1 AT2G39780 37.615 218 118 7 24 228 28 240 2.13e-35 126
MS.gene55237.t1 AT2G39780 31.336 217 101 7 24 228 28 208 2.30e-20 86.3

Find 45 sgRNAs with CRISPR-Local

Find 63 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TACATGTGTGCGGACATTTC+TGG 0.161608 5.2:+30788842 MS.gene55237:CDS
TTAAGGACTTGGAAAGTAAT+TGG 0.239444 5.2:+30788249 MS.gene55237:CDS
GTGGAGTAAAATTTATTATC+TGG 0.272659 5.2:-30788722 None:intergenic
TCTCTATTACATTCTATTCC+TGG 0.336181 5.2:-30788788 None:intergenic
AAGTGTCTTTGATAAATCTA+AGG 0.352998 5.2:+30788111 MS.gene55237:CDS
ACATGTGTGCGGACATTTCT+GGG 0.368274 5.2:+30788843 MS.gene55237:CDS
CTCAGACCTCATTAAGGACT+TGG 0.380669 5.2:+30788238 MS.gene55237:CDS
AAATAAATTCACTTAAAACT+TGG 0.386881 5.2:-30788927 None:intergenic
ATAGATCTCAGACCTCATTA+AGG 0.395778 5.2:+30788232 MS.gene55237:intron
CTCTATTACATTCTATTCCT+GGG 0.404362 5.2:-30788787 None:intergenic
AATAAATTCACTTAAAACTT+GGG 0.412849 5.2:-30788926 None:intergenic
TTGAGCTGCCCTAGTAGAAA+TGG 0.424487 5.2:+30788278 MS.gene55237:CDS
GAGTGCCCTGGTCTTCCAAT+GGG 0.481203 5.2:+30788878 MS.gene55237:CDS
AATCAAATTCTTGAGCAGAA+AGG 0.483669 5.2:-30787779 None:intergenic
TTGTTAATGATGCAGTGGCC+AGG 0.484767 5.2:+30787962 MS.gene55237:intron
TTTGAGTCACAGATTGCTCC+TGG 0.486696 5.2:-30787980 None:intergenic
TACCTGCATTCTGAAGGATC+TGG 0.492132 5.2:-30788415 None:intergenic
TTTCACTATGGTCACATGAA+TGG 0.494000 5.2:+30788303 MS.gene55237:CDS
TGAGTGCCCTGGTCTTCCAA+TGG 0.494252 5.2:+30788877 MS.gene55237:CDS
GATGCTATACAACAGGCTAC+AGG 0.501779 5.2:+30788758 MS.gene55237:CDS
AGTGAAATACCATTTCTACT+AGG 0.503226 5.2:-30788287 None:intergenic
CTACTAGGGCAGCTCAAAGA+TGG 0.503862 5.2:-30788272 None:intergenic
TACTTTCCAAGTCCTTAATG+AGG 0.504206 5.2:-30788244 None:intergenic
CAGCTACCCATTGGAAGACC+AGG 0.504798 5.2:-30788884 None:intergenic
CTTAGGCCTAACTTCAATGA+TGG 0.510786 5.2:+30788061 MS.gene55237:CDS
CTCCAGATCCTTCAGAATGC+AGG 0.518105 5.2:+30788413 MS.gene55237:CDS
GTAGAAATGGTATTTCACTA+TGG 0.526118 5.2:+30788291 MS.gene55237:CDS
GATGATCCATCATTGAAGTT+AGG 0.526231 5.2:-30788067 None:intergenic
GTGAAATACCATTTCTACTA+GGG 0.529497 5.2:-30788286 None:intergenic
TCAAAATTCATTGAGTGCCC+TGG 0.537116 5.2:+30788866 MS.gene55237:CDS
ATATTGAAGTATCAAAAGCT+TGG 0.542439 5.2:-30787742 None:intergenic
TCTTGTTACCTGCATTCTGA+AGG 0.544843 5.2:-30788421 None:intergenic
ACATGTAAACTTGATAAAGC+TGG 0.553440 5.2:-30788826 None:intergenic
ATAAATTCACTTAAAACTTG+GGG 0.560603 5.2:-30788925 None:intergenic
TTAGCGCCACAGCTACCCAT+TGG 0.584200 5.2:-30788893 None:intergenic
GGTCTTCCAATGGGTAGCTG+TGG 0.598566 5.2:+30788887 MS.gene55237:CDS
AGCATCTAAAATGTTACCTG+TGG 0.610310 5.2:-30788741 None:intergenic
ATGCTATACAACAGGCTACA+GGG 0.616264 5.2:+30788759 MS.gene55237:CDS
TTATCAAGTTTACATGTGTG+CGG 0.617597 5.2:+30788832 MS.gene55237:CDS
CAGGCTACAGGGTATTCCCC+AGG 0.622346 5.2:+30788770 MS.gene55237:CDS
TCTATTACATTCTATTCCTG+GGG 0.626261 5.2:-30788786 None:intergenic
GTTAGGCCTAAGTCCAGCAA+TGG 0.644262 5.2:-30788050 None:intergenic
GCAATGGTAAAATCTGATGT+CGG 0.657922 5.2:-30788034 None:intergenic
AGCTACCCATTGGAAGACCA+GGG 0.682922 5.2:-30788883 None:intergenic
TCACATGAATGGATGAAACA+TGG 0.720853 5.2:+30788314 MS.gene55237:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! AATTAAATGATTAGAAATTT+TGG - chr5.2:30788680-30788699 None:intergenic 10.0%
!! ATTTAATTGCATTGAATTTC+AGG + chr5.2:30788692-30788711 MS.gene55237:intron 20.0%
!! TTTAATTGCATTGAATTTCA+GGG + chr5.2:30788693-30788712 MS.gene55237:intron 20.0%
!!! ACTTTTAATATTACAGTTTG+AGG - chr5.2:30788095-30788114 None:intergenic 20.0%
!!! CTTTTAATATTACAGTTTGA+GGG - chr5.2:30788094-30788113 None:intergenic 20.0%
! AAGTGTCTTTGATAAATCTA+AGG + chr5.2:30788111-30788130 MS.gene55237:CDS 25.0%
! CTGACATATACATTTATACA+CGG + chr5.2:30788481-30788500 MS.gene55237:intron 25.0%
! GTGGAGTAAAATTTATTATC+TGG - chr5.2:30788725-30788744 None:intergenic 25.0%
! GTTACATAAGTAATCATCAA+AGG - chr5.2:30788460-30788479 None:intergenic 25.0%
!! ATATTGAAGTATCAAAAGCT+TGG - chr5.2:30787745-30787764 None:intergenic 25.0%
!! GATAATAAATTTTACTCCAC+AGG + chr5.2:30788725-30788744 MS.gene55237:CDS 25.0%
!! TTTCTTCTATTTTATTCTGC+AGG + chr5.2:30787800-30787819 MS.gene55237:CDS 25.0%
!!! TTAATTTGTTAATGATGCAG+TGG + chr5.2:30787957-30787976 MS.gene55237:intron 25.0%
AAGCTTGGACAAAAATGAAA+TGG - chr5.2:30787730-30787749 None:intergenic 30.0%
AATCAAATTCTTGAGCAGAA+AGG - chr5.2:30787782-30787801 None:intergenic 30.0%
ACATGTAAACTTGATAAAGC+TGG - chr5.2:30788829-30788848 None:intergenic 30.0%
AGTGAAATACCATTTCTACT+AGG - chr5.2:30788290-30788309 None:intergenic 30.0%
CTCTATTACATTCTATTCCT+GGG - chr5.2:30788790-30788809 None:intergenic 30.0%
GTAGAAATGGTATTTCACTA+TGG + chr5.2:30788291-30788310 MS.gene55237:CDS 30.0%
GTGAAATACCATTTCTACTA+GGG - chr5.2:30788289-30788308 None:intergenic 30.0%
TCTATTACATTCTATTCCTG+GGG - chr5.2:30788789-30788808 None:intergenic 30.0%
TCTCTATTACATTCTATTCC+TGG - chr5.2:30788791-30788810 None:intergenic 30.0%
TTAAGGACTTGGAAAGTAAT+TGG + chr5.2:30788249-30788268 MS.gene55237:CDS 30.0%
TTATCAAGTTTACATGTGTG+CGG + chr5.2:30788832-30788851 MS.gene55237:CDS 30.0%
! AGTGTATGTTGTTTATGTGT+CGG - chr5.2:30788528-30788547 None:intergenic 30.0%
! CATTTTAGATGCTATACAAC+AGG + chr5.2:30788751-30788770 MS.gene55237:CDS 30.0%
ATAGATCTCAGACCTCATTA+AGG + chr5.2:30788232-30788251 MS.gene55237:intron 35.0%
ATATATAGCTCTCGACACTT+TGG - chr5.2:30788655-30788674 None:intergenic 35.0%
GATGATCCATCATTGAAGTT+AGG - chr5.2:30788070-30788089 None:intergenic 35.0%
GCAATGGTAAAATCTGATGT+CGG - chr5.2:30788037-30788056 None:intergenic 35.0%
TACTTTCCAAGTCCTTAATG+AGG - chr5.2:30788247-30788266 None:intergenic 35.0%
TCACATGAATGGATGAAACA+TGG + chr5.2:30788314-30788333 MS.gene55237:CDS 35.0%
TTTCACTATGGTCACATGAA+TGG + chr5.2:30788303-30788322 MS.gene55237:CDS 35.0%
! ACATCAGATTTTACCATTGC+TGG + chr5.2:30788037-30788056 MS.gene55237:CDS 35.0%
! AGCATCTAAAATGTTACCTG+TGG - chr5.2:30788744-30788763 None:intergenic 35.0%
! ATTTTACCATTGCTGGACTT+AGG + chr5.2:30788044-30788063 MS.gene55237:CDS 35.0%
!!! AAAATCTGATGTCGGTTTTC+CGG - chr5.2:30788029-30788048 None:intergenic 35.0%
ATGCTATACAACAGGCTACA+GGG + chr5.2:30788759-30788778 MS.gene55237:CDS 40.0%
CTTAGGCCTAACTTCAATGA+TGG + chr5.2:30788061-30788080 MS.gene55237:CDS 40.0%
TCAAAATTCATTGAGTGCCC+TGG + chr5.2:30788866-30788885 MS.gene55237:CDS 40.0%
TCTTGTTACCTGCATTCTGA+AGG - chr5.2:30788424-30788443 None:intergenic 40.0%
ACATGTGTGCGGACATTTCT+GGG + chr5.2:30788843-30788862 MS.gene55237:CDS 45.0%
CTCAGACCTCATTAAGGACT+TGG + chr5.2:30788238-30788257 MS.gene55237:CDS 45.0%
GATGCTATACAACAGGCTAC+AGG + chr5.2:30788758-30788777 MS.gene55237:CDS 45.0%
TACATGTGTGCGGACATTTC+TGG + chr5.2:30788842-30788861 MS.gene55237:CDS 45.0%
TTGAGCTGCCCTAGTAGAAA+TGG + chr5.2:30788278-30788297 MS.gene55237:CDS 45.0%
TTGTTAATGATGCAGTGGCC+AGG + chr5.2:30787962-30787981 MS.gene55237:intron 45.0%
TTTGAGTCACAGATTGCTCC+TGG - chr5.2:30787983-30788002 None:intergenic 45.0%
! TACCTGCATTCTGAAGGATC+TGG - chr5.2:30788418-30788437 None:intergenic 45.0%
!!! AGCTGCTGTTTTCCGAAAAC+CGG + chr5.2:30788007-30788026 MS.gene55237:CDS 45.0%
!!! GATGTCGGTTTTCCGGTTTT+CGG - chr5.2:30788022-30788041 None:intergenic 45.0%
AGCTACCCATTGGAAGACCA+GGG - chr5.2:30788886-30788905 None:intergenic 50.0%
CGTGTCAGACGAGACAAGTA+TGG - chr5.2:30788624-30788643 None:intergenic 50.0%
CTACTAGGGCAGCTCAAAGA+TGG - chr5.2:30788275-30788294 None:intergenic 50.0%
CTCCAGATCCTTCAGAATGC+AGG + chr5.2:30788413-30788432 MS.gene55237:CDS 50.0%
GGTGTCTGACTGACACATTG+TGG - chr5.2:30788603-30788622 None:intergenic 50.0%
GTTAGGCCTAAGTCCAGCAA+TGG - chr5.2:30788053-30788072 None:intergenic 50.0%
CAGCTACCCATTGGAAGACC+AGG - chr5.2:30788887-30788906 None:intergenic 55.0%
GGTCTTCCAATGGGTAGCTG+TGG + chr5.2:30788887-30788906 MS.gene55237:CDS 55.0%
TTAGCGCCACAGCTACCCAT+TGG - chr5.2:30788896-30788915 None:intergenic 55.0%
! GAGTGCCCTGGTCTTCCAAT+GGG + chr5.2:30788878-30788897 MS.gene55237:CDS 55.0%
! TGAGTGCCCTGGTCTTCCAA+TGG + chr5.2:30788877-30788896 MS.gene55237:CDS 55.0%
! CAGGCTACAGGGTATTCCCC+AGG + chr5.2:30788770-30788789 MS.gene55237:CDS 60.0%


Chromosome Type Strat End Strand Name
chr5.2 gene 30787714 30788937 30787714 ID=MS.gene55237
chr5.2 mRNA 30787714 30788937 30787714 ID=MS.gene55237.t1;Parent=MS.gene55237
chr5.2 exon 30787714 30787821 30787714 ID=MS.gene55237.t1.exon1;Parent=MS.gene55237.t1
chr5.2 CDS 30787714 30787821 30787714 ID=cds.MS.gene55237.t1;Parent=MS.gene55237.t1
chr5.2 exon 30787977 30788132 30787977 ID=MS.gene55237.t1.exon2;Parent=MS.gene55237.t1
chr5.2 CDS 30787977 30788132 30787977 ID=cds.MS.gene55237.t1;Parent=MS.gene55237.t1
chr5.2 exon 30788236 30788434 30788236 ID=MS.gene55237.t1.exon3;Parent=MS.gene55237.t1
chr5.2 CDS 30788236 30788434 30788236 ID=cds.MS.gene55237.t1;Parent=MS.gene55237.t1
chr5.2 exon 30788714 30788937 30788714 ID=MS.gene55237.t1.exon4;Parent=MS.gene55237.t1
chr5.2 CDS 30788714 30788937 30788714 ID=cds.MS.gene55237.t1;Parent=MS.gene55237.t1
Gene Sequence

>MS.gene55237

ATGAAACTCAACACCATTTCATTTTTGTCCAAGCTTTTGATACTTCAATATCTTTCTGTTCAAAGCCTTTCTGCTCAAGAATTTGATTTCTTCTATTTTATTCTGCAGGTAATTAAATCACGAGTAGATCTCTTAATCATGACTATAGTGTATTCATTTAATTCTTATAAAAAAAAATAGTCGATTTATTTAAGCTTTATATTTATATTTACATTTTATTCTGATTCTTCAGTATTTGCACTGTTAATTTGTTAATGATGCAGTGGCCAGGAGCAATCTGTGACTCAAAGCAGAGCTGCTGTTTTCCGAAAACCGGAAAACCGACATCAGATTTTACCATTGCTGGACTTAGGCCTAACTTCAATGATGGATCATCTCCCTCAAACTGTAATATTAAAAGTGTCTTTGATAAATCTAAGGTATTTTTTTTTTAAATGAATTTAATTGCTCTTTATGATTTTAGTAGTGTATTTCTCTGCTGAAAAACTCATCTATGAGTCATATTTAATTTTGTATATATAGATCTCAGACCTCATTAAGGACTTGGAAAGTAATTGGCCATCTTTGAGCTGCCCTAGTAGAAATGGTATTTCACTATGGTCACATGAATGGATGAAACATGGTACATGTTCAGAATCTAAGCTTACTCAACATGACTACTTTCAAACAGCTCTCAAACTCAAGAAAAAATCAAATCTTCTCCAGATCCTTCAGAATGCAGGTAACAAGACATAATTTTGAAACCTTTGATGATTACTTATGTAACACTGACATATACATTTATACACGGATATTAGACACGACACTAACACCGACACATAAACAACATACACTGACACAGTACACGACACTGACATATGTGTCAAAGTTGTGTATGTGTCAGACACCACAATGTGTCAGTCAGACACCATACTTGTCTCGTCTGACACGCTTTTAATCCAAAGTGTCGAGAGCTATATATTTCCAAAATTTCTAATCATTTAATTGCATTGAATTTCAGGGATTGAACCAGATAATAAATTTTACTCCACAGGTAACATTTTAGATGCTATACAACAGGCTACAGGGTATTCCCCAGGAATAGAATGTAATAGAGATTCAGCTCATAACAGCCAGCTTTATCAAGTTTACATGTGTGCGGACATTTCTGGGTCAAAATTCATTGAGTGCCCTGGTCTTCCAATGGGTAGCTGTGGCGCTAATGTACATTTCCCCAAGTTTTAA
Protein sequence

>MS.gene55237.t1

MKLNTISFLSKLLILQYLSVQSLSAQEFDFFYFILQWPGAICDSKQSCCFPKTGKPTSDFTIAGLRPNFNDGSSPSNCNIKSVFDKSKISDLIKDLESNWPSLSCPSRNGISLWSHEWMKHGTCSESKLTQHDYFQTALKLKKKSNLLQILQNAGIEPDNKFYSTGNILDAIQQATGYSPGIECNRDSAHNSQLYQVYMCADISGSKFIECPGLPMGSCGANVHFPKF