AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene048844

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene048844.t1 MTR_8g098725 98.438 128 2 0 1 128 201 328 3.91e-92 269
MS.gene048844.t1 MTR_8g098725 98.438 128 2 0 1 128 197 324 5.05e-92 269
MS.gene048844.t1 MTR_5g010120 65.217 92 30 2 5 95 150 240 2.45e-33 117
MS.gene048844.t1 MTR_2g068730 77.419 62 14 0 15 76 149 210 4.76e-25 95.9
MS.gene048844.t1 MTR_1g073350 65.625 64 22 0 10 73 297 360 2.77e-23 93.6
MS.gene048844.t1 MTR_1g044785 48.544 103 47 2 15 117 120 216 3.74e-23 90.5
MS.gene048844.t1 MTR_2g096080 65.625 64 19 1 20 83 146 206 3.95e-21 85.5
MS.gene048844.t1 MTR_4g061823 62.712 59 22 0 15 73 131 189 3.14e-20 82.8
MS.gene048844.t1 MTR_4g061910 62.712 59 22 0 15 73 131 189 3.14e-20 82.8
MS.gene048844.t1 MTR_1g008220 53.623 69 30 1 5 73 210 276 2.37e-18 78.6
MS.gene048844.t1 MTR_3g091340 59.016 61 25 0 13 73 185 245 4.91e-18 77.4
MS.gene048844.t1 MTR_3g091340 59.016 61 25 0 13 73 178 238 5.30e-18 77.0
MS.gene048844.t1 MTR_3g091340 59.016 61 25 0 13 73 214 274 1.03e-17 77.0
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene048844.t1 AT1G63820 59.016 122 38 2 7 116 170 291 1.07e-37 129
MS.gene048844.t1 AT5G41380 65.686 102 26 3 15 113 201 296 6.45e-36 125
MS.gene048844.t1 AT3G12890 67.647 68 22 0 9 76 119 186 2.90e-24 93.6
MS.gene048844.t1 AT2G33350 63.768 69 24 1 6 73 295 363 8.29e-24 95.1
MS.gene048844.t1 AT2G33350 63.768 69 24 1 6 73 286 354 1.56e-23 94.0
MS.gene048844.t1 AT2G33350 63.768 69 24 1 6 73 287 355 1.78e-23 94.0
MS.gene048844.t1 AT2G33350 63.768 69 24 1 6 73 275 343 1.83e-23 94.0
MS.gene048844.t1 AT1G04500 68.254 63 20 0 20 82 279 341 9.36e-23 91.7
MS.gene048844.t1 AT1G04500 68.254 63 20 0 20 82 279 341 9.36e-23 91.7
MS.gene048844.t1 AT1G04500 68.254 63 20 0 20 82 270 332 3.23e-22 90.1
MS.gene048844.t1 AT5G59990 51.042 96 47 0 2 97 136 231 1.72e-18 78.6
MS.gene048844.t1 AT4G27900 49.206 63 32 0 11 73 196 258 3.06e-16 72.8
MS.gene048844.t1 AT4G27900 49.206 63 32 0 11 73 196 258 3.06e-16 72.8
MS.gene048844.t1 AT5G53420 59.184 49 20 0 25 73 135 183 5.88e-16 70.5
MS.gene048844.t1 AT5G53420 59.184 49 20 0 25 73 135 183 5.88e-16 70.5
MS.gene048844.t1 AT5G53420 59.184 49 20 0 25 73 135 183 5.88e-16 70.5
MS.gene048844.t1 AT5G53420 59.184 49 20 0 25 73 214 262 1.44e-15 70.9

Find 31 sgRNAs with CRISPR-Local

Find 38 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ATGAAGACGAAGTCGATTTC+TGG 0.227779 4.1:+5633380 MS.gene048844:CDS
GAACTTTAACAAGACTATTA+AGG 0.296751 4.1:+5633177 MS.gene048844:CDS
TGTTCTCTTGGCTCTGTACT+TGG 0.332786 4.1:-5633149 None:intergenic
AAAGTTCCTCTGTGTTCTCT+TGG 0.348760 4.1:-5633161 None:intergenic
GTTGGTCAATTTCAGTACTT+TGG 0.368744 4.1:+5633844 MS.gene048844:CDS
CTGATTAAACATGGAGCCTT+AGG 0.397252 4.1:-5633355 None:intergenic
TTGGTCAATTTCAGTACTTT+GGG 0.401778 4.1:+5633845 MS.gene048844:CDS
TGAAGACGAAGTCGATTTCT+GGG 0.449240 4.1:+5633381 MS.gene048844:CDS
AAGAATAGTGGTTACGGAGT+TGG 0.483748 4.1:+5633826 MS.gene048844:CDS
TCTTGCGAATTCCCCTCCGT+TGG 0.487308 4.1:-5633070 None:intergenic
GAACAATATCTGAAGAATAG+TGG 0.497442 4.1:+5633814 MS.gene048844:CDS
GAGGAACAAAATTTCAAAGT+AGG 0.499993 4.1:+5633091 MS.gene048844:CDS
TATCTGAAGAATAGTGGTTA+CGG 0.515829 4.1:+5633820 MS.gene048844:CDS
ATCGACCACGAGTACGTGGC+AGG 0.522107 4.1:+5633302 MS.gene048844:CDS
AATAATATGTCTCCAACGGA+GGG 0.534384 4.1:+5633058 MS.gene048844:CDS
AAATAATATGTCTCCAACGG+AGG 0.560154 4.1:+5633057 MS.gene048844:CDS
AGAAAATAATATGTCTCCAA+CGG 0.563673 4.1:+5633054 MS.gene048844:CDS
CGAGCCCACGGAGATTCCTA+AGG 0.567771 4.1:+5633339 MS.gene048844:CDS
TCTTCATCTCTGATTAAACA+TGG 0.570013 4.1:-5633364 None:intergenic
TGCACGCAATGACGAGCCCA+CGG 0.603558 4.1:+5633327 MS.gene048844:CDS
GCAAACCTGCCACGTACTCG+TGG 0.610525 4.1:-5633307 None:intergenic
GACAATCGACCACGAGTACG+TGG 0.635769 4.1:+5633298 MS.gene048844:CDS
TGATGTAGATGGAAGAATTG+CGG 0.651165 4.1:+5633758 MS.gene048844:intron
AACGGAGGGGAATTCGCAAG+AGG 0.653430 4.1:+5633072 MS.gene048844:CDS
ATAATATGTCTCCAACGGAG+GGG 0.654626 4.1:+5633059 MS.gene048844:CDS
CAAAGTAGGTCGTTATAGCG+CGG 0.657198 4.1:+5633105 MS.gene048844:CDS
CATGAAGATGATGTAACAGT+GGG 0.675111 4.1:+5633784 MS.gene048844:CDS
GGAGCCTTAGGAATCTCCGT+GGG 0.684622 4.1:-5633343 None:intergenic
GCATGAAGATGATGTAACAG+TGG 0.695685 4.1:+5633783 MS.gene048844:CDS
TGGAGCCTTAGGAATCTCCG+TGG 0.702219 4.1:-5633344 None:intergenic
ACAGAGCCAAGAGAACACAG+AGG 0.782868 4.1:+5633155 MS.gene048844:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! AGAAAATAATATGTCTCCAA+CGG + chr4.1:5633054-5633073 MS.gene048844:CDS 25.0%
! GAACTTTAACAAGACTATTA+AGG + chr4.1:5633177-5633196 MS.gene048844:CDS 25.0%
!! TTTGAAATAGTAAGCATGTA+AGG + chr4.1:5633467-5633486 MS.gene048844:intron 25.0%
GAACAATATCTGAAGAATAG+TGG + chr4.1:5633814-5633833 MS.gene048844:CDS 30.0%
GAGGAACAAAATTTCAAAGT+AGG + chr4.1:5633091-5633110 MS.gene048844:CDS 30.0%
TATCTGAAGAATAGTGGTTA+CGG + chr4.1:5633820-5633839 MS.gene048844:CDS 30.0%
TCTTCATCTCTGATTAAACA+TGG - chr4.1:5633367-5633386 None:intergenic 30.0%
TTGGTCAATTTCAGTACTTT+GGG + chr4.1:5633845-5633864 MS.gene048844:CDS 30.0%
! GATTTTACTTGTACAAGCTA+TGG - chr4.1:5633526-5633545 None:intergenic 30.0%
!! GACTATTGATTGAGTTGAAA+GGG + chr4.1:5633715-5633734 MS.gene048844:intron 30.0%
!! TGACTATTGATTGAGTTGAA+AGG + chr4.1:5633714-5633733 MS.gene048844:intron 30.0%
!!! AAAGGGTTTTGATTCTTATG+TGG + chr4.1:5633732-5633751 MS.gene048844:intron 30.0%
AAATAATATGTCTCCAACGG+AGG + chr4.1:5633057-5633076 MS.gene048844:CDS 35.0%
AATAATATGTCTCCAACGGA+GGG + chr4.1:5633058-5633077 MS.gene048844:CDS 35.0%
CATGAAGATGATGTAACAGT+GGG + chr4.1:5633784-5633803 MS.gene048844:CDS 35.0%
GCATGTAAGGATTGTACATT+TGG + chr4.1:5633480-5633499 MS.gene048844:intron 35.0%
GTTGGTCAATTTCAGTACTT+TGG + chr4.1:5633844-5633863 MS.gene048844:CDS 35.0%
TGATGTAGATGGAAGAATTG+CGG + chr4.1:5633758-5633777 MS.gene048844:intron 35.0%
!! TTATGTGGCTTTGATGTAGA+TGG + chr4.1:5633747-5633766 MS.gene048844:intron 35.0%
AAAGTTCCTCTGTGTTCTCT+TGG - chr4.1:5633164-5633183 None:intergenic 40.0%
AAGAATAGTGGTTACGGAGT+TGG + chr4.1:5633826-5633845 MS.gene048844:CDS 40.0%
ATAATATGTCTCCAACGGAG+GGG + chr4.1:5633059-5633078 MS.gene048844:CDS 40.0%
CTGATTAAACATGGAGCCTT+AGG - chr4.1:5633358-5633377 None:intergenic 40.0%
GCATGAAGATGATGTAACAG+TGG + chr4.1:5633783-5633802 MS.gene048844:CDS 40.0%
! ATGAAGACGAAGTCGATTTC+TGG + chr4.1:5633380-5633399 MS.gene048844:CDS 40.0%
! TGAAGACGAAGTCGATTTCT+GGG + chr4.1:5633381-5633400 MS.gene048844:CDS 40.0%
CAAAGTAGGTCGTTATAGCG+CGG + chr4.1:5633105-5633124 MS.gene048844:CDS 45.0%
!! TGTTCTCTTGGCTCTGTACT+TGG - chr4.1:5633152-5633171 None:intergenic 45.0%
ACAGAGCCAAGAGAACACAG+AGG + chr4.1:5633155-5633174 MS.gene048844:CDS 50.0%
AACGGAGGGGAATTCGCAAG+AGG + chr4.1:5633072-5633091 MS.gene048844:CDS 55.0%
GACAATCGACCACGAGTACG+TGG + chr4.1:5633298-5633317 MS.gene048844:CDS 55.0%
GGAGCCTTAGGAATCTCCGT+GGG - chr4.1:5633346-5633365 None:intergenic 55.0%
TCTTGCGAATTCCCCTCCGT+TGG - chr4.1:5633073-5633092 None:intergenic 55.0%
TGGAGCCTTAGGAATCTCCG+TGG - chr4.1:5633347-5633366 None:intergenic 55.0%
ATCGACCACGAGTACGTGGC+AGG + chr4.1:5633302-5633321 MS.gene048844:CDS 60.0%
CGAGCCCACGGAGATTCCTA+AGG + chr4.1:5633339-5633358 MS.gene048844:CDS 60.0%
GCAAACCTGCCACGTACTCG+TGG - chr4.1:5633310-5633329 None:intergenic 60.0%
TGCACGCAATGACGAGCCCA+CGG + chr4.1:5633327-5633346 MS.gene048844:CDS 60.0%


Chromosome Type Strat End Strand Name
chr4.1 gene 5633049 5633873 5633049 ID=MS.gene048844
chr4.1 mRNA 5633049 5633873 5633049 ID=MS.gene048844.t1;Parent=MS.gene048844
chr4.1 exon 5633049 5633198 5633049 ID=MS.gene048844.t1.exon1;Parent=MS.gene048844.t1
chr4.1 CDS 5633049 5633198 5633049 ID=cds.MS.gene048844.t1;Parent=MS.gene048844.t1
chr4.1 exon 5633274 5633402 5633274 ID=MS.gene048844.t1.exon2;Parent=MS.gene048844.t1
chr4.1 CDS 5633274 5633402 5633274 ID=cds.MS.gene048844.t1;Parent=MS.gene048844.t1
chr4.1 exon 5633766 5633873 5633766 ID=MS.gene048844.t1.exon3;Parent=MS.gene048844.t1
chr4.1 CDS 5633766 5633873 5633766 ID=cds.MS.gene048844.t1;Parent=MS.gene048844.t1
Gene Sequence

>MS.gene048844

ATGAAAGAAAATAATATGTCTCCAACGGAGGGGAATTCGCAAGAGGAACAAAATTTCAAAGTAGGTCGTTATAGCGCGGAAGAAAGAAAAGAAAAAATTTCCAAGTACAGAGCCAAGAGAACACAGAGGAACTTTAACAAGACTATTAAGGTAATCAAGATCATTAGACTGTAATTAAGAATGTTTGATTAGAAAGAGAAGAGTCTGAATGTGTTGTTTTTATAGTATGCATGTAGAAAGACACTAGCAGACAATCGACCACGAGTACGTGGCAGGTTTGCACGCAATGACGAGCCCACGGAGATTCCTAAGGCTCCATGTTTAATCAGAGATGAAGACGAAGTCGATTTCTGGGTAAATATTACTGATTCATTTTGTTGCTTTCTTCAATTTTAACATCAATGTGAGAGCAAACGTCTTTGAAATAGTAAGCATGTAAGGATTGTACATTTGGTTAAACGTGTCACACTCACACCATAGCTTGTACAAGTAAAATCTTATGTTATTTTAATTTGTATAATTGAAATTTGCTTTAGTAAATTTTTTTTTTTTTTTGACAAGCTAGAAAATGATAAAAATAAATAAATTTTATAATCTTCTAATGACACAATTTGCACAAGTGCTTTTCAGTTAAAACAATGACATTATGAAGATCACATTGTAAATGACTATTGATTGAGTTGAAAGGGTTTTGATTCTTATGTGGCTTTGATGTAGATGGAAGAATTGCGGTTGCATGAAGATGATGTAACAGTGGGAGTAGCAGAACAATATCTGAAGAATAGTGGTTACGGAGTTGGTCAATTTCAGTACTTTGGGTTATGA
Protein sequence

>MS.gene048844.t1

MKENNMSPTEGNSQEEQNFKVGRYSAEERKEKISKYRAKRTQRNFNKTIKYACRKTLADNRPRVRGRFARNDEPTEIPKAPCLIRDEDEVDFWMEELRLHEDDVTVGVAEQYLKNSGYGVGQFQYFGL