AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene52258

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene52258.t1 MTR_7g077620 62.903 372 101 4 1 337 1 370 3.76e-157 446
MS.gene52258.t1 MTR_7g077660 60.215 372 111 6 1 339 1 368 1.88e-143 410
MS.gene52258.t1 MTR_7g077650 59.474 380 105 6 1 339 1 372 5.66e-142 406
MS.gene52258.t1 MTR_7g076100 54.572 339 108 5 4 339 5 300 2.42e-110 323
MS.gene52258.t1 MTR_7g076110 54.513 277 116 5 72 339 38 313 1.89e-94 283
MS.gene52258.t1 MTR_1g108740 43.089 369 153 14 1 337 1 344 7.54e-79 244
MS.gene52258.t1 MTR_5g038260 39.796 392 173 14 1 339 2 383 3.42e-71 226
MS.gene52258.t1 MTR_5g082770 43.667 300 118 8 5 269 4 287 1.32e-65 209
MS.gene52258.t1 MTR_5g038230 38.381 383 153 14 5 337 4 353 3.94e-65 210
MS.gene52258.t1 MTR_1g064570 37.745 408 174 13 3 339 2 400 7.53e-64 207
MS.gene52258.t1 MTR_7g076130 62.097 124 44 1 135 255 25 148 5.42e-46 154
MS.gene52258.t1 MTR_1g016150 44.271 192 69 4 1 155 1 191 3.65e-40 141
MS.gene52258.t1 MTR_5g082780 36.000 250 124 9 81 317 1 227 3.85e-33 123
MS.gene52258.t1 MTR_1g108750 56.452 124 49 4 5 126 4 124 9.82e-31 113
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 64 sgRNAs with CRISPR-Local

Find 83 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CGAACTTCACGTTTACAAAT+TGG 0.193148 7.4:-28521436 MS.gene52258:CDS
TCAAGTGGATGCAATTGTTT+TGG 0.203842 7.4:-28521176 MS.gene52258:CDS
TGCATCCACTTGAAGGAAAT+TGG 0.206428 7.4:+28521186 None:intergenic
CGAGCTTTACATCTCTTAAA+AGG 0.209664 7.4:+28521873 None:intergenic
AAAGACCAAGCCAATCATTT+TGG 0.213196 7.4:-28521734 MS.gene52258:CDS
TTCTCATAGTAAGTCAAATT+AGG 0.238289 7.4:+28521579 None:intergenic
ATGTGGTTGCAGCAATTTAC+AGG 0.290741 7.4:-28521776 MS.gene52258:CDS
ACCTCTCGAATCTATCAAAA+AGG 0.312660 7.4:-28521838 MS.gene52258:CDS
AGCCTCTTGTTTCCCTGCAT+TGG 0.327895 7.4:-28521310 MS.gene52258:CDS
GCTGATCAATGGAATGGGTT+AGG 0.348133 7.4:-28521258 MS.gene52258:CDS
AAGAACACATAGATCATGTT+AGG 0.348741 7.4:-28522179 MS.gene52258:CDS
AGAAGCATATCCTCTTAGTT+TGG 0.367450 7.4:-28522217 MS.gene52258:CDS
AATTAACAGACTTAATAGTT+TGG 0.392756 7.4:-28521382 MS.gene52258:CDS
TCAGCATGACTAAGGTTGAT+TGG 0.394156 7.4:-28522248 None:intergenic
TCTCATAGTAAGTCAAATTA+GGG 0.396551 7.4:+28521580 None:intergenic
AAAAGGATTCACTAGAGTTA+TGG 0.411464 7.4:+28521890 None:intergenic
GTTGCAGCAATTTACAGGTT+TGG 0.412609 7.4:-28521771 MS.gene52258:CDS
GGGTTGTACCACAATTTCAA+TGG 0.418918 7.4:-28521155 MS.gene52258:CDS
CACATAGATCATGTTAGGTT+TGG 0.419733 7.4:-28522174 MS.gene52258:CDS
TTGTTTCCCTGCATTGGAAA+AGG 0.420899 7.4:-28521304 MS.gene52258:CDS
CAGCATGACTAAGGTTGATT+GGG 0.432229 7.4:-28522247 None:intergenic
TTTACTTATCAGCATGACTA+AGG 0.435408 7.4:-28522256 None:intergenic
TCACGTTTACAAATTGGATC+TGG 0.437953 7.4:-28521430 MS.gene52258:CDS
TAATTTCTAAAGCTGATCAA+TGG 0.449052 7.4:-28521269 MS.gene52258:CDS
CTTTACCAATTTCCTTCAAG+TGG 0.453302 7.4:-28521191 MS.gene52258:CDS
AAACAATTGCATCCACTTGA+AGG 0.458403 7.4:+28521179 None:intergenic
CTGATCAATGGAATGGGTTA+GGG 0.458755 7.4:-28521257 MS.gene52258:CDS
CCATGGTTGGCTTGCACTAG+TGG 0.460763 7.4:-28521925 MS.gene52258:CDS
AGAGTAGAATAACATTGGTC+TGG 0.461740 7.4:+28521531 None:intergenic
TCTAAAGCTGATCAATGGAA+TGG 0.466690 7.4:-28521264 MS.gene52258:CDS
ATGAGGATTGTTGAACTTGA+AGG 0.468030 7.4:+28521620 None:intergenic
GGTTGTACCACAATTTCAAT+GGG 0.477703 7.4:-28521154 MS.gene52258:CDS
CTACACGAATCCAAAATGAT+TGG 0.480728 7.4:+28521724 None:intergenic
CTAAAGCTGATCAATGGAAT+GGG 0.481933 7.4:-28521263 MS.gene52258:CDS
TAATCACTTGGATTTGTCAT+GGG 0.490766 7.4:+28521798 None:intergenic
TATTTCATGAAATCATTGAC+TGG 0.492434 7.4:-28521504 MS.gene52258:CDS
TTGTCAAGCACCAAACTAAG+AGG 0.503101 7.4:+28522207 None:intergenic
TAGTTTGGTGCTTGACAAGT+TGG 0.509534 7.4:-28522202 MS.gene52258:CDS
AATCATTGACTGGAGACATA+TGG 0.525440 7.4:-28521494 MS.gene52258:CDS
TACGAGACAATTTGTTTGAG+AGG 0.526510 7.4:+28522064 None:intergenic
AGAATCGAAAATGTGAAGGA+TGG 0.527327 7.4:-28521231 MS.gene52258:CDS
ATAATCACTTGGATTTGTCA+TGG 0.537229 7.4:+28521797 None:intergenic
GTTTGGGTTGTAGCCATGGT+TGG 0.537462 7.4:-28521938 MS.gene52258:intron
CGAATCCAAAATGATTGGCT+TGG 0.538749 7.4:+28521729 None:intergenic
GATCAATCCCATTGAAATTG+TGG 0.540140 7.4:+28521147 None:intergenic
TGTCATGGGGTCAGCAGACA+AGG 0.556574 7.4:+28521812 None:intergenic
TGCGGCTATCAGCAAATACC+AGG 0.564512 7.4:+28521658 None:intergenic
GACAAATCCAAGTGATTATG+TGG 0.574598 7.4:-28521793 MS.gene52258:CDS
AAGAAAGAGTAGAATAACAT+TGG 0.575599 7.4:+28521526 None:intergenic
TTTGAGAGGATCATTAGCAT+AGG 0.579338 7.4:+28522078 None:intergenic
GAGAAAATGTTTAATCGATG+AGG 0.590607 7.4:-28521466 MS.gene52258:CDS
GCTGCAACCACATAATCACT+TGG 0.591162 7.4:+28521786 None:intergenic
GTTAAGAATCGAAAATGTGA+AGG 0.593607 7.4:-28521235 MS.gene52258:CDS
AATCACTTGGATTTGTCATG+GGG 0.596697 7.4:+28521799 None:intergenic
GAGAGGATCATTAGCATAGG+TGG 0.597051 7.4:+28522081 None:intergenic
GTTGAACTTGAAGGATACAA+TGG 0.598885 7.4:+28521629 None:intergenic
TTGGTGTAGTGTGCAAGAGT+TGG 0.610851 7.4:-28522155 MS.gene52258:CDS
CCACTAGTGCAAGCCAACCA+TGG 0.620481 7.4:+28521925 None:intergenic
TTCCAATGCAGGGAAACAAG+AGG 0.623982 7.4:+28521308 None:intergenic
TCATTTAAGTCATCACAATG+AGG 0.632337 7.4:+28521603 None:intergenic
GTAGACAAGCAAAATCAAAG+AGG 0.655244 7.4:-28522044 MS.gene52258:intron
TTGGATCTGGATGTGCAAAG+TGG 0.695381 7.4:-28521417 MS.gene52258:CDS
ATTGACTGGAGACATATGGA+TGG 0.700403 7.4:-28521490 MS.gene52258:CDS
AGGATACAATGGTATCTCTG+CGG 0.749692 7.4:+28521640 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! AACATTTTATTTATCAAATA+TGG - chr7.4:28522038-28522057 MS.gene52258:intron 10.0%
!! ATATAAAACTAAAAGATGTT+TGG - chr7.4:28521437-28521456 MS.gene52258:CDS 15.0%
!! TATAAAACTAAAAGATGTTT+GGG - chr7.4:28521438-28521457 MS.gene52258:CDS 15.0%
!!! AAACATCTTTTAGTTTTATA+TGG + chr7.4:28521438-28521457 None:intergenic 15.0%
!!! ATTTTATTTATCAAATATGG+AGG - chr7.4:28522041-28522060 MS.gene52258:intron 15.0%
!! AATTAACAGACTTAATAGTT+TGG - chr7.4:28522010-28522029 MS.gene52258:intron 20.0%
!! ACCATAAAAATCATCTATTT+AGG - chr7.4:28521279-28521298 MS.gene52258:CDS 20.0%
!!! ACTGATGTTGTATTTTATAA+AGG - chr7.4:28521711-28521730 MS.gene52258:CDS 20.0%
!!! ATCTTTTAGTTTTATATGGA+AGG + chr7.4:28521434-28521453 None:intergenic 20.0%
!!! TCCTAAATAGATGATTTTTA+TGG + chr7.4:28521283-28521302 None:intergenic 20.0%
! AAGAAAGAGTAGAATAACAT+TGG + chr7.4:28521869-28521888 None:intergenic 25.0%
! TATTTCATGAAATCATTGAC+TGG - chr7.4:28521888-28521907 MS.gene52258:CDS 25.0%
! TCTCATAGTAAGTCAAATTA+GGG + chr7.4:28521815-28521834 None:intergenic 25.0%
! TTCTCATAGTAAGTCAAATT+AGG + chr7.4:28521816-28521835 None:intergenic 25.0%
!!! TAATTTCTAAAGCTGATCAA+TGG - chr7.4:28522123-28522142 MS.gene52258:CDS 25.0%
!!! TTAGTTTTATATGGAAGGAT+GGG + chr7.4:28521429-28521448 None:intergenic 25.0%
!!! TTTAGTTTTATATGGAAGGA+TGG + chr7.4:28521430-28521449 None:intergenic 25.0%
AAAAGGATTCACTAGAGTTA+TGG + chr7.4:28521505-28521524 None:intergenic 30.0%
AAGAACACATAGATCATGTT+AGG - chr7.4:28521213-28521232 MS.gene52258:CDS 30.0%
ATAATCACTTGGATTTGTCA+TGG + chr7.4:28521598-28521617 None:intergenic 30.0%
GAGAAAATGTTTAATCGATG+AGG - chr7.4:28521926-28521945 MS.gene52258:CDS 30.0%
GTTAAGAATCGAAAATGTGA+AGG - chr7.4:28522157-28522176 MS.gene52258:CDS 30.0%
TAATCACTTGGATTTGTCAT+GGG + chr7.4:28521597-28521616 None:intergenic 30.0%
TCATTTAAGTCATCACAATG+AGG + chr7.4:28521792-28521811 None:intergenic 30.0%
! CATTGGTCTGGAAAAATATA+CGG + chr7.4:28521852-28521871 None:intergenic 30.0%
! TGTTGTATTTTATAAAGGCC+TGG - chr7.4:28521716-28521735 MS.gene52258:CDS 30.0%
AAACAATTGCATCCACTTGA+AGG + chr7.4:28522216-28522235 None:intergenic 35.0%
AATCACTTGGATTTGTCATG+GGG + chr7.4:28521596-28521615 None:intergenic 35.0%
ACCTCTCGAATCTATCAAAA+AGG - chr7.4:28521554-28521573 MS.gene52258:CDS 35.0%
AGAATCGAAAATGTGAAGGA+TGG - chr7.4:28522161-28522180 MS.gene52258:CDS 35.0%
AGAGTAGAATAACATTGGTC+TGG + chr7.4:28521864-28521883 None:intergenic 35.0%
ATGAGGATTGTTGAACTTGA+AGG + chr7.4:28521775-28521794 None:intergenic 35.0%
CACATAGATCATGTTAGGTT+TGG - chr7.4:28521218-28521237 MS.gene52258:CDS 35.0%
CGAACTTCACGTTTACAAAT+TGG - chr7.4:28521956-28521975 MS.gene52258:intron 35.0%
CGAGCTTTACATCTCTTAAA+AGG + chr7.4:28521522-28521541 None:intergenic 35.0%
CTAAAGCTGATCAATGGAAT+GGG - chr7.4:28522129-28522148 MS.gene52258:CDS 35.0%
CTACACGAATCCAAAATGAT+TGG + chr7.4:28521671-28521690 None:intergenic 35.0%
CTTTACCAATTTCCTTCAAG+TGG - chr7.4:28522201-28522220 MS.gene52258:CDS 35.0%
GACAAATCCAAGTGATTATG+TGG - chr7.4:28521599-28521618 MS.gene52258:CDS 35.0%
GGTTGTACCACAATTTCAAT+GGG - chr7.4:28522238-28522257 MS.gene52258:CDS 35.0%
GTAGACAAGCAAAATCAAAG+AGG - chr7.4:28521348-28521367 MS.gene52258:CDS 35.0%
GTTGAACTTGAAGGATACAA+TGG + chr7.4:28521766-28521785 None:intergenic 35.0%
TCACGTTTACAAATTGGATC+TGG - chr7.4:28521962-28521981 MS.gene52258:intron 35.0%
TTTGAGAGGATCATTAGCAT+AGG + chr7.4:28521317-28521336 None:intergenic 35.0%
! AAAGACCAAGCCAATCATTT+TGG - chr7.4:28521658-28521677 MS.gene52258:CDS 35.0%
! AATCATTGACTGGAGACATA+TGG - chr7.4:28521898-28521917 MS.gene52258:CDS 35.0%
! ACCTTTTTGATAGATTCGAG+AGG + chr7.4:28521558-28521577 None:intergenic 35.0%
! AGAAGCATATCCTCTTAGTT+TGG - chr7.4:28521175-28521194 MS.gene52258:CDS 35.0%
! CAAGTGGATGCAATTGTTTT+GGG - chr7.4:28522217-28522236 MS.gene52258:CDS 35.0%
! TACGAGACAATTTGTTTGAG+AGG + chr7.4:28521331-28521350 None:intergenic 35.0%
! TCAAGTGGATGCAATTGTTT+TGG - chr7.4:28522216-28522235 MS.gene52258:CDS 35.0%
! TCTAAAGCTGATCAATGGAA+TGG - chr7.4:28522128-28522147 MS.gene52258:CDS 35.0%
! TTTTTGATAGATTCGAGAGG+TGG + chr7.4:28521555-28521574 None:intergenic 35.0%
AGGATACAATGGTATCTCTG+CGG + chr7.4:28521755-28521774 None:intergenic 40.0%
ATGTGGTTGCAGCAATTTAC+AGG - chr7.4:28521616-28521635 MS.gene52258:CDS 40.0%
ATTGACTGGAGACATATGGA+TGG - chr7.4:28521902-28521921 MS.gene52258:CDS 40.0%
GGGTTGTACCACAATTTCAA+TGG - chr7.4:28522237-28522256 MS.gene52258:CDS 40.0%
GTTGCAGCAATTTACAGGTT+TGG - chr7.4:28521621-28521640 MS.gene52258:CDS 40.0%
TGCATCCACTTGAAGGAAAT+TGG + chr7.4:28522209-28522228 None:intergenic 40.0%
TTGTCAAGCACCAAACTAAG+AGG + chr7.4:28521188-28521207 None:intergenic 40.0%
TTGTTTCCCTGCATTGGAAA+AGG - chr7.4:28522088-28522107 MS.gene52258:CDS 40.0%
! ATCGAATCCTTTTCCAATGC+AGG + chr7.4:28522098-28522117 None:intergenic 40.0%
! CGAATCCAAAATGATTGGCT+TGG + chr7.4:28521666-28521685 None:intergenic 40.0%
! TAGGGTACTCTTTCTCACTT+AGG + chr7.4:28521397-28521416 None:intergenic 40.0%
! TCGAATCCTTTTCCAATGCA+GGG + chr7.4:28522097-28522116 None:intergenic 40.0%
!! CTGATCAATGGAATGGGTTA+GGG - chr7.4:28522135-28522154 MS.gene52258:CDS 40.0%
!! TAGTTTGGTGCTTGACAAGT+TGG - chr7.4:28521190-28521209 MS.gene52258:CDS 40.0%
AAGGATGGGATAACCGACTA+GGG + chr7.4:28521415-28521434 None:intergenic 45.0%
GAGAGGATCATTAGCATAGG+TGG + chr7.4:28521314-28521333 None:intergenic 45.0%
GCTGCAACCACATAATCACT+TGG + chr7.4:28521609-28521628 None:intergenic 45.0%
TTCCAATGCAGGGAAACAAG+AGG + chr7.4:28522087-28522106 None:intergenic 45.0%
TTGGATCTGGATGTGCAAAG+TGG - chr7.4:28521975-28521994 MS.gene52258:intron 45.0%
TTGGTGTAGTGTGCAAGAGT+TGG - chr7.4:28521237-28521256 MS.gene52258:CDS 45.0%
! GCTGATCAATGGAATGGGTT+AGG - chr7.4:28522134-28522153 MS.gene52258:CDS 45.0%
!! AGATGTTTGGGTTGTAGCCA+TGG - chr7.4:28521450-28521469 MS.gene52258:CDS 45.0%
!! GTGAGAAAGAGTACCCTAGT+CGG - chr7.4:28521399-28521418 MS.gene52258:CDS 45.0%
GAAGGATGGGATAACCGACT+AGG + chr7.4:28521416-28521435 None:intergenic 50.0%
TGCGGCTATCAGCAAATACC+AGG + chr7.4:28521737-28521756 None:intergenic 50.0%
! AGCCTCTTGTTTCCCTGCAT+TGG - chr7.4:28522082-28522101 MS.gene52258:CDS 50.0%
!! GTTTGGGTTGTAGCCATGGT+TGG - chr7.4:28521454-28521473 MS.gene52258:CDS 50.0%
CCACTAGTGCAAGCCAACCA+TGG + chr7.4:28521470-28521489 None:intergenic 55.0%
TGTCATGGGGTCAGCAGACA+AGG + chr7.4:28521583-28521602 None:intergenic 55.0%
!! CCATGGTTGGCTTGCACTAG+TGG - chr7.4:28521467-28521486 MS.gene52258:CDS 55.0%


Chromosome Type Strat End Strand Name
chr7.4 gene 28521149 28522265 28521149 ID=MS.gene52258
chr7.4 mRNA 28521149 28522265 28521149 ID=MS.gene52258.t1;Parent=MS.gene52258
chr7.4 exon 28522045 28522265 28522045 ID=MS.gene52258.t1.exon1;Parent=MS.gene52258.t1
chr7.4 CDS 28522045 28522265 28522045 ID=cds.MS.gene52258.t1;Parent=MS.gene52258.t1
chr7.4 exon 28521149 28521947 28521149 ID=MS.gene52258.t1.exon2;Parent=MS.gene52258.t1
chr7.4 CDS 28521149 28521947 28521149 ID=cds.MS.gene52258.t1;Parent=MS.gene52258.t1
Gene Sequence

>MS.gene52258

ATGACTAAGGTTGATTGGGCAAATTTAGAAGCATATCCTCTTAGTTTGGTGCTTGACAAGTTGGAAGAACACATAGATCATGTTAGGTTTGGTGTAGTGTGCAAGAGTTGGCTATCAATTGCAAAGCTTAACCATAAAAATCATCTATTTAGGATTAATGTACCACCTATGCTAATGATCCTCTCAAACAAATTGTCTCGTAGACAAGCAAAATCAAAGAGGTATGAGAGATTGTTATATAGTATCCTAAGTGAGAAAGAGTACCCTAGTCGGTTATCCCATCCTTCCATATAAAACTAAAAGATGTTTGGGTTGTAGCCATGGTTGGCTTGCACTAGTGGATAATAACAATGCCATAACTCTAGTGAATCCTTTTAAGAGATGTAAAGCTCGCATTAGTCTGCCACCTCTCGAATCTATCAAAAAGGTTACCTTGTCTGCTGACCCCATGACAAATCCAAGTGATTATGTGGTTGCAGCAATTTACAGGTTTGGTTATCTCGCTTTCAAAAGACCAAGCCAATCATTTTGGATTCGTGTAGACAGAAATAGATTTTATTTCACTGATGTTGTATTTTATAAAGGCCTGGTATTTGCTGATAGCCGCAGAGATACCATTGTATCCTTCAAGTTCAACAATCCTCATTGTGATGACTTAAATGACCCTAATTTGACTTACTATGAGAAGATATCTAGTACTCCGTATATTTTTCCAGACCAATGTTATTCTACTCTTTCTTATTTCATGAAATCATTGACTGGAGACATATGGATGGTGAGAAAATGTTTAATCGATGAGGATTCATTCGAACTTCACGTTTACAAATTGGATCTGGATGTGCAAAGTGGAAGACTTGAACAAATTAACAGACTTAATAGTTTGGAAGACAACATTTTATTTATCAAATATGGAGGTGATTCACTTTCAGTGTCAGCCTCTTGTTTCCCTGCATTGGAAAAGGATTCGATTTATTTAATTTCTAAAGCTGATCAATGGAATGGGTTAGGGTTAAGAATCGAAAATGTGAAGGATGGAAGTTTTCACATTCGATCTTTACCAATTTCCTTCAAGTGGATGCAATTGTTTTGGGTTGTACCACAATTTCAATGGGATTGA
Protein sequence

>MS.gene52258.t1

MTKVDWANLEAYPLSLVLDKLEEHIDHVRFGVVCKSWLSIAKLNHKNHLFRINVPPMLMILSNKLSRRQAKSKSHGWLALVDNNNAITLVNPFKRCKARISLPPLESIKKVTLSADPMTNPSDYVVAAIYRFGYLAFKRPSQSFWIRVDRNRFYFTDVVFYKGLVFADSRRDTIVSFKFNNPHCDDLNDPNLTYYEKISSTPYIFPDQCYSTLSYFMKSLTGDIWMVRKCLIDEDSFELHVYKLDLDVQSGRLEQINRLNSLEDNILFIKYGGDSLSVSASCFPALEKDSIYLISKADQWNGLGLRIENVKDGSFHIRSLPISFKWMQLFWVVPQFQWD