AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene86857

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene86857.t1 MTR_5g021930 90.947 243 12 3 1 237 22 260 8.07e-163 452
MS.gene86857.t1 MTR_4g084550 62.687 67 24 1 5 71 60 125 4.20e-25 97.8
MS.gene86857.t1 MTR_8g107210 67.188 64 20 1 8 71 95 157 4.91e-24 98.6
MS.gene86857.t1 MTR_5g081990 58.108 74 27 2 9 79 33 105 5.80e-24 94.7
MS.gene86857.t1 MTR_4g063735 65.079 63 21 1 9 71 25 86 1.98e-22 92.8
MS.gene86857.t1 MTR_7g060630 64.062 64 22 1 8 71 7 69 2.41e-22 91.3
MS.gene86857.t1 MTR_1g019130 60.938 64 24 1 8 71 89 151 1.89e-21 89.7
MS.gene86857.t1 MTR_1g019130 60.938 64 24 1 8 71 89 151 2.05e-21 89.4
MS.gene86857.t1 MTR_8g095580 74.468 47 12 0 25 71 97 143 3.71e-18 79.0
MS.gene86857.t1 MTR_3g088485 72.340 47 13 0 25 71 95 141 5.22e-18 78.6
MS.gene86857.t1 MTR_7g025010 44.118 68 37 1 5 72 43 109 3.37e-14 71.6
MS.gene86857.t1 MTR_2g015000 43.478 69 38 1 3 71 49 116 8.34e-14 70.5
MS.gene86857.t1 MTR_4g088070 43.750 64 35 1 7 70 27 89 2.40e-13 68.9
MS.gene86857.t1 MTR_7g066060 84.848 33 5 0 54 86 465 497 2.28e-12 66.2
MS.gene86857.t1 MTR_4g088080 42.188 64 36 1 7 70 38 100 1.51e-11 63.2
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene86857.t1 AT2G17950 40.000 260 102 11 4 232 33 269 4.48e-46 155
MS.gene86857.t1 AT3G18010 67.188 64 20 1 8 71 75 137 3.88e-24 99.0
MS.gene86857.t1 AT5G59340 65.152 66 22 1 6 71 11 75 5.95e-24 96.7
MS.gene86857.t1 AT5G05770 60.870 69 26 1 9 77 29 96 8.82e-23 90.1
MS.gene86857.t1 AT3G11260 63.492 63 22 1 9 71 24 85 1.03e-22 91.7
MS.gene86857.t1 AT2G28610 62.500 64 23 1 8 71 7 69 1.23e-21 90.1
MS.gene86857.t1 AT1G46480 60.938 64 24 1 8 71 89 151 1.44e-21 89.0
MS.gene86857.t1 AT1G46480 60.938 64 24 1 8 71 89 151 8.39e-21 88.2
MS.gene86857.t1 AT2G01500 64.286 56 19 1 9 64 61 115 3.69e-19 84.3
MS.gene86857.t1 AT2G33880 44.286 70 38 1 3 72 49 117 2.12e-14 72.0
MS.gene86857.t1 AT5G45980 49.231 65 32 1 7 71 53 116 2.15e-14 71.6
MS.gene86857.t1 AT2G33880 44.286 70 38 1 3 72 49 117 2.20e-14 72.0

Find 44 sgRNAs with CRISPR-Local

Find 69 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CCATCCTAAGTGAGGGTTTA+TGG 0.166513 6.2:-52835245 None:intergenic
AAAGGGAGGGTTTCAATTTC+AGG 0.186091 6.2:-52835379 None:intergenic
ATGTTCTTCTGCTGATAATA+TGG 0.223760 6.2:+52834695 MS.gene86857:CDS
CTATTATTGCTGCTGCTAAT+TGG 0.230551 6.2:+52834473 MS.gene86857:CDS
CTAGAGAAAGACAGAATAAA+AGG 0.267042 6.2:+52834395 MS.gene86857:CDS
TTAGCATAAGCTGAAGAATA+TGG 0.320661 6.2:-52835286 None:intergenic
TCTTCCATGATTTCTTCATT+AGG 0.332083 6.2:-52835328 None:intergenic
TATGAACAAGGACAAGAAAA+TGG 0.342235 6.2:+52835352 MS.gene86857:CDS
TCACCATGCATAGGGAATAA+AGG 0.377353 6.2:-52835397 None:intergenic
CTCTGAATCTGTTCAACACT+TGG 0.394597 6.2:-52834298 None:intergenic
ATTCTTATCTGATCTGTTGT+TGG 0.397466 6.2:-52834238 None:intergenic
TTTCCATATAGTTACCAATC+TGG 0.403343 6.2:-52834728 None:intergenic
GCAATAATAGTATTGTTGTT+TGG 0.407919 6.2:-52834460 None:intergenic
CACCATGCATAGGGAATAAA+GGG 0.416329 6.2:-52835396 None:intergenic
TCTGCTAGGTTAAGACAGTA+TGG 0.419676 6.2:+52834325 MS.gene86857:CDS
TGATGTTGTTCATGATGATC+AGG 0.428226 6.2:-52834499 None:intergenic
AGGCCAGATTGGTAACTATA+TGG 0.432080 6.2:+52834725 MS.gene86857:CDS
GTTTGGTGCTCTTTGAATGA+TGG 0.443486 6.2:-52834443 None:intergenic
TTTGGTGCTCTTTGAATGAT+GGG 0.453249 6.2:-52834442 None:intergenic
AAGACCTAATGAAGAAATCA+TGG 0.463541 6.2:+52835324 MS.gene86857:CDS
AAGGATCTTTACTACAACAA+TGG 0.474991 6.2:+52834265 MS.gene86857:CDS
ATGGTTACTGCAGGCCAGAT+TGG 0.481591 6.2:+52834714 MS.gene86857:CDS
AACCCTCACTTAGGATGGAT+TGG 0.494244 6.2:+52835250 MS.gene86857:CDS
AGTTAGATGAGTTTCATTTG+TGG 0.497892 6.2:-52835444 None:intergenic
AGACAGTATGGTAAGATTGA+AGG 0.507784 6.2:+52834337 MS.gene86857:CDS
GGATGTAGCAGCAGTCAAGT+TGG 0.519817 6.2:+52835217 MS.gene86857:CDS
TAGGAGTGCACAATATCAGC+TGG 0.529304 6.2:+52835196 MS.gene86857:intron
CCATAAACCCTCACTTAGGA+TGG 0.538741 6.2:+52835245 MS.gene86857:CDS
GAATGTCTTCACCATGCATA+GGG 0.538890 6.2:-52835405 None:intergenic
CTCCCTTTATTCCCTATGCA+TGG 0.543247 6.2:+52835394 MS.gene86857:CDS
AAAATTGTAATTAGTATGGT+TGG 0.552762 6.2:-52834548 None:intergenic
ATGCATGGTGAAGACATTCA+TGG 0.571277 6.2:+52835409 MS.gene86857:CDS
TGAATGTCTTCACCATGCAT+AGG 0.574747 6.2:-52835406 None:intergenic
GCTGATAATATGGTTACTGC+AGG 0.581156 6.2:+52834705 MS.gene86857:CDS
AGTACCATAAACCCTCACTT+AGG 0.599826 6.2:+52835241 MS.gene86857:CDS
AGATTCAGAGAATCTCTGCT+AGG 0.608727 6.2:+52834311 MS.gene86857:CDS
GACCAATCCATCCTAAGTGA+GGG 0.618647 6.2:-52835252 None:intergenic
TGACCAATCCATCCTAAGTG+AGG 0.637357 6.2:-52835253 None:intergenic
CATGCATAGGGAATAAAGGG+AGG 0.658861 6.2:-52835393 None:intergenic
ATGCATAGGGAATAAAGGGA+GGG 0.659824 6.2:-52835392 None:intergenic
ATCATGGAAGAATATGAACA+AGG 0.690834 6.2:+52835340 MS.gene86857:CDS
GCAGCAGACAAAGTAGAACA+AGG 0.695509 6.2:+52834209 MS.gene86857:CDS
GCAGACAAAGTAGAACAAGG+TGG 0.752615 6.2:+52834212 MS.gene86857:CDS
CATGGTGAAGACATTCATGG+TGG 0.793972 6.2:+52835412 MS.gene86857:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAGAAAAAAAAGTAACAAAT+TGG + chr6.2:52834605-52834624 MS.gene86857:intron 15.0%
!! ATGAAAAATTGTAATTAGTA+TGG - chr6.2:52834555-52834574 None:intergenic 15.0%
!!! ATTAAAACTCTACTTTTTTT+AGG + chr6.2:52835094-52835113 MS.gene86857:intron 15.0%
!!! TCTTTTATTTAATAACCAAA+AGG + chr6.2:52834910-52834929 MS.gene86857:intron 15.0%
!!! TTTTTAATTCTTAGTTTATG+AGG - chr6.2:52834970-52834989 None:intergenic 15.0%
!!! TTTTTTTTTTTCTTCTTCTT+AGG + chr6.2:52835177-52835196 MS.gene86857:intron 15.0%
!! AAAATTGTAATTAGTATGGT+TGG - chr6.2:52834551-52834570 None:intergenic 20.0%
!! ACATACACAAGAATTAATAT+AGG - chr6.2:52834651-52834670 None:intergenic 20.0%
!! ATTCTTGTGTATGTTTATTT+AGG + chr6.2:52834657-52834676 MS.gene86857:intron 20.0%
!! TTCTTGTGTATGTTTATTTA+GGG + chr6.2:52834658-52834677 MS.gene86857:intron 20.0%
!!! TTCTTATTATGGAAATTTTC+TGG - chr6.2:52834941-52834960 None:intergenic 20.0%
!!! TTTTTTTTCTTGTCTCAAAA+AGG - chr6.2:52834596-52834615 None:intergenic 20.0%
! TTTCTATATCAAATCTCACA+TGG - chr6.2:52834861-52834880 None:intergenic 25.0%
!! AATTACAATTTTTCATCTGC+TGG + chr6.2:52834559-52834578 MS.gene86857:CDS 25.0%
!! ACTATATGGAAAAGAGTTTT+AGG + chr6.2:52834739-52834758 MS.gene86857:CDS 25.0%
!! AGATCAGATAAGAATTTTGA+AGG + chr6.2:52834246-52834265 MS.gene86857:CDS 25.0%
!! CTATATGGAAAAGAGTTTTA+GGG + chr6.2:52834740-52834759 MS.gene86857:CDS 25.0%
!! GCAATAATAGTATTGTTGTT+TGG - chr6.2:52834463-52834482 None:intergenic 25.0%
AAGACCTAATGAAGAAATCA+TGG + chr6.2:52835324-52835343 MS.gene86857:CDS 30.0%
AAGGATCTTTACTACAACAA+TGG + chr6.2:52834265-52834284 MS.gene86857:CDS 30.0%
ATCATGGAAGAATATGAACA+AGG + chr6.2:52835340-52835359 MS.gene86857:CDS 30.0%
ATGTTCTTCTGCTGATAATA+TGG + chr6.2:52834695-52834714 MS.gene86857:CDS 30.0%
ATTCTTATCTGATCTGTTGT+TGG - chr6.2:52834241-52834260 None:intergenic 30.0%
CTAGAGAAAGACAGAATAAA+AGG + chr6.2:52834395-52834414 MS.gene86857:CDS 30.0%
TATGAACAAGGACAAGAAAA+TGG + chr6.2:52835352-52835371 MS.gene86857:CDS 30.0%
TCTTCCATGATTTCTTCATT+AGG - chr6.2:52835331-52835350 None:intergenic 30.0%
TGAGGTTGTTCTTCTTATTA+TGG - chr6.2:52834952-52834971 None:intergenic 30.0%
TTAGCATAAGCTGAAGAATA+TGG - chr6.2:52835289-52835308 None:intergenic 30.0%
TTTCCATATAGTTACCAATC+TGG - chr6.2:52834731-52834750 None:intergenic 30.0%
! AAGGCAAAAATGTCTTTTAC+TGG + chr6.2:52834356-52834375 MS.gene86857:CDS 30.0%
! AATTTTCTGGATTGTCCTTT+TGG - chr6.2:52834928-52834947 None:intergenic 30.0%
!! ATGAAAACTATGATGGATCA+TGG - chr6.2:52834834-52834853 None:intergenic 30.0%
AGACAGTATGGTAAGATTGA+AGG + chr6.2:52834337-52834356 MS.gene86857:CDS 35.0%
CTATTATTGCTGCTGCTAAT+TGG + chr6.2:52834473-52834492 MS.gene86857:CDS 35.0%
TAGTGAAACTGAACTCTTGT+TGG - chr6.2:52835039-52835058 None:intergenic 35.0%
TGATGTTGTTCATGATGATC+AGG - chr6.2:52834502-52834521 None:intergenic 35.0%
TGGATGCATGAAAACTATGA+TGG - chr6.2:52834841-52834860 None:intergenic 35.0%
TGGATTGAATGCATTGCAAA+GGG - chr6.2:52834814-52834833 None:intergenic 35.0%
! ATGGATTGAATGCATTGCAA+AGG - chr6.2:52834815-52834834 None:intergenic 35.0%
!! TTTGGTGCTCTTTGAATGAT+GGG - chr6.2:52834445-52834464 None:intergenic 35.0%
AAAGGGAGGGTTTCAATTTC+AGG - chr6.2:52835382-52835401 None:intergenic 40.0%
AGATTCAGAGAATCTCTGCT+AGG + chr6.2:52834311-52834330 MS.gene86857:CDS 40.0%
AGTACCATAAACCCTCACTT+AGG + chr6.2:52835241-52835260 MS.gene86857:CDS 40.0%
ATGCATAGGGAATAAAGGGA+GGG - chr6.2:52835395-52835414 None:intergenic 40.0%
ATGCATGGTGAAGACATTCA+TGG + chr6.2:52835409-52835428 MS.gene86857:CDS 40.0%
CACCATGCATAGGGAATAAA+GGG - chr6.2:52835399-52835418 None:intergenic 40.0%
CTCTGAATCTGTTCAACACT+TGG - chr6.2:52834301-52834320 None:intergenic 40.0%
GAATGTCTTCACCATGCATA+GGG - chr6.2:52835408-52835427 None:intergenic 40.0%
GCTGATAATATGGTTACTGC+AGG + chr6.2:52834705-52834724 MS.gene86857:CDS 40.0%
TCACCATGCATAGGGAATAA+AGG - chr6.2:52835400-52835419 None:intergenic 40.0%
TCTGCTAGGTTAAGACAGTA+TGG + chr6.2:52834325-52834344 MS.gene86857:CDS 40.0%
TGAAACTGAACTCTTGTTGG+TGG - chr6.2:52835036-52835055 None:intergenic 40.0%
TGAATGTCTTCACCATGCAT+AGG - chr6.2:52835409-52835428 None:intergenic 40.0%
! AGGCCAGATTGGTAACTATA+TGG + chr6.2:52834725-52834744 MS.gene86857:CDS 40.0%
!! GTTTGGTGCTCTTTGAATGA+TGG - chr6.2:52834446-52834465 None:intergenic 40.0%
AACCCTCACTTAGGATGGAT+TGG + chr6.2:52835250-52835269 MS.gene86857:CDS 45.0%
CATGCATAGGGAATAAAGGG+AGG - chr6.2:52835396-52835415 None:intergenic 45.0%
CATGGTGAAGACATTCATGG+TGG + chr6.2:52835412-52835431 MS.gene86857:CDS 45.0%
CCATAAACCCTCACTTAGGA+TGG + chr6.2:52835245-52835264 MS.gene86857:CDS 45.0%
CCATCCTAAGTGAGGGTTTA+TGG - chr6.2:52835248-52835267 None:intergenic 45.0%
CTCCCTTTATTCCCTATGCA+TGG + chr6.2:52835394-52835413 MS.gene86857:CDS 45.0%
GACCAATCCATCCTAAGTGA+GGG - chr6.2:52835255-52835274 None:intergenic 45.0%
GCAGACAAAGTAGAACAAGG+TGG + chr6.2:52834212-52834231 MS.gene86857:CDS 45.0%
GCAGCAGACAAAGTAGAACA+AGG + chr6.2:52834209-52834228 MS.gene86857:CDS 45.0%
TGACCAATCCATCCTAAGTG+AGG - chr6.2:52835256-52835275 None:intergenic 45.0%
! TAGGAGTGCACAATATCAGC+TGG + chr6.2:52835196-52835215 MS.gene86857:intron 45.0%
!! AAGAAAAAAAAAAATTAAAA+TGG - chr6.2:52835171-52835190 None:intergenic 5.0%
ATGGTTACTGCAGGCCAGAT+TGG + chr6.2:52834714-52834733 MS.gene86857:CDS 50.0%
GGATGTAGCAGCAGTCAAGT+TGG + chr6.2:52835217-52835236 MS.gene86857:CDS 50.0%


Chromosome Type Strat End Strand Name
chr6.2 gene 52834205 52835453 52834205 ID=MS.gene86857
chr6.2 mRNA 52834205 52835453 52834205 ID=MS.gene86857.t1;Parent=MS.gene86857
chr6.2 exon 52834205 52834580 52834205 ID=MS.gene86857.t1.exon1;Parent=MS.gene86857.t1
chr6.2 CDS 52834205 52834580 52834205 ID=cds.MS.gene86857.t1;Parent=MS.gene86857.t1
chr6.2 exon 52834679 52834761 52834679 ID=MS.gene86857.t1.exon2;Parent=MS.gene86857.t1
chr6.2 CDS 52834679 52834761 52834679 ID=cds.MS.gene86857.t1;Parent=MS.gene86857.t1
chr6.2 exon 52835199 52835453 52835199 ID=MS.gene86857.t1.exon3;Parent=MS.gene86857.t1
chr6.2 CDS 52835199 52835453 52835199 ID=cds.MS.gene86857.t1;Parent=MS.gene86857.t1
Gene Sequence

>MS.gene86857

ATGGGCAGCAGACAAAGTAGAACAAGGTGGACACCAACAACAGATCAGATAAGAATTTTGAAGGATCTTTACTACAACAATGGAATTAGATCACCAAGTGTTGAACAGATTCAGAGAATCTCTGCTAGGTTAAGACAGTATGGTAAGATTGAAGGCAAAAATGTCTTTTACTGGTTTCAAAATCATAAAGCTAGAGAAAGACAGAATAAAAGGTTCACTTCTGATGTTAATGTTGTTCCCATCATTCAAAGAGCACCAAACAACAATACTATTATTGCTGCTGCTAATTGGAAACCTGATCATCATGAACAACATCAACAACAACAAAACATTAATGTTCACACCAACCATACTAATTACAATTTTTCATCTGCTGGTATATTTTGTTCCTTTTTGAGACAAGAAAAAAAAGTAACAAATTGGTTAAATATTATATACTATATCCTATATTAATTCTTGTGTATGTTTATTTAGGGCTTTCTTCTGCTTCATGTTCTTCTGCTGATAATATGGTTACTGCAGGCCAGATTGGTAACTATATGGAAAAGAGTTTTAGGGTAAGTTATTGACATGAAAAACTTTATACTATTATTACAAGTTTTCTTTCCCTTTGCAATGCATTCAATCCATGATCCATCATAGTTTTCATGCATCCATGTGAGATTTGATATAGAAAACTACACAAGCAAGTGATCATAGTAATGATCTTTTATTTAATAACCAAAAGGACAATCCAGAAAATTTCCATAATAAGAAGAACAACCTCATAAACTAAGAATTAAAAATAAAACTTTAATTTATGAAGTGAAAGTATCACTTGTATTGAATCCACCAACAAGAGTTCAGTTTCACTAGCTCAGCTCATAACTAGTTAATGCTTTTATAGATTATTAAAACTCTACTTTTTTTAGGTATAGCTTTAGACATGTCACATATATTTATTTTCTTCTGCAAAATGTTGAACCATTTTAATTTTTTTTTTTCTTCTTCTTAGGAGTGCACAATATCAGCTGGATGTAGCAGCAGTCAAGTTGGAAGTACCATAAACCCTCACTTAGGATGGATTGGTCATCATGTTGATCCATATTCTTCAGCTTATGCTAACTTATTTGAAAAAATAAGACCTAATGAAGAAATCATGGAAGAATATGAACAAGGACAAGAAAATGGTTCACCTGAAATTGAAACCCTCCCTTTATTCCCTATGCATGGTGAAGACATTCATGGTGGCTATTGTAACCACAAATGA
Protein sequence

>MS.gene86857.t1

MGSRQSRTRWTPTTDQIRILKDLYYNNGIRSPSVEQIQRISARLRQYGKIEGKNVFYWFQNHKARERQNKRFTSDVNVVPIIQRAPNNNTIIAAANWKPDHHEQHQQQQNINVHTNHTNYNFSSAGLSSASCSSADNMVTAGQIGNYMEKSFRECTISAGCSSSQVGSTINPHLGWIGHHVDPYSSAYANLFEKIRPNEEIMEEYEQGQENGSPEIETLPLFPMHGEDIHGGYCNHK