AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene03617

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene03617.t1 MTR_3g438070 98.913 92 1 0 1 92 1 92 2.06e-59 176
MS.gene03617.t1 MTR_7g010120 71.277 94 24 2 1 92 1 93 3.71e-37 120
MS.gene03617.t1 MTR_5g039180 71.429 77 20 1 17 91 17 93 1.32e-32 108
MS.gene03617.t1 MTR_6g011670 71.795 78 20 1 17 92 15 92 7.32e-32 107
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene03617.t1 AT3G47710 72.043 93 24 2 1 92 1 92 1.50e-38 124
MS.gene03617.t1 AT1G74500 76.623 77 17 1 17 92 17 93 3.29e-35 115
MS.gene03617.t1 AT1G26945 78.378 74 14 1 19 90 19 92 5.43e-34 112
MS.gene03617.t1 AT3G28857 67.021 94 26 3 1 91 1 92 1.60e-33 111
MS.gene03617.t1 AT5G39860 70.513 78 20 2 17 91 15 92 1.65e-30 103
MS.gene03617.t1 AT5G15160 65.333 75 23 2 19 90 18 92 1.28e-26 94.0

Find 18 sgRNAs with CRISPR-Local

Find 69 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTCAGCTTCAAGGGTGTTGC+AGG 0.328305 3.4:-33688315 MS.gene03617:CDS
TGAGCGTTTGTCTGAGCTAT+TGG 0.392203 3.4:-33688243 MS.gene03617:CDS
TATATCAGGTTTCAGCTTCA+AGG 0.403696 3.4:-33688325 MS.gene03617:intron
ACTATATTAGAAACTTGAAC+AGG 0.414262 3.4:-33688283 MS.gene03617:CDS
GAGCTCCTATTGCGAATCTC+AGG 0.466230 3.4:+33689191 None:intergenic
TTCTTCCTGAGATTCGCAAT+AGG 0.484861 3.4:-33689196 MS.gene03617:CDS
AGGAAGAAGTTGCTGCAGCT+TGG 0.493730 3.4:+33689211 None:intergenic
ATATCAGGTTTCAGCTTCAA+GGG 0.502020 3.4:-33688324 MS.gene03617:intron
CTAGCAGGAGGTCGCGGTCA+CGG 0.548676 3.4:-33689286 MS.gene03617:CDS
GCTCAGACAAACGCTCACTT+AGG 0.559789 3.4:+33688249 None:intergenic
GCAGCTTGGAGACAAGATCA+TGG 0.563717 3.4:+33689225 None:intergenic
AGATGTCTAGCAGGAGGTCG+CGG 0.564343 3.4:-33689292 MS.gene03617:CDS
TCGCAATAGGAGCTCTGACA+AGG 0.593557 3.4:-33689183 MS.gene03617:intron
GTCTGAGCTATTGGCTACAA+CGG 0.609233 3.4:-33688234 MS.gene03617:CDS
AAGATCATGGATCTGATCGT+CGG 0.643584 3.4:+33689238 None:intergenic
TTATAAAGATGTCTAGCAGG+AGG 0.648667 3.4:-33689298 None:intergenic
CTATATTAGAAACTTGAACA+GGG 0.660572 3.4:-33688282 MS.gene03617:CDS
CACGGCAAACAAGTAGCTCG+AGG 0.663330 3.4:-33689268 MS.gene03617:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAAAAAAAAAAAAACTTGAA+AGG - chr3.4:33688865-33688884 MS.gene03617:intron 10.0%
!! TGTATTAAAAATATAGTATA+TGG + chr3.4:33688544-33688563 None:intergenic 10.0%
!!! ATGACTTTTATAAAAAATAA+TGG + chr3.4:33688450-33688469 None:intergenic 10.0%
!!! TTATTTTTTATAAAAGTCAT+TGG - chr3.4:33688450-33688469 MS.gene03617:intron 10.0%
!!! AAATTGAATTTTACTATATC+AGG - chr3.4:33689141-33689160 MS.gene03617:intron 15.0%
!!! CAAGTTTTTTTTTTTTTTCT+TGG + chr3.4:33688863-33688882 None:intergenic 15.0%
! ACTATATTAGAAACTTGAAC+AGG - chr3.4:33689197-33689216 MS.gene03617:CDS 25.0%
! ATATAGTATATGGTAGTTAC+AGG + chr3.4:33688534-33688553 None:intergenic 25.0%
! ATTTAAACCAACTTAATCCT+AGG - chr3.4:33688955-33688974 MS.gene03617:intron 25.0%
! CAAGAAAAAGAAACAACAAT+AGG - chr3.4:33688991-33689010 MS.gene03617:intron 25.0%
! CTAGGAAACAAATAATATGT+AGG + chr3.4:33688329-33688348 None:intergenic 25.0%
! CTATATTAGAAACTTGAACA+GGG - chr3.4:33689198-33689217 MS.gene03617:CDS 25.0%
!!! AGAAGAGATTAGTTTTATAG+CGG - chr3.4:33688565-33688584 MS.gene03617:intron 25.0%
ACATCAACAATTCTTGTAGA+TGG + chr3.4:33689067-33689086 None:intergenic 30.0%
ACCATACTTATTCACCTTTA+AGG - chr3.4:33688814-33688833 MS.gene03617:intron 30.0%
ACCTTAAAGGTGAATAAGTA+TGG + chr3.4:33688818-33688837 None:intergenic 30.0%
CATCAACAATTCTTGTAGAT+GGG + chr3.4:33689066-33689085 None:intergenic 30.0%
GATAATGCATACTATATGCA+GGG - chr3.4:33688770-33688789 MS.gene03617:intron 30.0%
! ACACTAGAGAAAGTATAAGA+GGG - chr3.4:33688931-33688950 MS.gene03617:intron 30.0%
! TACACTAGAGAAAGTATAAG+AGG - chr3.4:33688930-33688949 MS.gene03617:intron 30.0%
!! CTAGTCTTTTGATTAAGACT+AGG + chr3.4:33688347-33688366 None:intergenic 30.0%
AATAGGCCTAACAAATACGA+GGG - chr3.4:33689008-33689027 MS.gene03617:intron 35.0%
ATATCAGGTTTCAGCTTCAA+GGG - chr3.4:33689156-33689175 MS.gene03617:intron 35.0%
GAGATACCCTATTAATCTAC+CGG - chr3.4:33688609-33688628 MS.gene03617:intron 35.0%
GAGCTTAGTTCATTTGGTAA+GGG - chr3.4:33688748-33688767 MS.gene03617:intron 35.0%
GGATAATGCATACTATATGC+AGG - chr3.4:33688769-33688788 MS.gene03617:intron 35.0%
TATATCAGGTTTCAGCTTCA+AGG - chr3.4:33689155-33689174 MS.gene03617:intron 35.0%
TCTTGTAGATGGGAAAAAAC+TGG + chr3.4:33689056-33689075 None:intergenic 35.0%
TGAGCTTAGTTCATTTGGTA+AGG - chr3.4:33688747-33688766 MS.gene03617:intron 35.0%
TTAATCCCCTCGTATTTGTT+AGG + chr3.4:33689017-33689036 None:intergenic 35.0%
! TTTCTTGGTCAATTAGCCTA+GGG + chr3.4:33688848-33688867 None:intergenic 35.0%
!! TCTTTTTCTTGTTATGTCCC+TGG + chr3.4:33688982-33689001 None:intergenic 35.0%
!! TTATTCACCTTTAAGGTCTC+TGG - chr3.4:33688821-33688840 MS.gene03617:intron 35.0%
!! TTTTCTTGGTCAATTAGCCT+AGG + chr3.4:33688849-33688868 None:intergenic 35.0%
AAGATCATGGATCTGATCGT+CGG + chr3.4:33688245-33688264 None:intergenic 40.0%
AGCTCAGAAGGACTTCTTTA+CGG + chr3.4:33688733-33688752 None:intergenic 40.0%
AGGTGAATAAGTATGGTGTC+TGG + chr3.4:33688811-33688830 None:intergenic 40.0%
ATAGGCCTAACAAATACGAG+GGG - chr3.4:33689009-33689028 MS.gene03617:intron 40.0%
CAATAGGCCTAACAAATACG+AGG - chr3.4:33689007-33689026 MS.gene03617:intron 40.0%
CCAAATGAACTAAGCTCAGA+AGG + chr3.4:33688745-33688764 None:intergenic 40.0%
CCTTCTGAGCTTAGTTCATT+TGG - chr3.4:33688742-33688761 MS.gene03617:intron 40.0%
GACTCTCCGGTAGATTAATA+GGG + chr3.4:33688618-33688637 None:intergenic 40.0%
GGTGAATAAGTATGGTGTCT+GGG + chr3.4:33688810-33688829 None:intergenic 40.0%
GTGAATAAGTATGGTGTCTG+GGG + chr3.4:33688809-33688828 None:intergenic 40.0%
TGACTCTCCGGTAGATTAAT+AGG + chr3.4:33688619-33688638 None:intergenic 40.0%
TTCTTCCTGAGATTCGCAAT+AGG - chr3.4:33688284-33688303 MS.gene03617:CDS 40.0%
! TTCTTGGTCAATTAGCCTAG+GGG + chr3.4:33688847-33688866 None:intergenic 40.0%
!! GAGCTGTTTTGTGAGCTTTT+AGG + chr3.4:33688661-33688680 None:intergenic 40.0%
ACCAACTTAATCCTAGGTCC+AGG - chr3.4:33688961-33688980 MS.gene03617:intron 45.0%
CCAACTTAATCCTAGGTCCA+GGG - chr3.4:33688962-33688981 MS.gene03617:intron 45.0%
TGAGCGTTTGTCTGAGCTAT+TGG - chr3.4:33689237-33689256 MS.gene03617:CDS 45.0%
TGCATACTATATGCAGGGAC+CGG - chr3.4:33688775-33688794 MS.gene03617:intron 45.0%
! AGAGTCAGCTCTAACTATGG+TGG - chr3.4:33688632-33688651 MS.gene03617:intron 45.0%
! CATAGTTAGAGCTGACTCTC+CGG + chr3.4:33688631-33688650 None:intergenic 45.0%
! GTCTGAGCTATTGGCTACAA+CGG - chr3.4:33689246-33689265 MS.gene03617:CDS 45.0%
AGGAAGAAGTTGCTGCAGCT+TGG + chr3.4:33688272-33688291 None:intergenic 50.0%
CCCTGGACCTAGGATTAAGT+TGG + chr3.4:33688965-33688984 None:intergenic 50.0%
GAGCTCCTATTGCGAATCTC+AGG + chr3.4:33688292-33688311 None:intergenic 50.0%
GCAGCTTGGAGACAAGATCA+TGG + chr3.4:33688258-33688277 None:intergenic 50.0%
GCTCAGACAAACGCTCACTT+AGG + chr3.4:33689234-33689253 None:intergenic 50.0%
! CGGAGAGTCAGCTCTAACTA+TGG - chr3.4:33688629-33688648 MS.gene03617:intron 50.0%
! CTTGTTATGTCCCTGGACCT+AGG + chr3.4:33688975-33688994 None:intergenic 50.0%
! TCGCAATAGGAGCTCTGACA+AGG - chr3.4:33688297-33688316 MS.gene03617:CDS 50.0%
!! TTCAGCTTCAAGGGTGTTGC+AGG - chr3.4:33689165-33689184 MS.gene03617:intron 50.0%
CACGGCAAACAAGTAGCTCG+AGG - chr3.4:33688212-33688231 MS.gene03617:CDS 55.0%
CTAGGGGCCAGAGACCTTAA+AGG + chr3.4:33688831-33688850 None:intergenic 55.0%
!! CTTTAAGGTCTCTGGCCCCT+AGG - chr3.4:33688829-33688848 MS.gene03617:intron 55.0%
! GGTGTCTGGGGTTCGAACTC+CGG + chr3.4:33688797-33688816 None:intergenic 60.0%
CTAGCAGGAGGTCGCGGTCA+CGG - chr3.4:33688194-33688213 MS.gene03617:CDS 65.0%


Chromosome Type Strat End Strand Name
chr3.4 gene 33688190 33689312 33688190 ID=MS.gene03617
chr3.4 mRNA 33688190 33689312 33688190 ID=MS.gene03617.t1;Parent=MS.gene03617
chr3.4 exon 33689184 33689312 33689184 ID=MS.gene03617.t1.exon1;Parent=MS.gene03617.t1
chr3.4 CDS 33689184 33689312 33689184 ID=cds.MS.gene03617.t1;Parent=MS.gene03617.t1
chr3.4 exon 33688190 33688339 33688190 ID=MS.gene03617.t1.exon2;Parent=MS.gene03617.t1
chr3.4 CDS 33688190 33688339 33688190 ID=cds.MS.gene03617.t1;Parent=MS.gene03617.t1
Gene Sequence

>MS.gene03617

ATGTCTAGCAGGAGGTCGCGGTCACGGCAAACAAGTAGCTCGAGGAATATCACCGACGATCAGATCCATGATCTTGTCTCCAAGCTGCAGCAACTTCTTCCTGAGATTCGCAATAGGAGCTCTGACAAGGTTTGTTCCTACATATTATTTGTTTCCTAGTCTTAATCAAAAGACTAGAGTATTTCTTTTTACTTCGTTTTTTGCTTAATTACATTCATATTATTCAATTAATGTGATTTTGTTGCTTAACTACACTACCATTATTTTTTATAAAAGTCATTGGTAAGAGATAAGTAGAAAAAAGTAAATGAAAACTATAATGATGATGAGAAGAATCTAAGCCTGTAACTACCATATACTATATTTTTAATACATAGAAGAGATTAGTTTTATAGCGGATCAAAGAATCTAAGCTTGTAGAGATACCCTATTAATCTACCGGAGAGTCAGCTCTAACTATGGTGGACTCCTAAAAGCTCACAAAACAGCTCTTAATATAATTTTGCTTATAAAAAAACAAAATTTAATTGAATAAAAAAACCGTAAAGAAGTCCTTCTGAGCTTAGTTCATTTGGTAAGGGATAATGCATACTATATGCAGGGACCGGAGTTCGAACCCCAGACACCATACTTATTCACCTTTAAGGTCTCTGGCCCCTAGGCTAATTGACCAAGAAAAAAAAAAAAAACTTGAAAGGTGCAAGAGTGAGATTTTGTCATTTTTAAGCATCATAAATAAATACACTAGAGAAAGTATAAGAGGGTATTTAAACCAACTTAATCCTAGGTCCAGGGACATAACAAGAAAAAGAAACAACAATAGGCCTAACAAATACGAGGGGATTAAGTACTTCTATCTAGCACCAGTTTTTTCCCATCTACAAGAATTGTTGATGTTTTCAATTTTCAACTATATATTTTAAGAGAATAGTTAAATATATAGCATTTACTAAATTGAATTTTACTATATCAGGTTTCAGCTTCAAGGGTGTTGCAGGAGACTTGCAACTATATTAGAAACTTGAACAGGGAAGTTGACAACCTAAGTGAGCGTTTGTCTGAGCTATTGGCTACAACGGACACAGCACAAGCAGCAATAATAAGAAATTTACTTATGCAATAG
Protein sequence

>MS.gene03617.t1

MSSRRSRSRQTSSSRNITDDQIHDLVSKLQQLLPEIRNRSSDKVSASRVLQETCNYIRNLNREVDNLSERLSELLATTDTAQAAIIRNLLMQ