AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene83524

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene83524.t1 MTR_2g105340 74.074 135 18 3 1 133 1 120 2.13e-37 124
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 51 sgRNAs with CRISPR-Local

Find 66 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CCCCATTTCTTTCAGTTTCC+CGG 0.179440 2.2:+343425 None:intergenic
TTAACTGTGCCAGCAACTTC+TGG 0.273818 2.2:-343247 MS.gene83524:CDS
GAGTTGGCCCAGGATTATAT+TGG 0.353506 2.2:+343278 None:intergenic
TCCCGGGAAACTGAAAGAAA+TGG 0.360508 2.2:-343427 MS.gene83524:CDS
AGTTGGCCCAGGATTATATT+GGG 0.360873 2.2:+343279 None:intergenic
AGAGATTAGGAGGAGAATTC+TGG 0.378079 2.2:+343194 None:intergenic
CCCGGGAAACTGAAAGAAAT+GGG 0.394159 2.2:-343426 MS.gene83524:CDS
CAGAGCGTCTGCGGCGGGAG+TGG 0.394365 2.2:+343333 None:intergenic
GTTGGGTTTCCAGAAGTTGC+TGG 0.414499 2.2:+343238 None:intergenic
AAAATATGTATCTGAGCTGT+TGG 0.415022 2.2:+343220 None:intergenic
CCCGGCGAATGGTGCGGAGG+TGG 0.417570 2.2:+343382 None:intergenic
CCTCCTCCCCAATATAATCC+TGG 0.422464 2.2:-343286 MS.gene83524:CDS
CCCATTTCTTTCAGTTTCCC+GGG 0.433130 2.2:+343426 None:intergenic
AAGAGAGTAGAAAGACAGAT+TGG 0.434084 2.2:+344092 None:intergenic
GAATGGTGCGGAGGTGGTGG+TGG 0.448834 2.2:+343388 None:intergenic
TATAATCCTGGGCCAACTCC+AGG 0.450650 2.2:-343274 MS.gene83524:CDS
GGAGAATTCAGTTTCTGAAC+TGG 0.452981 2.2:+343358 None:intergenic
AGAGCGTCTGCGGCGGGAGT+GGG 0.453808 2.2:+343334 None:intergenic
GGCGAATGGTGCGGAGGTGG+TGG 0.454424 2.2:+343385 None:intergenic
TTATATTGGGGAGGAGGTGG+TGG 0.459881 2.2:+343292 None:intergenic
ACCACCTCCGCACCATTCGC+CGG 0.460281 2.2:-343383 MS.gene83524:CDS
TTCAGTTTCTGAACTGGTCC+CGG 0.467126 2.2:+343364 None:intergenic
GGATTATATTGGGGAGGAGG+TGG 0.471962 2.2:+343289 None:intergenic
GCTGAAGCTGCAAAGAGATT+AGG 0.479618 2.2:+343181 None:intergenic
AAATATGTATCTGAGCTGTT+GGG 0.496619 2.2:+343221 None:intergenic
AAGAGCCCTGGAGTTGGCCC+AGG 0.496989 2.2:+343268 None:intergenic
TAGAAACAAACAGCAAGGCT+TGG 0.507692 2.2:+344056 None:intergenic
CTCCTCCCCAATATAATCCT+GGG 0.521004 2.2:-343285 MS.gene83524:CDS
TGTCTCAGAGCGTCTGCGGC+GGG 0.521606 2.2:+343328 None:intergenic
TCTGAACTGGTCCCGGCGAA+TGG 0.523874 2.2:+343371 None:intergenic
CCACCTCCGCACCATTCGCC+GGG 0.524394 2.2:-343382 MS.gene83524:CDS
GCTGGCACAGTTAAGAGCCC+TGG 0.549638 2.2:+343256 None:intergenic
CCAGGATTATATTGGGGAGG+AGG 0.552901 2.2:+343286 None:intergenic
CAGCAAGCATCTAGCTTCTG+TGG 0.554315 2.2:+344030 None:intergenic
TAGAAACTGAATTCTCCTCC+CGG 0.559431 2.2:-343444 MS.gene83524:CDS
GAAGCTGCAAAGAGATTAGG+AGG 0.563505 2.2:+343184 None:intergenic
ACAGTTAAGAGCCCTGGAGT+TGG 0.564303 2.2:+343262 None:intergenic
ACTGGTCCCGGCGAATGGTG+CGG 0.568557 2.2:+343376 None:intergenic
AGAAACTGAATTCTCCTCCC+GGG 0.573887 2.2:-343443 MS.gene83524:CDS
GCGTCTGCGGCGGGAGTGGG+AGG 0.581224 2.2:+343337 None:intergenic
CTGTTGCAGACTATGTCACT+AGG 0.582810 2.2:-344010 MS.gene83524:intron
ATGTCTCAGAGCGTCTGCGG+CGG 0.587729 2.2:+343327 None:intergenic
ATAATCCTGGGCCAACTCCA+GGG 0.596363 2.2:-343273 MS.gene83524:CDS
GGTCCCGGCGAATGGTGCGG+AGG 0.622064 2.2:+343379 None:intergenic
GTTGGCCCAGGATTATATTG+GGG 0.622956 2.2:+343280 None:intergenic
GGCCCAGGATTATATTGGGG+AGG 0.624273 2.2:+343283 None:intergenic
CCGGGAAACTGAAAGAAATG+GGG 0.639431 2.2:-343425 MS.gene83524:CDS
GGCAGTAGAAACAAACAGCA+AGG 0.643990 2.2:+344051 None:intergenic
ATGATGTCTCAGAGCGTCTG+CGG 0.676100 2.2:+343324 None:intergenic
CGGGAAACTGAAAGAAATGG+GGG 0.677386 2.2:-343424 MS.gene83524:CDS
ATTTCTTTCAGTTTCCCGGG+AGG 0.690454 2.2:+343429 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAATTATTCTTATTAGTTAT+TGG - chr2.2:343442-343461 MS.gene83524:CDS 10.0%
!! AATTATTCTTATTAGTTATT+GGG - chr2.2:343443-343462 MS.gene83524:CDS 10.0%
!!! TAAAAGAATTTTATTTGAAT+TGG + chr2.2:343362-343381 None:intergenic 10.0%
!! AAACAATATATTTATGTGAT+TGG + chr2.2:343723-343742 None:intergenic 15.0%
!! GAAAATATAATATAACGAAA+TGG - chr2.2:343536-343555 MS.gene83524:intron 15.0%
!! TATTTATGTGATTGGAATAA+TGG + chr2.2:343715-343734 None:intergenic 20.0%
!!! AAGAATTTTATTTGAATTGG+AGG + chr2.2:343359-343378 None:intergenic 20.0%
!!! AATATTTTTTCAGTTACATG+AGG + chr2.2:343692-343711 None:intergenic 20.0%
!!! AGAATTTTATTTGAATTGGA+GGG + chr2.2:343358-343377 None:intergenic 20.0%
!!! TATTTTGTTTTGAATATGTG+CGG + chr2.2:343396-343415 None:intergenic 20.0%
AAAATATGTATCTGAGCTGT+TGG + chr2.2:344063-344082 None:intergenic 30.0%
AAATATGTATCTGAGCTGTT+GGG + chr2.2:344062-344081 None:intergenic 30.0%
ACGAAATGGTTGAATTTAAG+TGG - chr2.2:343550-343569 MS.gene83524:intron 30.0%
!!! GATATCTTTTTGAGTTCGAA+TGG + chr2.2:343661-343680 None:intergenic 30.0%
AAGAGAGTAGAAAGACAGAT+TGG + chr2.2:343191-343210 None:intergenic 35.0%
TCAGTTACATGAGGTGAAAA+AGG + chr2.2:343683-343702 None:intergenic 35.0%
AGAGATTAGGAGGAGAATTC+TGG + chr2.2:344089-344108 None:intergenic 40.0%
AGTTGGCCCAGGATTATATT+GGG + chr2.2:344004-344023 None:intergenic 40.0%
GGAGAATTCAGTTTCTGAAC+TGG + chr2.2:343925-343944 None:intergenic 40.0%
TAGAAACAAACAGCAAGGCT+TGG + chr2.2:343227-343246 None:intergenic 40.0%
TAGAAACTGAATTCTCCTCC+CGG - chr2.2:343836-343855 MS.gene83524:intron 40.0%
AGAAACTGAATTCTCCTCCC+GGG - chr2.2:343837-343856 MS.gene83524:intron 45.0%
ATTTCTTTCAGTTTCCCGGG+AGG + chr2.2:343854-343873 None:intergenic 45.0%
CCCATTTCTTTCAGTTTCCC+GGG + chr2.2:343857-343876 None:intergenic 45.0%
CCCCATTTCTTTCAGTTTCC+CGG + chr2.2:343858-343877 None:intergenic 45.0%
CCCGGGAAACTGAAAGAAAT+GGG - chr2.2:343854-343873 MS.gene83524:intron 45.0%
CCGGGAAACTGAAAGAAATG+GGG - chr2.2:343855-343874 MS.gene83524:intron 45.0%
CGGGAAACTGAAAGAAATGG+GGG - chr2.2:343856-343875 MS.gene83524:intron 45.0%
CTCCTCCCCAATATAATCCT+GGG - chr2.2:343995-344014 MS.gene83524:intron 45.0%
CTGTTGCAGACTATGTCACT+AGG - chr2.2:343270-343289 MS.gene83524:CDS 45.0%
GAAGCTGCAAAGAGATTAGG+AGG + chr2.2:344099-344118 None:intergenic 45.0%
GAGTTGGCCCAGGATTATAT+TGG + chr2.2:344005-344024 None:intergenic 45.0%
GCTGAAGCTGCAAAGAGATT+AGG + chr2.2:344102-344121 None:intergenic 45.0%
GGCAGTAGAAACAAACAGCA+AGG + chr2.2:343232-343251 None:intergenic 45.0%
GTTGGCCCAGGATTATATTG+GGG + chr2.2:344003-344022 None:intergenic 45.0%
TCCCGGGAAACTGAAAGAAA+TGG - chr2.2:343853-343872 MS.gene83524:intron 45.0%
TTAACTGTGCCAGCAACTTC+TGG - chr2.2:344033-344052 MS.gene83524:CDS 45.0%
TTCAGTTTCTGAACTGGTCC+CGG + chr2.2:343919-343938 None:intergenic 45.0%
!! AATTGGAGGGAGTACTGACT+AGG + chr2.2:343345-343364 None:intergenic 45.0%
!! TATAATATAATATAATTAGT+TGG - chr2.2:343478-343497 MS.gene83524:intron 5.0%
ACAGTTAAGAGCCCTGGAGT+TGG + chr2.2:344021-344040 None:intergenic 50.0%
ATAATCCTGGGCCAACTCCA+GGG - chr2.2:344007-344026 MS.gene83524:intron 50.0%
CCAGGATTATATTGGGGAGG+AGG + chr2.2:343997-344016 None:intergenic 50.0%
CCTCCTCCCCAATATAATCC+TGG - chr2.2:343994-344013 MS.gene83524:intron 50.0%
GGATTATATTGGGGAGGAGG+TGG + chr2.2:343994-344013 None:intergenic 50.0%
GTTGGGTTTCCAGAAGTTGC+TGG + chr2.2:344045-344064 None:intergenic 50.0%
TATAATCCTGGGCCAACTCC+AGG - chr2.2:344006-344025 MS.gene83524:intron 50.0%
TTATATTGGGGAGGAGGTGG+TGG + chr2.2:343991-344010 None:intergenic 50.0%
! ATGATGTCTCAGAGCGTCTG+CGG + chr2.2:343959-343978 None:intergenic 50.0%
! CAGCAAGCATCTAGCTTCTG+TGG + chr2.2:343253-343272 None:intergenic 50.0%
GGCCCAGGATTATATTGGGG+AGG + chr2.2:344000-344019 None:intergenic 55.0%
GCTGGCACAGTTAAGAGCCC+TGG + chr2.2:344027-344046 None:intergenic 60.0%
TCTGAACTGGTCCCGGCGAA+TGG + chr2.2:343912-343931 None:intergenic 60.0%
! ATGTCTCAGAGCGTCTGCGG+CGG + chr2.2:343956-343975 None:intergenic 60.0%
AAGAGCCCTGGAGTTGGCCC+AGG + chr2.2:344015-344034 None:intergenic 65.0%
ACCACCTCCGCACCATTCGC+CGG - chr2.2:343897-343916 MS.gene83524:intron 65.0%
ACTGGTCCCGGCGAATGGTG+CGG + chr2.2:343907-343926 None:intergenic 65.0%
! GAATGGTGCGGAGGTGGTGG+TGG + chr2.2:343895-343914 None:intergenic 65.0%
! TGTCTCAGAGCGTCTGCGGC+GGG + chr2.2:343955-343974 None:intergenic 65.0%
CCACCTCCGCACCATTCGCC+GGG - chr2.2:343898-343917 MS.gene83524:intron 70.0%
GGCGAATGGTGCGGAGGTGG+TGG + chr2.2:343898-343917 None:intergenic 70.0%
! AGAGCGTCTGCGGCGGGAGT+GGG + chr2.2:343949-343968 None:intergenic 70.0%
CCCGGCGAATGGTGCGGAGG+TGG + chr2.2:343901-343920 None:intergenic 75.0%
GGTCCCGGCGAATGGTGCGG+AGG + chr2.2:343904-343923 None:intergenic 75.0%
! CAGAGCGTCTGCGGCGGGAG+TGG + chr2.2:343950-343969 None:intergenic 75.0%
! GCGTCTGCGGCGGGAGTGGG+AGG + chr2.2:343946-343965 None:intergenic 80.0%


Chromosome Type Strat End Strand Name
chr2.2 gene 343177 344125 343177 ID=MS.gene83524
chr2.2 mRNA 343177 344125 343177 ID=MS.gene83524.t1;Parent=MS.gene83524
chr2.2 exon 344011 344125 344011 ID=MS.gene83524.t1.exon1;Parent=MS.gene83524.t1
chr2.2 CDS 344011 344125 344011 ID=cds.MS.gene83524.t1;Parent=MS.gene83524.t1
chr2.2 exon 343177 343463 343177 ID=MS.gene83524.t1.exon2;Parent=MS.gene83524.t1
chr2.2 CDS 343177 343463 343177 ID=cds.MS.gene83524.t1;Parent=MS.gene83524.t1
Gene Sequence

>MS.gene83524

ATGAAGACTCTCCAATCTGTCTTTCTACTCTCTTCACTCTTTGCATTCCAAGCCTTGCTGTTTGTTTCTACTGCCACAGAAGCTAGATGCTTGCTGTTGCAGACTATGTCACTAGGTAAATTCTTTACTTATAGCTTATTAACTTATATGTGCATGCACTTTGTACCTAGTCAGTACTCCCTCCAATTCAAATAAAATTCTTTTAAAGCTTTTTCGCCGCACATATTCAAAACAAAATAAATGAACAAAGTGTAATAATCTTTTAAAATTATTCTTATTAGTTATTGGGTTGTATAGTACGTATAATATAATATAATTAGTTGGACGTAAAATTGAAAAATTAATTAATTGATTGTCTTGAAAATATAATATAACGAAATGGTTGAATTTAAGTGGTTAATAAATTTTATTTTAAATAATTCAAAAGAACACGAATTTAAAATTTTAAATAAAATAATCATTGATCAAGCTATACTTATATCCATTCGAACTCAAAAAGATATCCTTTTTCACCTCATGTAACTGAAAAAATATTCCATTATTCCAATCACATAAATATATTGTTTAGAAAAAGAAAAGCATATCACAATGTCAGTTTGTCATACTAGTTATTAATATATTTTCACAAATATTTATACAACTAGACGTGATTTGATGTATAGAAACTGAATTCTCCTCCCGGGAAACTGAAAGAAATGGGGGAAGACATCATGCACCACCACCACCTCCGCACCATTCGCCGGGACCAGTTCAGAAACTGAATTCTCCTCCCACTCCCGCCGCAGACGCTCTGAGACATCATCGACACTCACCACCACCTCCTCCCCAATATAATCCTGGGCCAACTCCAGGGCTCTTAACTGTGCCAGCAACTTCTGGAAACCCAACAGCTCAGATACATATTTTGTACCAGAATTCTCCTCCTAATCTCTTTGCAGCTTCAGCCTGA
Protein sequence

>MS.gene83524.t1

MKTLQSVFLLSSLFAFQALLFVSTATEARCLLLQTMSLETEFSSRETERNGGRHHAPPPPPHHSPGPVQKLNSPPTPAADALRHHRHSPPPPPQYNPGPTPGLLTVPATSGNPTAQIHILYQNSPPNLFAASA