AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene77466

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene77466.t1 MTR_3g083050 77.707 157 10 2 1 132 52 208 1.61e-80 236
MS.gene77466.t1 MTR_3g083030 77.707 157 10 2 1 132 75 231 1.87e-80 236
MS.gene77466.t1 MTR_3g083080 51.266 158 51 1 1 132 50 207 6.59e-48 153
MS.gene77466.t1 MTR_3g086030 55.556 81 36 0 1 81 23 103 1.65e-24 92.0
MS.gene77466.t1 MTR_3g082420 42.105 95 51 1 1 95 61 151 2.37e-21 85.5
MS.gene77466.t1 MTR_3g082340 42.105 95 51 1 1 95 62 152 5.46e-21 84.7
MS.gene77466.t1 MTR_3g083150 34.810 158 69 4 7 131 56 212 9.54e-15 68.2
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 28 sgRNAs with CRISPR-Local

Find 48 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GCGCTTTATTTACAAGAATA+AGG 0.246265 3.2:+71959351 MS.gene77466:CDS
CGCGCGCATATAAACATAAA+AGG 0.298624 3.2:-71959331 None:intergenic
CAGCCCTGTTATATCTTTCC+AGG 0.337582 3.2:+71959843 MS.gene77466:CDS
CAATTACAATGCTGAGAATC+AGG 0.359881 3.2:+71959631 MS.gene77466:CDS
TCCAGGCCGAAGTCAGGAAT+TGG 0.401904 3.2:+71959860 MS.gene77466:CDS
TCGGCCTGGAAAGATATAAC+AGG 0.404862 3.2:-71959847 None:intergenic
ATGGCACATGACTTGATGAT+AGG 0.460123 3.2:-71959895 None:intergenic
AGGCGACGATCATCGGTCAT+AGG 0.464071 3.2:-71959575 None:intergenic
TATCTTTCCAGGCCGAAGTC+AGG 0.478343 3.2:+71959854 MS.gene77466:CDS
AAAGATATAACAGGGCTGTT+GGG 0.481315 3.2:-71959838 None:intergenic
TCCAATTCCTGACTTCGGCC+TGG 0.483561 3.2:-71959861 None:intergenic
GAAAGATATAACAGGGCTGT+TGG 0.497566 3.2:-71959839 None:intergenic
GAGACGAAGGCGACGATCAT+CGG 0.531298 3.2:-71959582 None:intergenic
TACAATGCTGAGAATCAGGC+AGG 0.531649 3.2:+71959635 MS.gene77466:CDS
TCAGGAAAATGTGGCGGTGT+CGG 0.534211 3.2:+71959545 MS.gene77466:CDS
GTCTAACGCAAGCTTGCAGA+CGG 0.539023 3.2:-71959609 None:intergenic
GACGATCATCGGTCATAGGA+AGG 0.543064 3.2:-71959571 None:intergenic
CGATCATCGGTCATAGGAAG+GGG 0.552083 3.2:-71959569 None:intergenic
ACGATCATCGGTCATAGGAA+GGG 0.583505 3.2:-71959570 None:intergenic
TAAGGAGATTGAAGTAGCCA+TGG 0.591215 3.2:+71959390 MS.gene77466:CDS
AGGCCGAAGTCAGGAATTGG+AGG 0.613344 3.2:+71959863 MS.gene77466:CDS
TGCAGACGGGAGTGAGACGA+AGG 0.616805 3.2:-71959595 None:intergenic
ACTCCTCCAATTCCTGACTT+CGG 0.621511 3.2:-71959866 None:intergenic
TCTAACGCAAGCTTGCAGAC+GGG 0.623247 3.2:-71959608 None:intergenic
GCACTCATCATACTCAGCCA+TGG 0.631008 3.2:-71959407 None:intergenic
CGGCCTGGAAAGATATAACA+GGG 0.637548 3.2:-71959846 None:intergenic
GCACATGACTTGATGATAGG+TGG 0.677186 3.2:-71959892 None:intergenic
AAAATCTCAGGAAAATGTGG+CGG 0.681893 3.2:+71959539 MS.gene77466:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! ATTTTTTTTTTTTTTTTTTT+AGG + chr3.2:71959726-71959745 MS.gene77466:intron 0.0%
!!! TTTTTTTTTTTTTTTTTTTA+GGG + chr3.2:71959727-71959746 MS.gene77466:intron 0.0%
!!! TTAATTTTAATGATTCATTC+TGG + chr3.2:71959473-71959492 MS.gene77466:intron 15.0%
AATTTCTTCTTGTGCTTGAA+AGG - chr3.2:71959818-71959837 None:intergenic 30.0%
ACGTCAACAAAAACGAAATT+TGG - chr3.2:71959754-71959773 None:intergenic 30.0%
TAGTTGAGTTACTTACACTT+AGG - chr3.2:71959441-71959460 None:intergenic 30.0%
! CTCCTTATCTTTTTGAATCT+GGG - chr3.2:71959377-71959396 None:intergenic 30.0%
! TCTCCTTATCTTTTTGAATC+TGG - chr3.2:71959378-71959397 None:intergenic 30.0%
!! GCGCTTTATTTACAAGAATA+AGG + chr3.2:71959351-71959370 MS.gene77466:CDS 30.0%
!! TTTTCCTGAGATTTTTGGAA+CGG - chr3.2:71959534-71959553 None:intergenic 30.0%
AAAATCTCAGGAAAATGTGG+CGG + chr3.2:71959539-71959558 MS.gene77466:CDS 35.0%
AAAGATATAACAGGGCTGTT+GGG - chr3.2:71959841-71959860 None:intergenic 35.0%
CAATTACAATGCTGAGAATC+AGG + chr3.2:71959631-71959650 MS.gene77466:CDS 35.0%
CCAAAAATCTCAGGAAAATG+TGG + chr3.2:71959536-71959555 MS.gene77466:CDS 35.0%
GTAATGTAATAGAAACCACC+AGG - chr3.2:71959796-71959815 None:intergenic 35.0%
! CCACATTTTCCTGAGATTTT+TGG - chr3.2:71959539-71959558 None:intergenic 35.0%
!!! TTTCCTGAGATTTTTGGAAC+GGG - chr3.2:71959533-71959552 None:intergenic 35.0%
ATAGAAACCACCAGGTCTAT+AGG - chr3.2:71959788-71959807 None:intergenic 40.0%
CGCGCGCATATAAACATAAA+AGG - chr3.2:71959334-71959353 None:intergenic 40.0%
GAAAGATATAACAGGGCTGT+TGG - chr3.2:71959842-71959861 None:intergenic 40.0%
GGCCCAGATTCAAAAAGATA+AGG + chr3.2:71959372-71959391 MS.gene77466:CDS 40.0%
TAAGGAGATTGAAGTAGCCA+TGG + chr3.2:71959390-71959409 MS.gene77466:CDS 40.0%
! ATGGCACATGACTTGATGAT+AGG - chr3.2:71959898-71959917 None:intergenic 40.0%
!!! TTCCTGAGATTTTTGGAACG+GGG - chr3.2:71959532-71959551 None:intergenic 40.0%
AAGACAACCTATAGACCTGG+TGG + chr3.2:71959778-71959797 MS.gene77466:intron 45.0%
ACGATCATCGGTCATAGGAA+GGG - chr3.2:71959573-71959592 None:intergenic 45.0%
ACTCCTCCAATTCCTGACTT+CGG - chr3.2:71959869-71959888 None:intergenic 45.0%
ATCCCCGTTCCAAAAATCTC+AGG + chr3.2:71959527-71959546 MS.gene77466:CDS 45.0%
CAGCCCTGTTATATCTTTCC+AGG + chr3.2:71959843-71959862 MS.gene77466:CDS 45.0%
CGGCCTGGAAAGATATAACA+GGG - chr3.2:71959849-71959868 None:intergenic 45.0%
GTCAAGACAACCTATAGACC+TGG + chr3.2:71959775-71959794 MS.gene77466:intron 45.0%
TACAATGCTGAGAATCAGGC+AGG + chr3.2:71959635-71959654 MS.gene77466:CDS 45.0%
TCGGCCTGGAAAGATATAAC+AGG - chr3.2:71959850-71959869 None:intergenic 45.0%
TGGACAACACAACACAACAC+AGG + chr3.2:71959493-71959512 MS.gene77466:intron 45.0%
! GCACATGACTTGATGATAGG+TGG - chr3.2:71959895-71959914 None:intergenic 45.0%
CGATCATCGGTCATAGGAAG+GGG - chr3.2:71959572-71959591 None:intergenic 50.0%
GACGATCATCGGTCATAGGA+AGG - chr3.2:71959574-71959593 None:intergenic 50.0%
GCACTCATCATACTCAGCCA+TGG - chr3.2:71959410-71959429 None:intergenic 50.0%
GTCTAACGCAAGCTTGCAGA+CGG - chr3.2:71959612-71959631 None:intergenic 50.0%
TATCTTTCCAGGCCGAAGTC+AGG + chr3.2:71959854-71959873 MS.gene77466:CDS 50.0%
TCAGGAAAATGTGGCGGTGT+CGG + chr3.2:71959545-71959564 MS.gene77466:CDS 50.0%
TCTAACGCAAGCTTGCAGAC+GGG - chr3.2:71959611-71959630 None:intergenic 50.0%
AGGCCGAAGTCAGGAATTGG+AGG + chr3.2:71959863-71959882 MS.gene77466:CDS 55.0%
AGGCGACGATCATCGGTCAT+AGG - chr3.2:71959578-71959597 None:intergenic 55.0%
GAGACGAAGGCGACGATCAT+CGG - chr3.2:71959585-71959604 None:intergenic 55.0%
TCCAATTCCTGACTTCGGCC+TGG - chr3.2:71959864-71959883 None:intergenic 55.0%
TCCAGGCCGAAGTCAGGAAT+TGG + chr3.2:71959860-71959879 MS.gene77466:CDS 55.0%
TGCAGACGGGAGTGAGACGA+AGG - chr3.2:71959598-71959617 None:intergenic 60.0%


Chromosome Type Strat End Strand Name
chr3.2 gene 71959295 71959930 71959295 ID=MS.gene77466
chr3.2 mRNA 71959295 71959930 71959295 ID=MS.gene77466.t1;Parent=MS.gene77466
chr3.2 exon 71959295 71959444 71959295 ID=MS.gene77466.t1.exon1;Parent=MS.gene77466.t1
chr3.2 CDS 71959295 71959444 71959295 ID=cds.MS.gene77466.t1;Parent=MS.gene77466.t1
chr3.2 exon 71959515 71959656 71959515 ID=MS.gene77466.t1.exon2;Parent=MS.gene77466.t1
chr3.2 CDS 71959515 71959656 71959515 ID=cds.MS.gene77466.t1;Parent=MS.gene77466.t1
chr3.2 exon 71959824 71959930 71959824 ID=MS.gene77466.t1.exon3;Parent=MS.gene77466.t1
chr3.2 CDS 71959824 71959930 71959824 ID=cds.MS.gene77466.t1;Parent=MS.gene77466.t1
Gene Sequence

>MS.gene77466

ATGAGTGACTTCTCTATGTATGACGATGACATTGAGCCTTTTATGTTTATATGCGCGCGCTTTATTTACAAGAATAAGGCCCAGATTCAAAAAGATAAGGAGATTGAAGTAGCCATGGCTGAGTATGATGAGTGCTCTCGCAACCTAAGTGTAAGTAACTCAACTATCTATCTTAATTTTAATTTTAATGATTCATTCTGGACAACACAACACAACACAGGTGTTCGATGCTATCCCCGTTCCAAAAATCTCAGGAAAATGTGGCGGTGTCGGTCCCCTTCCTATGACCGATGATCGTCGCCTTCGTCTCACTCCCGTCTGCAAGCTTGCGTTAGACAATTACAATGCTGAGAATCAGGCAGGTTTCAATACTTATGATGATTATAATATGTTTATGTTTATTTATTCATTCATTGATCATCTAATATACTATTTTTTTTTTTTTTTTTTTAGGGTCCAAATTTCGTTTTTGTTGACGTTGTCAAGACAACCTATAGACCTGGTGGTTTCTATTACATTACCTTTCAAGCACAAGAAGAAATTCCCAACAGCCCTGTTATATCTTTCCAGGCCGAAGTCAGGAATTGGAGGAGTCAGCCACCTATCATCAAGTCATGTGCCATTAAAACTACTTAA
Protein sequence

>MS.gene77466.t1

MSDFSMYDDDIEPFMFICARFIYKNKAQIQKDKEIEVAMAEYDECSRNLSVFDAIPVPKISGKCGGVGPLPMTDDRRLRLTPVCKLALDNYNAENQAAQEEIPNSPVISFQAEVRNWRSQPPIIKSCAIKTT