AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene071546


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 22 sgRNAs with CRISPR-Local

Find 28 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CAGTATGTTGCGGTATATAC+TGG 0.218929 5.3:+246706 MS.gene071546:intron
ATCCCCAATGGTCCCGATTA+TGG 0.250985 5.3:-246491 None:intergenic
ACTCTTACAAAAGCCATAAT+CGG 0.362269 5.3:+246478 MS.gene071546:CDS
TGGTGACTTCTTAAGAGAAT+TGG 0.365879 5.3:+246441 MS.gene071546:CDS
AAGCCATAATCGGGACCATT+GGG 0.373438 5.3:+246488 MS.gene071546:CDS
GGGATCACGATAAGACAAAA+AGG 0.416539 5.3:-246383 None:intergenic
TTCATACCTACTATAACCTT+TGG 0.427406 5.3:-246539 None:intergenic
CTACTATAACCTTTGGCATC+AGG 0.430815 5.3:-246532 None:intergenic
TTTGGCATCAGGAAGTTGAT+AGG 0.461058 5.3:-246521 None:intergenic
CTGATGCCAAAGGTTATAGT+AGG 0.492789 5.3:+246533 MS.gene071546:CDS
AAAACACTTGAGGTATATGA+TGG 0.499301 5.3:+246415 MS.gene071546:CDS
CTCTTACAAAAGCCATAATC+GGG 0.515937 5.3:+246479 MS.gene071546:CDS
AAAGCCATAATCGGGACCAT+TGG 0.520667 5.3:+246487 MS.gene071546:CDS
TGGGTATCACAGAGGAAGAA+AGG 0.534259 5.3:+246726 MS.gene071546:CDS
AGTATGTTGCGGTATATACT+GGG 0.560882 5.3:+246707 MS.gene071546:intron
CTTGAGGTATATGATGGAAC+TGG 0.561746 5.3:+246421 MS.gene071546:CDS
TATCAACTTCCTGATGCCAA+AGG 0.598450 5.3:+246523 MS.gene071546:CDS
GAAGAAAGGCAAAAGAGACG+TGG 0.599903 5.3:+246740 MS.gene071546:CDS
ATAGGAGTCTACATCCCCAA+TGG 0.650682 5.3:-246503 None:intergenic
AGCCATAATCGGGACCATTG+GGG 0.686109 5.3:+246489 MS.gene071546:CDS
GTATATACTGGGTATCACAG+AGG 0.779699 5.3:+246718 MS.gene071546:CDS
GTGGAGAGATATTATCTACG+AGG 0.781070 5.3:+246759 MS.gene071546:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! AATAAAAAAGCAGCATGATT+TGG - chr5.3:246650-246669 None:intergenic 25.0%
!! ATTTCATTTTCAGTATGTTG+CGG + chr5.3:246696-246715 MS.gene071546:intron 25.0%
AAAACACTTGAGGTATATGA+TGG + chr5.3:246415-246434 MS.gene071546:CDS 30.0%
ACTCTTACAAAAGCCATAAT+CGG + chr5.3:246478-246497 MS.gene071546:CDS 30.0%
TTCATACCTACTATAACCTT+TGG - chr5.3:246542-246561 None:intergenic 30.0%
! GCATGATTTGGAAATTTAGA+AGG - chr5.3:246638-246657 None:intergenic 30.0%
!!! TCAAGTGTTTTTAGCAAGTT+GGG - chr5.3:246406-246425 None:intergenic 30.0%
AGTATGTTGCGGTATATACT+GGG + chr5.3:246707-246726 MS.gene071546:intron 35.0%
CTCTTACAAAAGCCATAATC+GGG + chr5.3:246479-246498 MS.gene071546:CDS 35.0%
TGGTGACTTCTTAAGAGAAT+TGG + chr5.3:246441-246460 MS.gene071546:CDS 35.0%
!! CAACTTGCTAAAAACACTTG+AGG + chr5.3:246405-246424 MS.gene071546:CDS 35.0%
!!! CTCAAGTGTTTTTAGCAAGT+TGG - chr5.3:246407-246426 None:intergenic 35.0%
CAGTATGTTGCGGTATATAC+TGG + chr5.3:246706-246725 MS.gene071546:intron 40.0%
CTACTATAACCTTTGGCATC+AGG - chr5.3:246535-246554 None:intergenic 40.0%
CTGATGCCAAAGGTTATAGT+AGG + chr5.3:246533-246552 MS.gene071546:CDS 40.0%
GGGATCACGATAAGACAAAA+AGG - chr5.3:246386-246405 None:intergenic 40.0%
GTATATACTGGGTATCACAG+AGG + chr5.3:246718-246737 MS.gene071546:CDS 40.0%
GTGGAGAGATATTATCTACG+AGG + chr5.3:246759-246778 MS.gene071546:CDS 40.0%
TATCAACTTCCTGATGCCAA+AGG + chr5.3:246523-246542 MS.gene071546:CDS 40.0%
! CTTGAGGTATATGATGGAAC+TGG + chr5.3:246421-246440 MS.gene071546:CDS 40.0%
! TTTGGCATCAGGAAGTTGAT+AGG - chr5.3:246524-246543 None:intergenic 40.0%
AAAGCCATAATCGGGACCAT+TGG + chr5.3:246487-246506 MS.gene071546:CDS 45.0%
AAGCCATAATCGGGACCATT+GGG + chr5.3:246488-246507 MS.gene071546:CDS 45.0%
ATAGGAGTCTACATCCCCAA+TGG - chr5.3:246506-246525 None:intergenic 45.0%
GAAGAAAGGCAAAAGAGACG+TGG + chr5.3:246740-246759 MS.gene071546:CDS 45.0%
TGGGTATCACAGAGGAAGAA+AGG + chr5.3:246726-246745 MS.gene071546:CDS 45.0%
AGCCATAATCGGGACCATTG+GGG + chr5.3:246489-246508 MS.gene071546:CDS 50.0%
ATCCCCAATGGTCCCGATTA+TGG - chr5.3:246494-246513 None:intergenic 50.0%


Chromosome Type Strat End Strand Name
chr5.3 gene 246374 246780 246374 ID=MS.gene071546
chr5.3 mRNA 246374 246780 246374 ID=MS.gene071546.t1;Parent=MS.gene071546
chr5.3 exon 246374 246554 246374 ID=MS.gene071546.t1.exon1;Parent=MS.gene071546.t1
chr5.3 CDS 246374 246554 246374 ID=cds.MS.gene071546.t1;Parent=MS.gene071546.t1
chr5.3 exon 246709 246780 246709 ID=MS.gene071546.t1.exon2;Parent=MS.gene071546.t1
chr5.3 CDS 246709 246780 246709 ID=cds.MS.gene071546.t1;Parent=MS.gene071546.t1
Gene Sequence

>MS.gene071546

GAGTGTTCTCCTTTTTGTCTTATCGTGATCCCAACTTGCTAAAAACACTTGAGGTATATGATGGAACTGGTGACTTCTTAAGAGAATTGGAAATAGATGATGATACTCTTACAAAAGCCATAATCGGGACCATTGGGGATGTAGACTCCTATCAACTTCCTGATGCCAAAGGTTATAGTAGGTATGAATGAGCTAATTGATGCTTTTGTAGTTTGTTTACTGTAGATTTTTTTTTAGTTCTTCGTTAAATTATTAGTGATTCCTTCTAAATTTCCAAATCATGCTGCTTTTTTATTATAGTTGCAAATTATGCTTGCTTTTCATTTCATTTTCAGTATGTTGCGGTATATACTGGGTATCACAGAGGAAGAAAGGCAAAAGAGACGTGGAGAGATATTATCTACGAG

Protein sequence

>MS.gene071546.t1

ECSPFCLIVIPTCUKHLRYMMELVTSUENWKUMMILLQKPUSGPLGMUTPINFLMPKVIVVCCGIYWVSQRKKGKRDVERYYLR