AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene39479

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene39479.t1 MTR_1g085590 52.212 226 61 11 7 203 15 222 9.92e-53 171
MS.gene39479.t1 MTR_1g063150 54.286 175 46 5 24 198 30 170 5.14e-49 158
MS.gene39479.t1 MTR_1g046810 36.948 249 77 12 22 204 82 316 1.02e-31 117
MS.gene39479.t1 MTR_1g063140 48.462 130 40 5 81 200 2 114 5.45e-21 86.3
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 31 sgRNAs with CRISPR-Local

Find 35 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TCTGAGTGCCTGGCGTTTCT+TGG 0.234001 4.2:-22449746 None:intergenic
GAAAGAGAAAGAAGGGTATT+TGG 0.272932 4.2:-22449488 None:intergenic
AACCAAGACGAGACACTAAT+TGG 0.312675 4.2:-22450058 None:intergenic
TGAATCACAGCGGCACTAAA+AGG 0.331082 4.2:+22449875 MS.gene39479:CDS
CTGAGTGCCTGGCGTTTCTT+GGG 0.381627 4.2:-22449745 None:intergenic
TTCATTGATATTAATCATGC+TGG 0.416806 4.2:+22449508 MS.gene39479:CDS
GGGTATTTGGCATTGGTTGT+TGG 0.420713 4.2:-22449475 None:intergenic
AAGCATTGAATGAACATAAG+AGG 0.452841 4.2:+22449650 MS.gene39479:CDS
CTGGAAAACAAAAGATTACA+TGG 0.458402 4.2:+22449527 MS.gene39479:CDS
GAAAGAAGGGTATTTGGCAT+TGG 0.461253 4.2:-22449482 None:intergenic
CATAATCACAATGATGTTGT+TGG 0.465144 4.2:+22449574 MS.gene39479:CDS
CTCTGTTGCATATATCTCGC+GGG 0.495665 4.2:+22449821 MS.gene39479:CDS
TATCAATGAAAGAGAAAGAA+GGG 0.506201 4.2:-22449495 None:intergenic
GCTGTGATTCACATCGATAT+TGG 0.509973 4.2:-22449863 None:intergenic
TGGTAGAAACTGATCATCAA+TGG 0.511864 4.2:-22449722 None:intergenic
CTCATGTGATGTTTGCAACA+AGG 0.514548 4.2:+22449612 MS.gene39479:CDS
TCATCTTCAAAATCATCACT+TGG 0.541142 4.2:-22450033 None:intergenic
ATATCAATGAAAGAGAAAGA+AGG 0.543310 4.2:-22449496 None:intergenic
AACTGATCATCAATGGAAGA+TGG 0.551680 4.2:-22449715 None:intergenic
AAGAGGTGTCACTCTCAAAA+CGG 0.554314 4.2:+22449667 MS.gene39479:CDS
TCGTTCAAATCCATATTGCT+TGG 0.555538 4.2:-22449907 None:intergenic
TTAACTTCAAAATCATCACT+TGG 0.557014 4.2:-22449934 None:intergenic
GTGATTCACATCGATATTGG+CGG 0.581021 4.2:-22449860 None:intergenic
AGTGCCTGGCGTTTCTTGGG+TGG 0.592687 4.2:-22449742 None:intergenic
ATGGAAGATGGTGCTGCAGT+TGG 0.597422 4.2:-22449703 None:intergenic
TCTACCACCCAAGAAACGCC+AGG 0.621690 4.2:+22449738 MS.gene39479:CDS
TCTGTTGCATATATCTCGCG+GGG 0.628828 4.2:+22449822 MS.gene39479:CDS
ACATCATTGTGATTATGAGT+AGG 0.629847 4.2:-22449568 None:intergenic
ACTCTGTTGCATATATCTCG+CGG 0.638755 4.2:+22449820 MS.gene39479:CDS
CTGTTGCATATATCTCGCGG+GGG 0.734296 4.2:+22449823 MS.gene39479:CDS
AATATCGATGTGAATCACAG+CGG 0.784403 4.2:+22449865 MS.gene39479:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! ACTCAGAAGAAAAAGATATA+TGG + chr4.2:22449762-22449781 MS.gene39479:CDS 25.0%
! ATATCAATGAAAGAGAAAGA+AGG - chr4.2:22449499-22449518 None:intergenic 25.0%
! TATCAATGAAAGAGAAAGAA+GGG - chr4.2:22449498-22449517 None:intergenic 25.0%
! TTAACTTCAAAATCATCACT+TGG - chr4.2:22449937-22449956 None:intergenic 25.0%
! TTCATTGATATTAATCATGC+TGG + chr4.2:22449508-22449527 MS.gene39479:CDS 25.0%
!!! TGATGATTTTGAAGTTAATG+AGG + chr4.2:22449939-22449958 MS.gene39479:CDS 25.0%
ACATCATTGTGATTATGAGT+AGG - chr4.2:22449571-22449590 None:intergenic 30.0%
CATAATCACAATGATGTTGT+TGG + chr4.2:22449574-22449593 MS.gene39479:CDS 30.0%
CTGGAAAACAAAAGATTACA+TGG + chr4.2:22449527-22449546 MS.gene39479:CDS 30.0%
GCAAAAAATTCCAAGCAATA+TGG + chr4.2:22449897-22449916 MS.gene39479:CDS 30.0%
TCATCTTCAAAATCATCACT+TGG - chr4.2:22450036-22450055 None:intergenic 30.0%
!! AAGCATTGAATGAACATAAG+AGG + chr4.2:22449650-22449669 MS.gene39479:CDS 30.0%
AACTGATCATCAATGGAAGA+TGG - chr4.2:22449718-22449737 None:intergenic 35.0%
AATATCGATGTGAATCACAG+CGG + chr4.2:22449865-22449884 MS.gene39479:CDS 35.0%
TCGTTCAAATCCATATTGCT+TGG - chr4.2:22449910-22449929 None:intergenic 35.0%
TGGTAGAAACTGATCATCAA+TGG - chr4.2:22449725-22449744 None:intergenic 35.0%
!! GAAAGAGAAAGAAGGGTATT+TGG - chr4.2:22449491-22449510 None:intergenic 35.0%
ACTCTGTTGCATATATCTCG+CGG + chr4.2:22449820-22449839 MS.gene39479:CDS 40.0%
CTCATGTGATGTTTGCAACA+AGG + chr4.2:22449612-22449631 MS.gene39479:CDS 40.0%
GCTGTGATTCACATCGATAT+TGG - chr4.2:22449866-22449885 None:intergenic 40.0%
GTGATTCACATCGATATTGG+CGG - chr4.2:22449863-22449882 None:intergenic 40.0%
! ATCTTTTTCTTCTGAGTGCC+TGG - chr4.2:22449759-22449778 None:intergenic 40.0%
!! AAGAGGTGTCACTCTCAAAA+CGG + chr4.2:22449667-22449686 MS.gene39479:CDS 40.0%
!! GAAAGAAGGGTATTTGGCAT+TGG - chr4.2:22449485-22449504 None:intergenic 40.0%
CTCTGTTGCATATATCTCGC+GGG + chr4.2:22449821-22449840 MS.gene39479:CDS 45.0%
TCTGTTGCATATATCTCGCG+GGG + chr4.2:22449822-22449841 MS.gene39479:CDS 45.0%
TGAATCACAGCGGCACTAAA+AGG + chr4.2:22449875-22449894 MS.gene39479:CDS 45.0%
!! GGGTATTTGGCATTGGTTGT+TGG - chr4.2:22449478-22449497 None:intergenic 45.0%
ATATCTCGCGGGGGTTATGA+AGG + chr4.2:22449832-22449851 MS.gene39479:CDS 50.0%
CTGTTGCATATATCTCGCGG+GGG + chr4.2:22449823-22449842 MS.gene39479:CDS 50.0%
!! ATGGAAGATGGTGCTGCAGT+TGG - chr4.2:22449706-22449725 None:intergenic 50.0%
CTGAGTGCCTGGCGTTTCTT+GGG - chr4.2:22449748-22449767 None:intergenic 55.0%
TCTACCACCCAAGAAACGCC+AGG + chr4.2:22449738-22449757 MS.gene39479:CDS 55.0%
TCTGAGTGCCTGGCGTTTCT+TGG - chr4.2:22449749-22449768 None:intergenic 55.0%
AGTGCCTGGCGTTTCTTGGG+TGG - chr4.2:22449745-22449764 None:intergenic 60.0%


Chromosome Type Strat End Strand Name
chr4.2 gene 22449451 22450065 22449451 ID=MS.gene39479
chr4.2 mRNA 22449451 22450065 22449451 ID=MS.gene39479.t1;Parent=MS.gene39479
chr4.2 exon 22449451 22450065 22449451 ID=MS.gene39479.t1.exon1;Parent=MS.gene39479.t1
chr4.2 CDS 22449451 22450065 22449451 ID=cds.MS.gene39479.t1;Parent=MS.gene39479.t1
Gene Sequence

>MS.gene39479

ATGAACAAGAAAATGTCTCATAAACCAACAACCAATGCCAAATACCCTTCTTTCTCTTTCATTGATATTAATCATGCTGGAAAACAAAAGATTACATGGTTTTTTTCTTATTCTGTTCCTACTCATAATCACAATGATGTTGTTGGTAAACAAAACAAACACTCATGTGATGTTTGCAACAAGGTTTTTACTTTTAACAAAGCATTGAATGAACATAAGAGGTGTCACTCTCAAAACGGTATTACTAACACACCAACTGCAGCACCATCTTCCATTGATGATCAGTTTCTACCACCCAAGAAACGCCAGGCACTCAGAAGAAAAAGATATATGGATATCGATGATGATGATGAAGTTACTGTTGCTGAAACTCTGTTGCATATATCTCGCGGGGGTTATGAAGGATCAACCGCCAATATCGATGTGAATCACAGCGGCACTAAAAGGCAAAAAATTCCAAGCAATATGGATTTGAACGAGCTTCCAAGTGATGATTTTGAAGTTAATGAGGAGAAGAAGATTAACGAAGCTGAAACTGAAGTCGAGTCAAAAGTTGTGAAGAATTTTGATTTGAACGAGCTTCCAAGTGATGATTTTGAAGATGAATCCAATTAG
Protein sequence

>MS.gene39479.t1

MNKKMSHKPTTNAKYPSFSFIDINHAGKQKITWFFSYSVPTHNHNDVVGKQNKHSCDVCNKVFTFNKALNEHKRCHSQNGITNTPTAAPSSIDDQFLPPKKRQALRRKRYMDIDDDDEVTVAETLLHISRGGYEGSTANIDVNHSGTKRQKIPSNMDLNELPSDDFEVNEEKKINEAETEVESKVVKNFDLNELPSDDFEDESN