AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene024855

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene024855.t1 MTR_5g006510 87.565 193 22 1 1 193 1 191 3.25e-122 344
MS.gene024855.t1 MTR_5g006460 80.829 193 29 3 9 193 1 193 1.34e-108 310
MS.gene024855.t1 MTR_5g006470 70.157 191 48 4 9 193 1 188 9.07e-90 261
MS.gene024855.t1 MTR_5g006450 70.681 191 49 3 9 193 1 190 3.86e-89 260
MS.gene024855.t1 MTR_5g006520 66.667 192 57 3 8 193 1718 1908 1.31e-77 253
MS.gene024855.t1 MTR_1g103110 61.538 182 63 4 16 193 12 190 3.75e-74 222
MS.gene024855.t1 MTR_1g103150 59.659 176 66 3 20 193 18 190 1.84e-71 215
MS.gene024855.t1 MTR_7g114410 44.186 172 90 3 21 190 4 171 4.68e-43 142
MS.gene024855.t1 MTR_7g024760 47.024 168 83 4 24 190 7 169 2.05e-42 141
MS.gene024855.t1 MTR_7g024780 45.349 172 89 3 20 190 3 170 2.84e-42 140
MS.gene024855.t1 MTR_3g463610 42.105 171 98 1 21 190 3 173 3.26e-41 139
MS.gene024855.t1 MTR_7g024765 44.970 169 85 4 24 190 7 169 4.63e-39 132
MS.gene024855.t1 MTR_7g114410 43.312 157 83 3 21 175 4 156 1.77e-37 128
MS.gene024855.t1 MTR_1g103320 50.000 82 39 1 53 134 10 89 1.48e-17 75.5
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene024855.t1 AT2G32030 48.705 193 86 6 1 190 3 185 2.17e-54 172
MS.gene024855.t1 AT2G32020 51.765 170 72 5 24 190 18 180 3.24e-52 166
MS.gene024855.t1 AT3G22560 38.857 175 99 4 20 190 2 172 5.36e-34 119

Find 36 sgRNAs with CRISPR-Local

Find 47 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTGTTGATGTGGATAATTTA+AGG 0.203228 5.3:-1594267 MS.gene024855:CDS
CAAATCAATGATCTCTTCTT+TGG 0.204931 5.3:+1594654 None:intergenic
GTTGATGCCTTGGTCTTTGC+TGG 0.262298 5.3:+1594531 None:intergenic
GCTTGAAGCCTTTCCAAGTA+TGG 0.276638 5.3:+1594292 None:intergenic
TGCCATAACGATCATGCTAT+TGG 0.288303 5.3:-1594463 MS.gene024855:CDS
GCAGAACTTGGGTATGTTCT+AGG 0.307665 5.3:-1594388 MS.gene024855:CDS
ATGTTCTAGGCTCTAAATAC+TGG 0.313478 5.3:-1594375 MS.gene024855:CDS
CCTTGGTCTTTGCTGGTGTA+AGG 0.327596 5.3:+1594538 None:intergenic
GAAAAGATCGGAGTGTGATT+TGG 0.386444 5.3:+1594629 None:intergenic
ACCTCGATGATCTCATGGTT+TGG 0.401354 5.3:-1594597 MS.gene024855:CDS
GGCTCTAAATACTGGGGTAA+AGG 0.409375 5.3:-1594367 MS.gene024855:CDS
ATTCAGTGAATTTCCATACT+TGG 0.413337 5.3:-1594305 MS.gene024855:CDS
GCCATAACGATCATGCTATT+GGG 0.423146 5.3:-1594462 MS.gene024855:CDS
TTCTGACCTCGATGATCTCA+TGG 0.433346 5.3:-1594602 MS.gene024855:CDS
GCTCTAAATACTGGGGTAAA+GGG 0.442106 5.3:-1594366 MS.gene024855:CDS
TGAGTTCACTTGATGATAAG+AGG 0.442621 5.3:-1594423 MS.gene024855:CDS
CAAAGAGTAGTTGAGAAAGT+TGG 0.450786 5.3:-1594241 MS.gene024855:CDS
AGGATCGCATGTGCAGAACT+TGG 0.454084 5.3:-1594400 MS.gene024855:CDS
ACCCAATAGCATGATCGTTA+TGG 0.457877 5.3:+1594461 None:intergenic
CTACTGATCTTAAACTAATG+AGG 0.474389 5.3:-1594138 MS.gene024855:CDS
GTAAGGTTCACCCCAGAACT+TGG 0.480302 5.3:+1594555 None:intergenic
TAAACTAATGAGGATGTTCA+AGG 0.483858 5.3:-1594128 MS.gene024855:CDS
GTGAATTTCCATACTTGGAA+AGG 0.490341 5.3:-1594300 MS.gene024855:CDS
TGCTGTGAAACAAATGGTTA+AGG 0.500098 5.3:-1594332 MS.gene024855:CDS
TGTTCTAGGCTCTAAATACT+GGG 0.526941 5.3:-1594374 MS.gene024855:CDS
CTTATCATCAAGTGAACTCA+AGG 0.556721 5.3:+1594426 None:intergenic
GCTTCAAGCTCTTGTTGATG+TGG 0.560091 5.3:-1594278 MS.gene024855:CDS
GGATCGCATGTGCAGAACTT+GGG 0.585194 5.3:-1594399 MS.gene024855:CDS
GGTCAGAAAGATGAAAAGAT+CGG 0.592412 5.3:+1594617 None:intergenic
CATTTGTTTCACAGCACATG+TGG 0.625218 5.3:+1594339 None:intergenic
TAATGAGGATGTTCAAGGTG+AGG 0.626914 5.3:-1594123 MS.gene024855:CDS
CACATGTGCTGTGAAACAAA+TGG 0.647600 5.3:-1594338 MS.gene024855:CDS
GTTCACTTGATGATAAGAGG+AGG 0.664638 5.3:-1594420 MS.gene024855:CDS
CCTTACACCAGCAAAGACCA+AGG 0.673207 5.3:-1594538 MS.gene024855:CDS
GTTCTAGGCTCTAAATACTG+GGG 0.712321 5.3:-1594373 MS.gene024855:CDS
GCCAAACCATGAGATCATCG+AGG 0.781144 5.3:+1594596 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! CATCAACTTCATTAAAAATA+TGG - chr5.3:1594284-1594303 MS.gene024855:CDS 20.0%
!!! AGGAAGTATGTATTTTTTAA+AGG - chr5.3:1594603-1594622 MS.gene024855:CDS 20.0%
! TTGTTGATGTGGATAATTTA+AGG - chr5.3:1594532-1594551 MS.gene024855:CDS 25.0%
!!! AAAGTTGGTTTTCAAAAAGA+GGG - chr5.3:1594573-1594592 MS.gene024855:CDS 25.0%
ATTCAGTGAATTTCCATACT+TGG - chr5.3:1594494-1594513 MS.gene024855:CDS 30.0%
CAAATCAATGATCTCTTCTT+TGG + chr5.3:1594148-1594167 None:intergenic 30.0%
CTACTGATCTTAAACTAATG+AGG - chr5.3:1594661-1594680 MS.gene024855:CDS 30.0%
TAAACTAATGAGGATGTTCA+AGG - chr5.3:1594671-1594690 MS.gene024855:CDS 30.0%
TCATTAAAAATATGGCAAGC+AGG - chr5.3:1594292-1594311 MS.gene024855:CDS 30.0%
!!! GAAAGTTGGTTTTCAAAAAG+AGG - chr5.3:1594572-1594591 MS.gene024855:CDS 30.0%
!!! TTTTAATGAAGTTGATGCCT+TGG + chr5.3:1594281-1594300 None:intergenic 30.0%
CAAAGAGTAGTTGAGAAAGT+TGG - chr5.3:1594558-1594577 MS.gene024855:CDS 35.0%
CTTATCATCAAGTGAACTCA+AGG + chr5.3:1594376-1594395 None:intergenic 35.0%
GGTCAGAAAGATGAAAAGAT+CGG + chr5.3:1594185-1594204 None:intergenic 35.0%
GTGAATTTCCATACTTGGAA+AGG - chr5.3:1594499-1594518 MS.gene024855:CDS 35.0%
TGCTGTGAAACAAATGGTTA+AGG - chr5.3:1594467-1594486 MS.gene024855:CDS 35.0%
TTCAAAAAGAGGGAGTTCTT+AGG - chr5.3:1594583-1594602 MS.gene024855:CDS 35.0%
TTGGCATACTGATGAAAAAG+TGG - chr5.3:1594221-1594240 MS.gene024855:CDS 35.0%
! TGAGTTCACTTGATGATAAG+AGG - chr5.3:1594376-1594395 MS.gene024855:CDS 35.0%
!! ATGTTCTAGGCTCTAAATAC+TGG - chr5.3:1594424-1594443 MS.gene024855:CDS 35.0%
!! TGTTCTAGGCTCTAAATACT+GGG - chr5.3:1594425-1594444 MS.gene024855:CDS 35.0%
ACCCAATAGCATGATCGTTA+TGG + chr5.3:1594341-1594360 None:intergenic 40.0%
ATGAAAAAGTGGCCAAGTTC+TGG - chr5.3:1594232-1594251 MS.gene024855:CDS 40.0%
CACATGTGCTGTGAAACAAA+TGG - chr5.3:1594461-1594480 MS.gene024855:CDS 40.0%
CATTTGTTTCACAGCACATG+TGG + chr5.3:1594463-1594482 None:intergenic 40.0%
GAAAAGATCGGAGTGTGATT+TGG + chr5.3:1594173-1594192 None:intergenic 40.0%
GCCATAACGATCATGCTATT+GGG - chr5.3:1594337-1594356 MS.gene024855:CDS 40.0%
TAATGAGGATGTTCAAGGTG+AGG - chr5.3:1594676-1594695 MS.gene024855:CDS 40.0%
TGAAAAAGTGGCCAAGTTCT+GGG - chr5.3:1594233-1594252 MS.gene024855:CDS 40.0%
TGCCATAACGATCATGCTAT+TGG - chr5.3:1594336-1594355 MS.gene024855:CDS 40.0%
! GCTCTAAATACTGGGGTAAA+GGG - chr5.3:1594433-1594452 MS.gene024855:CDS 40.0%
! GTTCACTTGATGATAAGAGG+AGG - chr5.3:1594379-1594398 MS.gene024855:CDS 40.0%
!! GTTCTAGGCTCTAAATACTG+GGG - chr5.3:1594426-1594445 MS.gene024855:CDS 40.0%
ACCTCGATGATCTCATGGTT+TGG - chr5.3:1594202-1594221 MS.gene024855:CDS 45.0%
GAAAAAGTGGCCAAGTTCTG+GGG - chr5.3:1594234-1594253 MS.gene024855:CDS 45.0%
GCAGAACTTGGGTATGTTCT+AGG - chr5.3:1594411-1594430 MS.gene024855:CDS 45.0%
GCTTCAAGCTCTTGTTGATG+TGG - chr5.3:1594521-1594540 MS.gene024855:CDS 45.0%
GCTTGAAGCCTTTCCAAGTA+TGG + chr5.3:1594510-1594529 None:intergenic 45.0%
TTCTGACCTCGATGATCTCA+TGG - chr5.3:1594197-1594216 MS.gene024855:CDS 45.0%
!! GGCTCTAAATACTGGGGTAA+AGG - chr5.3:1594432-1594451 MS.gene024855:CDS 45.0%
AGGATCGCATGTGCAGAACT+TGG - chr5.3:1594399-1594418 MS.gene024855:CDS 50.0%
CCTTACACCAGCAAAGACCA+AGG - chr5.3:1594261-1594280 MS.gene024855:CDS 50.0%
GCCAAACCATGAGATCATCG+AGG + chr5.3:1594206-1594225 None:intergenic 50.0%
GGATCGCATGTGCAGAACTT+GGG - chr5.3:1594400-1594419 MS.gene024855:CDS 50.0%
GTAAGGTTCACCCCAGAACT+TGG + chr5.3:1594247-1594266 None:intergenic 50.0%
! CCTTGGTCTTTGCTGGTGTA+AGG + chr5.3:1594264-1594283 None:intergenic 50.0%
! GTTGATGCCTTGGTCTTTGC+TGG + chr5.3:1594271-1594290 None:intergenic 50.0%


Chromosome Type Strat End Strand Name
chr5.3 gene 1594099 1594722 1594099 ID=MS.gene024855
chr5.3 mRNA 1594099 1594722 1594099 ID=MS.gene024855.t1;Parent=MS.gene024855
chr5.3 exon 1594099 1594722 1594099 ID=MS.gene024855.t1.exon1;Parent=MS.gene024855.t1
chr5.3 CDS 1594099 1594722 1594099 ID=cds.MS.gene024855.t1;Parent=MS.gene024855.t1
Gene Sequence

>MS.gene024855

ATGGAGCAAAACACAAGTATTATGATAGAGCAACTTTCTATTTCTTCCAAAGAAGAGATCATTGATTTGAACCAAATCACACTCCGATCTTTTCATCTTTCTGACCTCGATGATCTCATGGTTTGGCATACTGATGAAAAAGTGGCCAAGTTCTGGGGTGAACCTTACACCAGCAAAGACCAAGGCATCAACTTCATTAAAAATATGGCAAGCAGGTATCTAAGTTGCAAAGCAATATGCCATAACGATCATGCTATTGGGTGTATTAAGTTGTCCTTGAGTTCACTTGATGATAAGAGGAGGATCGCATGTGCAGAACTTGGGTATGTTCTAGGCTCTAAATACTGGGGTAAAGGGATTGCCACATGTGCTGTGAAACAAATGGTTAAGGTTGCATTCAGTGAATTTCCATACTTGGAAAGGCTTCAAGCTCTTGTTGATGTGGATAATTTAAGGTCGCAAAGAGTAGTTGAGAAAGTTGGTTTTCAAAAAGAGGGAGTTCTTAGGAAGTATGTATTTTTTAAAGGAAAAAGCAGAGATATGATCATGTTCAGTCTTCTTTCTACTGATCTTAAACTAATGAGGATGTTCAAGGTGAGGAACTTATATATTGCTGAAATGTAA
Protein sequence

>MS.gene024855.t1

MEQNTSIMIEQLSISSKEEIIDLNQITLRSFHLSDLDDLMVWHTDEKVAKFWGEPYTSKDQGINFIKNMASRYLSCKAICHNDHAIGCIKLSLSSLDDKRRIACAELGYVLGSKYWGKGIATCAVKQMVKVAFSEFPYLERLQALVDVDNLRSQRVVEKVGFQKEGVLRKYVFFKGKSRDMIMFSLLSTDLKLMRMFKVRNLYIAEM