AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene065960

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene065960.t1 MTR_8g087450 80.479 292 9 1 1 244 1 292 6.32e-159 442
MS.gene065960.t1 MTR_2g017960 56.849 292 61 7 1 243 1 276 7.53e-72 221
MS.gene065960.t1 MTR_2g017970 56.667 210 41 3 76 237 67 274 4.16e-66 206
MS.gene065960.t1 MTR_4g059840 43.568 241 73 7 58 240 53 288 9.61e-49 162
MS.gene065960.t1 MTR_4g053380 40.984 305 100 9 2 243 7 294 1.89e-48 161
MS.gene065960.t1 MTR_4g059790 46.269 201 50 4 58 200 53 253 1.68e-46 156
MS.gene065960.t1 MTR_2g093980 39.661 295 109 10 1 240 1 281 7.25e-45 152
MS.gene065960.t1 MTR_2g093970 37.671 292 101 8 10 237 13 287 1.07e-39 139
MS.gene065960.t1 MTR_2g017950 35.811 296 109 9 6 237 12 290 1.59e-37 133
MS.gene065960.t1 MTR_4g059780 39.483 271 95 6 21 236 45 301 3.81e-37 132
MS.gene065960.t1 MTR_8g087470 35.849 265 105 6 41 240 51 315 6.76e-36 129
MS.gene065960.t1 MTR_8g087460 35.974 303 124 10 8 240 13 315 4.92e-35 127
MS.gene065960.t1 MTR_4g059720 34.061 229 62 5 1 180 4 192 8.86e-28 107
MS.gene065960.t1 MTR_2g093990 33.495 206 79 4 77 231 41 239 1.28e-23 95.9
MS.gene065960.t1 MTR_7g101080 33.735 166 60 2 58 174 21 185 3.66e-21 89.4
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene065960.t1 AT5G03170 34.659 176 65 2 70 196 29 203 5.12e-22 91.7
MS.gene065960.t1 AT5G60490 34.247 146 46 2 77 173 39 183 8.73e-18 80.1

Find 41 sgRNAs with CRISPR-Local

Find 65 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GGTGCTGGAGCTTTAGCTTT+AGG 0.270473 4.1:+13242572 None:intergenic
GAATTCTCTTTCTCAGCTTT+AGG 0.296501 4.1:+13242533 None:intergenic
TGCTATATATCATGTGAATA+AGG 0.305049 4.1:-13242621 MS.gene065960:CDS
CAGATTAATGTGACTGCATA+TGG 0.308276 4.1:-13242716 MS.gene065960:CDS
GGTGCTGGAGCAGGTGTTGA+AGG 0.331645 4.1:+13243111 None:intergenic
ATGCATGTTATTCAAGCTAA+TGG 0.337878 4.1:+13242460 None:intergenic
GAATAAGGTTCTTATTCCTT+TGG 0.338628 4.1:-13242606 MS.gene065960:CDS
TCTTGGTTTCCTGACGAATC+AGG 0.343060 4.1:+13243042 None:intergenic
TGTGGTAATGCTGGGACTAA+TGG 0.407871 4.1:+13243081 None:intergenic
GATTAGTGTGTTGAATGATT+TGG 0.407894 4.1:+13242996 None:intergenic
TTAGAATCTTGATTATGTCT+TGG 0.417666 4.1:+13243025 None:intergenic
GCCTTAGCAAGAGCTGGTGC+TGG 0.431209 4.1:+13242557 None:intergenic
TCTGAAAAGGCACCATCATC+TGG 0.442423 4.1:+13242889 None:intergenic
AGAAGATAGAGGCAAGTAGT+AGG 0.446057 4.1:+13243223 None:intergenic
ATATCAGTGTTGGTTTCCCT+TGG 0.450067 4.1:-13242434 MS.gene065960:CDS
AACAGTGTGAATATTTCAAC+TGG 0.459076 4.1:-13242692 MS.gene065960:CDS
GTAGGTGATTGTGGTAATGC+TGG 0.464029 4.1:+13243072 None:intergenic
GACGAATCAGGATTTGTTGT+AGG 0.471829 4.1:+13243054 None:intergenic
GTGCTGGAGCAGGTGTTGAA+GGG 0.481443 4.1:+13243112 None:intergenic
TTAGGTGCCTTAGCAAGAGC+TGG 0.489973 4.1:+13242551 None:intergenic
GGATTTGTTGTAGGTGATTG+TGG 0.513333 4.1:+13243063 None:intergenic
ACAATTCTTGCACCAGATGA+TGG 0.514841 4.1:-13242901 MS.gene065960:CDS
GGAGCAGGTGTTGAAGGGGT+AGG 0.521942 4.1:+13243117 None:intergenic
ACAACAAATCCTGATTCGTC+AGG 0.522883 4.1:-13243051 MS.gene065960:CDS
AACCTGCTTGAGTTCTGAAA+AGG 0.528957 4.1:+13242876 None:intergenic
AGTGGTGATTGAGAAGATAG+AGG 0.531658 4.1:+13243212 None:intergenic
TTTGTGTTGTCTTGAGCAAA+CGG 0.534377 4.1:+13242974 None:intergenic
TCCAGCACCAGCTCTTGCTA+AGG 0.542557 4.1:-13242558 MS.gene065960:CDS
AGCGTAAACGATTCCAGTGA+TGG 0.545525 4.1:+13242655 None:intergenic
TTACAAGCTGTGCATTGACT+TGG 0.551173 4.1:+13242944 None:intergenic
CATGCATGGAATATCAGTGT+TGG 0.573529 4.1:-13242444 MS.gene065960:CDS
TGCTGGAGCAGGTGTTGAAG+GGG 0.574142 4.1:+13243113 None:intergenic
CTGCAAGCAGAGAAATTCCA+AGG 0.575775 4.1:+13242417 None:intergenic
AGCTGGTGATTGAGCTAAAG+TGG 0.578327 4.1:+13243194 None:intergenic
ATTAGCTTGAATAACATGCA+TGG 0.579278 4.1:-13242458 MS.gene065960:CDS
TAGGTGATTGTGGTAATGCT+GGG 0.582717 4.1:+13243073 None:intergenic
GTTGTTGATACAACCATCAC+TGG 0.593007 4.1:-13242668 MS.gene065960:CDS
TTAGGCTTAACAAAATCCAA+AGG 0.601169 4.1:+13242590 None:intergenic
TGATCAGACTCAGGCACACA+AGG 0.622744 4.1:-13242495 MS.gene065960:CDS
AGATGATGATGATCAGACTC+AGG 0.626792 4.1:-13242504 MS.gene065960:CDS
TGCAAGCAGAGAAATTCCAA+GGG 0.658685 4.1:+13242418 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! TGCTATATATCATGTGAATA+AGG - chr4.1:13243022-13243041 MS.gene065960:CDS 25.0%
! TTAGAATCTTGATTATGTCT+TGG + chr4.1:13242621-13242640 None:intergenic 25.0%
AACAGTGTGAATATTTCAAC+TGG - chr4.1:13242951-13242970 MS.gene065960:CDS 30.0%
ATGCATGTTATTCAAGCTAA+TGG + chr4.1:13243186-13243205 None:intergenic 30.0%
CAGCTTGTAACTACAAAAAA+TGG - chr4.1:13242712-13242731 MS.gene065960:CDS 30.0%
CTTGTAACTACAAAAAATGG+AGG - chr4.1:13242715-13242734 MS.gene065960:CDS 30.0%
GAATAAGGTTCTTATTCCTT+TGG - chr4.1:13243037-13243056 MS.gene065960:CDS 30.0%
GATTAGTGTGTTGAATGATT+TGG + chr4.1:13242650-13242669 None:intergenic 30.0%
TTAGGCTTAACAAAATCCAA+AGG + chr4.1:13243056-13243075 None:intergenic 30.0%
TTCGAACTTGATACATATTC+AGG + chr4.1:13242849-13242868 None:intergenic 30.0%
! ACATTAATCTGAAATCCTTG+TGG + chr4.1:13242918-13242937 None:intergenic 30.0%
! ATTAGCTTGAATAACATGCA+TGG - chr4.1:13243185-13243204 MS.gene065960:CDS 30.0%
! CATTAATCTGAAATCCTTGT+GGG + chr4.1:13242917-13242936 None:intergenic 30.0%
CAGATTAATGTGACTGCATA+TGG - chr4.1:13242927-13242946 MS.gene065960:CDS 35.0%
GAATTCTCTTTCTCAGCTTT+AGG + chr4.1:13243113-13243132 None:intergenic 35.0%
TTTGTGTTGTCTTGAGCAAA+CGG + chr4.1:13242672-13242691 None:intergenic 35.0%
!! TTTTTGTTGTCTTTCTCCCA+AGG + chr4.1:13242802-13242821 None:intergenic 35.0%
ACAATTCTTGCACCAGATGA+TGG - chr4.1:13242742-13242761 MS.gene065960:intron 40.0%
AGAAGATAGAGGCAAGTAGT+AGG + chr4.1:13242423-13242442 None:intergenic 40.0%
AGTGGTGATTGAGAAGATAG+AGG + chr4.1:13242434-13242453 None:intergenic 40.0%
CATGCATGGAATATCAGTGT+TGG - chr4.1:13243199-13243218 MS.gene065960:CDS 40.0%
GTTGTTGATACAACCATCAC+TGG - chr4.1:13242975-13242994 MS.gene065960:CDS 40.0%
TGCAAGCAGAGAAATTCCAA+GGG + chr4.1:13243228-13243247 None:intergenic 40.0%
! ACAACAAATCCTGATTCGTC+AGG - chr4.1:13242592-13242611 MS.gene065960:CDS 40.0%
! AGATGATGATGATCAGACTC+AGG - chr4.1:13243139-13243158 MS.gene065960:CDS 40.0%
! TAGGTGATTGTGGTAATGCT+GGG + chr4.1:13242573-13242592 None:intergenic 40.0%
!! AACCTGCTTGAGTTCTGAAA+AGG + chr4.1:13242770-13242789 None:intergenic 40.0%
!! ATATCAGTGTTGGTTTCCCT+TGG - chr4.1:13243209-13243228 MS.gene065960:CDS 40.0%
!! GACGAATCAGGATTTGTTGT+AGG + chr4.1:13242592-13242611 None:intergenic 40.0%
!! GGATTTGTTGTAGGTGATTG+TGG + chr4.1:13242583-13242602 None:intergenic 40.0%
!! TTACAAGCTGTGCATTGACT+TGG + chr4.1:13242702-13242721 None:intergenic 40.0%
!! TTGAAGGGGTAGGTTTTGTA+GGG + chr4.1:13242519-13242538 None:intergenic 40.0%
!!! TTTGTAGGTGCTGGTTTTTC+TGG + chr4.1:13242490-13242509 None:intergenic 40.0%
AGCAGGTTACTTCAACTCCT+TGG - chr4.1:13242782-13242801 MS.gene065960:intron 45.0%
AGCGTAAACGATTCCAGTGA+TGG + chr4.1:13242991-13243010 None:intergenic 45.0%
AGCTGGTGATTGAGCTAAAG+TGG + chr4.1:13242452-13242471 None:intergenic 45.0%
CACTAGCTAGTGTCAACACA+GGG + chr4.1:13242890-13242909 None:intergenic 45.0%
CTGCAAGCAGAGAAATTCCA+AGG + chr4.1:13243229-13243248 None:intergenic 45.0%
GCAGGTTACTTCAACTCCTT+GGG - chr4.1:13242783-13242802 MS.gene065960:intron 45.0%
TCACTAGCTAGTGTCAACAC+AGG + chr4.1:13242891-13242910 None:intergenic 45.0%
TCTTGGTTTCCTGACGAATC+AGG + chr4.1:13242604-13242623 None:intergenic 45.0%
! GTAGGTGATTGTGGTAATGC+TGG + chr4.1:13242574-13242593 None:intergenic 45.0%
! TGCCTTTTCAGAACTCAAGC+AGG - chr4.1:13242765-13242784 MS.gene065960:intron 45.0%
! TGTGGTAATGCTGGGACTAA+TGG + chr4.1:13242565-13242584 None:intergenic 45.0%
!! ACTAATGGTTTTGCTGGTGC+TGG + chr4.1:13242550-13242569 None:intergenic 45.0%
!! GTTGAAGGGGTAGGTTTTGT+AGG + chr4.1:13242520-13242539 None:intergenic 45.0%
!! TCTGAAAAGGCACCATCATC+TGG + chr4.1:13242757-13242776 None:intergenic 45.0%
!! TGAAGGGGTAGGTTTTGTAG+GGG + chr4.1:13242518-13242537 None:intergenic 45.0%
!!! GCTGGTTTTTCTGGTGCTTT+TGG + chr4.1:13242481-13242500 None:intergenic 45.0%
!!! TTTGTAGGGGCTGGTTTTGT+AGG + chr4.1:13242505-13242524 None:intergenic 45.0%
CTAGCTAGTGATAGCCCACA+AGG - chr4.1:13242900-13242919 MS.gene065960:CDS 50.0%
TGATCAGACTCAGGCACACA+AGG - chr4.1:13243148-13243167 MS.gene065960:CDS 50.0%
TTAGGTGCCTTAGCAAGAGC+TGG + chr4.1:13243095-13243114 None:intergenic 50.0%
!! GCTGGGACTAATGGTTTTGC+TGG + chr4.1:13242556-13242575 None:intergenic 50.0%
!! GGTGCTGGAGCTTTAGCTTT+AGG + chr4.1:13243074-13243093 None:intergenic 50.0%
TCCAGCACCAGCTCTTGCTA+AGG - chr4.1:13243085-13243104 MS.gene065960:CDS 55.0%
!! GTGCTGGAGCAGGTGTTGAA+GGG + chr4.1:13242534-13242553 None:intergenic 55.0%
!! TGCTGGAGCAGGTGTTGAAG+GGG + chr4.1:13242533-13242552 None:intergenic 55.0%
GCCTTAGCAAGAGCTGGTGC+TGG + chr4.1:13243089-13243108 None:intergenic 60.0%
!! GGAGCAGGTGTTGAAGGGGT+AGG + chr4.1:13242529-13242548 None:intergenic 60.0%
!! GGGGTAGGTTTTGTAGGGGC+TGG + chr4.1:13242514-13242533 None:intergenic 60.0%
!! GGTGCTGGAGCAGGTGTTGA+AGG + chr4.1:13242535-13242554 None:intergenic 60.0%
!! GGTTTTGCTGGTGCTGGAGC+AGG + chr4.1:13242544-13242563 None:intergenic 60.0%
!!! GGGGCTGGTTTTGTAGGTGC+TGG + chr4.1:13242499-13242518 None:intergenic 60.0%
!!! GGTGCTTTTGGTGCTGCAGC+TGG + chr4.1:13242469-13242488 None:intergenic 60.0%


Chromosome Type Strat End Strand Name
chr4.1 gene 13242394 13243271 13242394 ID=MS.gene065960
chr4.1 mRNA 13242394 13243271 13242394 ID=MS.gene065960.t1;Parent=MS.gene065960
chr4.1 exon 13242879 13243271 13242879 ID=MS.gene065960.t1.exon1;Parent=MS.gene065960.t1
chr4.1 CDS 13242879 13243271 13242879 ID=cds.MS.gene065960.t1;Parent=MS.gene065960.t1
chr4.1 exon 13242394 13242735 13242394 ID=MS.gene065960.t1.exon2;Parent=MS.gene065960.t1
chr4.1 CDS 13242394 13242735 13242394 ID=cds.MS.gene065960.t1;Parent=MS.gene065960.t1
Gene Sequence

>MS.gene065960

ATGAATCAAATTTTCTTGTTCTCACTCCTACTACTTGCCTCTATCTTCTCAATCACCACTTTAGCTCAATCACCAGCTGCAGCACCAAAAGCACCAGAAAAACCAGCACCTACAAAACCAGCCCCTACAAAACCTACCCCTTCAACACCTGCTCCAGCACCAGCAAAACCATTAGTCCCAGCATTACCACAATCACCTACAACAAATCCTGATTCGTCAGGAAACCAAGACATAATCAAGATTCTAAGAAAAGCCAAATCATTCAACACACTAATCCGTTTGCTCAAGACAACACAAATCATCAACCAAGTCAATGCACAGCTTGTAACTACAAAAAATGGAGGCTTGACAATTCTTGCACCAGATGATGGTGCCTTTTCAGAACTCAAGCAGGTTACTTCAACTCCTTGGGAGAAAGACAACAAAAAGAATTGATTCAGTATCATGTTCTTCCTGAATATGTATCAAGTTCGAACTTTGATTCTCTCAGCAACCCTGTGTTGACACTAGCTAGTGATAGCCCACAAGGATTTCAGATTAATGTGACTGCATATGGAAACAGTGTGAATATTTCAACTGGCGTTGTTGATACAACCATCACTGGAATCGTTTACGCTGATAAAACACTTGCTATATATCATGTGAATAAGGTTCTTATTCCTTTGGATTTTGTTAAGCCTAAAGCTAAAGCTCCAGCACCAGCTCTTGCTAAGGCACCTAAAGCTGAGAAAGAGAATTCATCTGCAGATGATGATGATCAGACTCAGGCACACAAGGATAGTTCTGATGCCATTAGCTTGAATAACATGCATGGAATATCAGTGTTGGTTTCCCTTGGAATTTCTCTGCTTGCAGTTGCAGTAACAACTATGTTGTGA
Protein sequence

>MS.gene065960.t1

MNQIFLFSLLLLASIFSITTLAQSPAAAPKAPEKPAPTKPAPTKPTPSTPAPAPAKPLVPALPQSPTTNPDSSGNQDIIKILRKAKSFNTLIRLLKTTQIINQVNAQLVTTKNGGLTILAPDDGAFSELKQINVTAYGNSVNISTGVVDTTITGIVYADKTLAIYHVNKVLIPLDFVKPKAKAPAPALAKAPKAEKENSSADDDDQTQAHKDSSDAISLNNMHGISVLVSLGISLLAVAVTTML