AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene001465


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene001465.t1 MTR_3g102980 86.975 238 7 4 1 216 1 236 3.18e-130 366
MS.gene001465.t1 MTR_1g018420 50.204 245 76 10 1 214 1 230 5.44e-62 193
MS.gene001465.t1 MTR_1g106730 43.580 257 85 14 1 211 3 245 2.29e-41 141
MS.gene001465.t1 MTR_0160s0030 36.885 122 52 4 84 196 240 345 4.36e-12 64.7
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene001465.t1 AT1G27730 45.992 237 91 10 1 212 1 225 3.60e-49 160
MS.gene001465.t1 AT5G04340 43.644 236 93 10 1 203 1 229 6.36e-43 144
MS.gene001465.t1 AT5G43170 46.429 224 71 11 1 207 1 192 4.00e-37 128
MS.gene001465.t1 AT3G19580 40.000 260 101 9 1 208 1 257 2.23e-35 126
MS.gene001465.t1 AT3G19580 40.000 260 101 9 1 208 1 257 2.23e-35 126
MS.gene001465.t1 AT5G67450 37.295 244 83 10 1 181 1 237 2.82e-28 107
MS.gene001465.t1 AT3G49930 40.805 174 65 5 30 181 36 193 1.22e-26 102
MS.gene001465.t1 AT2G45120 36.420 162 75 6 44 181 143 300 3.04e-16 76.3
MS.gene001465.t1 AT3G60580 33.533 167 73 4 44 181 119 276 2.15e-15 73.6
MS.gene001465.t1 AT1G49900 42.222 90 37 2 85 159 194 283 8.19e-12 64.3
MS.gene001465.t1 AT2G28200 29.744 195 80 8 46 184 70 263 5.41e-11 61.2

Find 54 sgRNAs with CRISPR-Local

Find 67 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTGCGGACATAACAGCTTTC+CGG 0.302034 3.2:+24588325 None:intergenic
GTTTCAAGATAACTCAGATT+TGG 0.369889 3.2:+24588582 None:intergenic
CCTTCCTACTGACAGGCTTT+GGG 0.379008 3.2:-24588201 MS.gene001465:intron
TACTCCTTTCACACCCTTTG+AGG 0.385893 3.2:-24588607 MS.gene001465:CDS
GGCAGCGTTGGTGCCGGTGC+CGG 0.399502 3.2:-24588153 MS.gene001465:CDS
CTCAGATTTGGTTCCTCAAA+GGG 0.424837 3.2:+24588594 None:intergenic
GTTGGTGCCGGTGCCGGTGC+TGG 0.425482 3.2:-24588147 MS.gene001465:CDS
CATAACAGCTTTCCGGTGAC+TGG 0.439265 3.2:+24588332 None:intergenic
GGCTTCTTTGCAGCAGGTAA+AGG 0.446061 3.2:+24587997 None:intergenic
AATTTCCAGCTTGAAAAGAC+AGG 0.452679 3.2:+24587975 None:intergenic
CTGATCTTCAGCGGTGGTTG+CGG 0.460016 3.2:+24588308 None:intergenic
TTTGAAAAGTCCGGAAAAGC+CGG 0.466243 3.2:+24588051 None:intergenic
ACTGGCTTTGTGTCCACCTA+GGG 0.475209 3.2:+24588350 None:intergenic
GATCGTTTACCTTTCGTCCA+CGG 0.485045 3.2:+24588558 None:intergenic
GCATTTGTGACTGAGTTTAA+CGG 0.491121 3.2:+24588407 None:intergenic
AGACAGGGCTTCTTTGCAGC+AGG 0.516606 3.2:+24587991 None:intergenic
GGTTCCTCAAAGGGTGTGAA+AGG 0.517530 3.2:+24588603 None:intergenic
ACGATCAAAGCGTTCTCGCA+TGG 0.518878 3.2:-24588541 MS.gene001465:CDS
TACGAAGGCAGCGTTGGTGC+CGG 0.519961 3.2:-24588159 MS.gene001465:CDS
TTGAAAAGTCCGGAAAAGCC+GGG 0.523321 3.2:+24588052 None:intergenic
GACTGGCTTTGTGTCCACCT+AGG 0.526559 3.2:+24588349 None:intergenic
TCTTACGTTGGAAGCAGAGC+TGG 0.528912 3.2:+24588257 None:intergenic
CTGAGTTTAACGGTGGTTAG+CGG 0.533899 3.2:+24588417 None:intergenic
ACTCAGATTTGGTTCCTCAA+AGG 0.539745 3.2:+24588593 None:intergenic
TTCTCATCTTATCAAGCCCT+AGG 0.550654 3.2:-24588366 MS.gene001465:CDS
GTAACTGCCTCTGAAGGAGT+TGG 0.551176 3.2:-24588114 MS.gene001465:CDS
CTTGAAACACCGTGGACGAA+AGG 0.563216 3.2:-24588567 MS.gene001465:CDS
TGTGAAAGGAGTAGCAGTGG+TGG 0.569120 3.2:+24588617 None:intergenic
TGTCACTACGAAGGCAGCGT+TGG 0.571767 3.2:-24588165 MS.gene001465:CDS
TCCTACTGACAGGCTTTGGG+AGG 0.574945 3.2:-24588198 MS.gene001465:intron
GGTAGTCACGGCGGATGAAG+TGG 0.575582 3.2:+24588278 None:intergenic
GCTACTTCCAGCACCGGCAC+CGG 0.578492 3.2:+24588140 None:intergenic
TAAGATCAAAATCACGGTGG+TGG 0.583762 3.2:+24588079 None:intergenic
GGAAGCAGAGCTGGTAGTCA+CGG 0.585255 3.2:+24588266 None:intergenic
CTCATCATGCTTGCTCGCAG+CGG 0.585296 3.2:-24588477 MS.gene001465:CDS
GTGGACACAAAGCCAGTCAC+CGG 0.585980 3.2:-24588344 MS.gene001465:CDS
ATTTCCAGCTTGAAAAGACA+GGG 0.591447 3.2:+24587976 None:intergenic
TACAGCGCTACTTCCAGCAC+CGG 0.591699 3.2:+24588134 None:intergenic
ATTATTGATCAGTAATGAGA+AGG 0.592327 3.2:+24587952 None:intergenic
GTGAAAGGAGTAGCAGTGGT+GGG 0.592634 3.2:+24588618 None:intergenic
AGCGCTGTAACTGCCTCTGA+AGG 0.607763 3.2:-24588120 MS.gene001465:CDS
TCATCTTATCAAGCCCTAGG+TGG 0.625860 3.2:-24588363 MS.gene001465:CDS
TGACGATCCAACTCCTTCAG+AGG 0.633382 3.2:+24588107 None:intergenic
GGGTGTGAAAGGAGTAGCAG+TGG 0.640901 3.2:+24588614 None:intergenic
GGAGGTTAAGATCAAAATCA+CGG 0.658091 3.2:+24588073 None:intergenic
AGTCACGGCGGATGAAGTGG+TGG 0.674100 3.2:+24588281 None:intergenic
CACAAGCGTTGTCACTACGA+AGG 0.677003 3.2:-24588174 MS.gene001465:CDS
TTTGTGACTGAGTTTAACGG+TGG 0.692042 3.2:+24588410 None:intergenic
AGCAGAGCTGGTAGTCACGG+CGG 0.700777 3.2:+24588269 None:intergenic
GGTGATCTGATCTTCAGCGG+TGG 0.700953 3.2:+24588302 None:intergenic
GGTGGTGATCTGATCTTCAG+CGG 0.704088 3.2:+24588299 None:intergenic
AAAAGTCCGGAAAAGCCGGG+AGG 0.720865 3.2:+24588055 None:intergenic
TGAGTTATCTTGAAACACCG+TGG 0.739154 3.2:-24588575 MS.gene001465:CDS
GGTTAAGATCAAAATCACGG+TGG 0.807668 3.2:+24588076 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAAAACTTCTTTGAAAAGTC+CGG + chr3.2:24588563-24588582 None:intergenic 25.0%
GTTTCAAGATAACTCAGATT+TGG + chr3.2:24588023-24588042 None:intergenic 30.0%
! CTTTTCAAAGAAGTTTTTCG+TGG - chr3.2:24588565-24588584 MS.gene001465:CDS 30.0%
AATTTCCAGCTTGAAAAGAC+AGG + chr3.2:24588630-24588649 None:intergenic 35.0%
ATTTCCAGCTTGAAAAGACA+GGG + chr3.2:24588629-24588648 None:intergenic 35.0%
CAACGACAAAAAGTCTGATT+CGG - chr3.2:24588154-24588173 MS.gene001465:CDS 35.0%
GCATTTGTGACTGAGTTTAA+CGG + chr3.2:24588198-24588217 None:intergenic 35.0%
GGAGGTTAAGATCAAAATCA+CGG + chr3.2:24588532-24588551 None:intergenic 35.0%
!! TGATTTTGATCTTAACCTCC+CGG - chr3.2:24588532-24588551 MS.gene001465:CDS 35.0%
GGTTAAGATCAAAATCACGG+TGG + chr3.2:24588529-24588548 None:intergenic 40.0%
TAAGATCAAAATCACGGTGG+TGG + chr3.2:24588526-24588545 None:intergenic 40.0%
TAGGAAGGATTTGTGACAGA+TGG + chr3.2:24588389-24588408 None:intergenic 40.0%
TGAGTTATCTTGAAACACCG+TGG - chr3.2:24588027-24588046 MS.gene001465:CDS 40.0%
TTCTCATCTTATCAAGCCCT+AGG - chr3.2:24588236-24588255 MS.gene001465:intron 40.0%
TTTGAAAAGTCCGGAAAAGC+CGG + chr3.2:24588554-24588573 None:intergenic 40.0%
TTTGTGACTGAGTTTAACGG+TGG + chr3.2:24588195-24588214 None:intergenic 40.0%
! ACTCAGATTTGGTTCCTCAA+AGG + chr3.2:24588012-24588031 None:intergenic 40.0%
! CTCAGATTTGGTTCCTCAAA+GGG + chr3.2:24588011-24588030 None:intergenic 40.0%
!! CATGAGTCTTGTTCTTACGT+TGG + chr3.2:24588360-24588379 None:intergenic 40.0%
CACAAATCCTTCCTACTGAC+AGG - chr3.2:24588394-24588413 MS.gene001465:CDS 45.0%
CTGAGTTTAACGGTGGTTAG+CGG + chr3.2:24588188-24588207 None:intergenic 45.0%
GATCGTTTACCTTTCGTCCA+CGG + chr3.2:24588047-24588066 None:intergenic 45.0%
TACTCCTTTCACACCCTTTG+AGG - chr3.2:24587995-24588014 MS.gene001465:CDS 45.0%
TCATCTTATCAAGCCCTAGG+TGG - chr3.2:24588239-24588258 MS.gene001465:intron 45.0%
TTGAAAAGTCCGGAAAAGCC+GGG + chr3.2:24588553-24588572 None:intergenic 45.0%
TTGCGGACATAACAGCTTTC+CGG + chr3.2:24588280-24588299 None:intergenic 45.0%
! GAAGTTTTTCGTGGATGACG+AGG - chr3.2:24588574-24588593 MS.gene001465:CDS 45.0%
!! CGACAAAAAGTCTGATTCGG+TGG - chr3.2:24588157-24588176 MS.gene001465:CDS 45.0%
CATAACAGCTTTCCGGTGAC+TGG + chr3.2:24588273-24588292 None:intergenic 50.0%
CCTTCCTACTGACAGGCTTT+GGG - chr3.2:24588401-24588420 MS.gene001465:CDS 50.0%
CTTGAAACACCGTGGACGAA+AGG - chr3.2:24588035-24588054 MS.gene001465:CDS 50.0%
GGCTTCTTTGCAGCAGGTAA+AGG + chr3.2:24588608-24588627 None:intergenic 50.0%
GGTGGTGATCTGATCTTCAG+CGG + chr3.2:24588306-24588325 None:intergenic 50.0%
GTGAAAGGAGTAGCAGTGGT+GGG + chr3.2:24587987-24588006 None:intergenic 50.0%
TCCTTCCTACTGACAGGCTT+TGG - chr3.2:24588400-24588419 MS.gene001465:CDS 50.0%
TCTTACGTTGGAAGCAGAGC+TGG + chr3.2:24588348-24588367 None:intergenic 50.0%
TGACGATCCAACTCCTTCAG+AGG + chr3.2:24588498-24588517 None:intergenic 50.0%
TGTGAAAGGAGTAGCAGTGG+TGG + chr3.2:24587988-24588007 None:intergenic 50.0%
! ACGATCAAAGCGTTCTCGCA+TGG - chr3.2:24588061-24588080 MS.gene001465:CDS 50.0%
! CACAAGCGTTGTCACTACGA+AGG - chr3.2:24588428-24588447 MS.gene001465:CDS 50.0%
! GGTTCCTCAAAGGGTGTGAA+AGG + chr3.2:24588002-24588021 None:intergenic 50.0%
! GTAACTGCCTCTGAAGGAGT+TGG - chr3.2:24588488-24588507 MS.gene001465:CDS 50.0%
! TCTTAACCTCCCGGCTTTTC+CGG - chr3.2:24588541-24588560 MS.gene001465:CDS 50.0%
!! ACTGGCTTTGTGTCCACCTA+GGG + chr3.2:24588255-24588274 None:intergenic 50.0%
!! GAAGCCCTGTCTTTTCAAGC+TGG - chr3.2:24588622-24588641 MS.gene001465:CDS 50.0%
AAAAGTCCGGAAAAGCCGGG+AGG + chr3.2:24588550-24588569 None:intergenic 55.0%
AGACAGGGCTTCTTTGCAGC+AGG + chr3.2:24588614-24588633 None:intergenic 55.0%
AGCGCTGTAACTGCCTCTGA+AGG - chr3.2:24588482-24588501 MS.gene001465:CDS 55.0%
CCCAAAGCCTGTCAGTAGGA+AGG + chr3.2:24588404-24588423 None:intergenic 55.0%
CTCATCATGCTTGCTCGCAG+CGG - chr3.2:24588125-24588144 MS.gene001465:CDS 55.0%
CTGATCTTCAGCGGTGGTTG+CGG + chr3.2:24588297-24588316 None:intergenic 55.0%
GGAAGCAGAGCTGGTAGTCA+CGG + chr3.2:24588339-24588358 None:intergenic 55.0%
GGGTGTGAAAGGAGTAGCAG+TGG + chr3.2:24587991-24588010 None:intergenic 55.0%
GGTGATCTGATCTTCAGCGG+TGG + chr3.2:24588303-24588322 None:intergenic 55.0%
GTGGACACAAAGCCAGTCAC+CGG - chr3.2:24588258-24588277 MS.gene001465:intron 55.0%
TACAGCGCTACTTCCAGCAC+CGG + chr3.2:24588471-24588490 None:intergenic 55.0%
TCCTCCCAAAGCCTGTCAGT+AGG + chr3.2:24588408-24588427 None:intergenic 55.0%
TGTCACTACGAAGGCAGCGT+TGG - chr3.2:24588437-24588456 MS.gene001465:CDS 55.0%
!! GACTGGCTTTGTGTCCACCT+AGG + chr3.2:24588256-24588275 None:intergenic 55.0%
!! TCCTACTGACAGGCTTTGGG+AGG - chr3.2:24588404-24588423 MS.gene001465:CDS 55.0%
AGCAGAGCTGGTAGTCACGG+CGG + chr3.2:24588336-24588355 None:intergenic 60.0%
AGTCACGGCGGATGAAGTGG+TGG + chr3.2:24588324-24588343 None:intergenic 60.0%
GGTAGTCACGGCGGATGAAG+TGG + chr3.2:24588327-24588346 None:intergenic 60.0%
!! TACGAAGGCAGCGTTGGTGC+CGG - chr3.2:24588443-24588462 MS.gene001465:CDS 60.0%
!! GCTACTTCCAGCACCGGCAC+CGG + chr3.2:24588465-24588484 None:intergenic 65.0%
!! GGCAGCGTTGGTGCCGGTGC+CGG - chr3.2:24588449-24588468 MS.gene001465:CDS 75.0%
!! GTTGGTGCCGGTGCCGGTGC+TGG - chr3.2:24588455-24588474 MS.gene001465:CDS 75.0%


Chromosome Type Strat End Strand Name
chr3.2 gene 24587960 24588664 24587960 ID=MS.gene001465
chr3.2 mRNA 24587960 24588664 24587960 ID=MS.gene001465.t1;Parent=MS.gene001465
chr3.2 exon 24588263 24588664 24588263 ID=MS.gene001465.t1.exon1;Parent=MS.gene001465.t1
chr3.2 CDS 24588263 24588664 24588263 ID=cds.MS.gene001465.t1;Parent=MS.gene001465.t1
chr3.2 exon 24587960 24588208 24587960 ID=MS.gene001465.t1.exon2;Parent=MS.gene001465.t1
chr3.2 CDS 24587960 24588208 24587960 ID=cds.MS.gene001465.t1;Parent=MS.gene001465.t1
Gene Sequence

>MS.gene001465

ATGGCTATGGAAGCACTTAACTCACCCACCACTGCTACTCCTTTCACACCCTTTGAGGAACCAAATCTGAGTTATCTTGAAACACCGTGGACGAAAGGTAAACGATCAAAGCGTTCTCGCATGGATCAATCTTCATGCACTGAAGAAGAGTATCTCGCTCTTTGTCTCATCATGCTTGCTCGCAGCGGTAACAACAACGACAAAAAGTCTGATTCGGTGGCGACGCCGCTAACCACCGTTAAACTCAGTCACAAATGCTCAGTCTGCAACAAAGCTTTCTCATCTTATCAAGCCCTAGGTGGACACAAAGCCAGTCACCGGAAAGCTGTTATGTCCGCAACCACCGCTGAAGATCAGATCACCACCACTTCATCCGCCGTGACTACCAGCTCTGCTTCCAACGTAAGAACAAGACTCATGAGTGTTCCATCTGTCACAAATCCTTCCTACTGACAGGCTTTGGGAGGACACAAGCGTTGTCACTACGAAGGCAGCGTTGGTGCCGGTGCCGGTGCTGGAAGTAGCGCTGTAACTGCCTCTGAAGGAGTTGGATCGTCACACAGCCACCACCGTGATTTTGATCTTAACCTCCCGGCTTTTCCGGACTTTTCAAAGAAGTTTTTCGTGGATGACGAGGTTTCTAGTCCTTTACCTGCTGCAAAGAAGCCCTGTCTTTTCAAGCTGGAAATTCCTTCTCATTACTGA

Protein sequence

>MS.gene001465.t1

MAMEALNSPTTATPFTPFEEPNLSYLETPWTKGKRSKRSRMDQSSCTEEEYLALCLIMLARSGNNNDKKSDSVATPLTTVKLSHKCSVCNKAFSSYQALGGHKASHRKAVMSATTAEDQITTTSSAVTTSSASNALGGHKRCHYEGSVGAGAGAGSSAVTASEGVGSSHSHHRDFDLNLPAFPDFSKKFFVDDEVSSPLPAAKKPCLFKLEIPSHY