AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0275400


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0275400 MtrunA17_Chr2g0287451 100.000 194 0 0 1 194 1 194 3.77e-140 390
Msa0275400 MtrunA17_Chr7g0217561 30.288 208 113 6 11 194 18 217 1.32e-19 83.2
Msa0275400 MtrunA17_Chr6g0453281 32.961 179 98 6 32 192 60 234 1.39e-18 80.9
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0275400 AT3G06180.1 53.723 188 57 3 32 194 45 227 9.87e-52 167
Msa0275400 AT5G19025.1 48.768 203 64 4 32 194 43 245 2.65e-46 154
Msa0275400 AT5G19025.2 48.529 204 65 4 32 195 43 246 4.35e-46 153
Msa0275400 AT3G01170.1 31.343 201 124 5 3 192 15 212 2.87e-22 90.5
Msa0275400 AT5G15260.2 36.264 182 94 7 32 194 52 230 3.04e-21 88.2
Msa0275400 AT5G15260.1 36.264 182 94 7 32 194 52 230 3.04e-21 88.2
Msa0275400 AT3G06180.2 49.618 131 46 3 32 142 45 175 4.84e-19 81.6

Find 74 sgRNAs with CRISPR-Local

Find 75 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AGGAAAATGGCTCCTGTTAA+TGG 0.248247 2_3:-7437373 Msa0275400:CDS
GTTGCTAAGCTTGAAGCTTC+TGG 0.282017 2_3:-7437310 Msa0275400:CDS
TTCTCCATCGGTTTCGTCTT+CGG 0.286647 2_3:-7437583 Msa0275400:CDS
GAGGTCGAGGGTGGCGGATG+GGG 0.291939 2_3:+7437738 None:intergenic
ATTTGAAGATAGAGAGATTA+GGG 0.294551 2_3:-7437480 Msa0275400:CDS
AAAAGAGCTTTCCCATTAAC+AGG 0.315760 2_3:+7437361 None:intergenic
AGGAAGGGAGGAGGAGAGAG+AGG 0.319372 2_3:+7437644 None:intergenic
TTCTGACGCTTTCCTTTCTT+AGG 0.324406 2_3:+7437286 None:intergenic
AGATAGAGAGATTAGGGTTA+GGG 0.332443 2_3:-7437474 Msa0275400:CDS
ATGATGAATGCGAGGATGTA+AGG 0.334695 2_3:+7437607 None:intergenic
TGGGGAGAGAGAAGGAAGGG+AGG 0.363640 2_3:+7437632 None:intergenic
AAGATAGAGAGATTAGGGTT+AGG 0.375742 2_3:-7437475 Msa0275400:CDS
GAGGTCTGAGTTAAGGAAAA+TGG 0.398152 2_3:-7437386 Msa0275400:CDS
GAGAGATTAGGGTTAGGGTT+TGG 0.401531 2_3:-7437469 Msa0275400:CDS
AGAGAACGAGGAGGAGGATG+AGG 0.403514 2_3:+7437716 None:intergenic
CGAGGAAGTGTGAGCGGAAA+GGG 0.417141 2_3:-7437534 Msa0275400:CDS
GGAAAATGGCTCCTGTTAAT+GGG 0.417774 2_3:-7437372 Msa0275400:CDS
GATGAGGAGGTCGAGGGTGG+CGG 0.419973 2_3:+7437732 None:intergenic
GACCTCAAACACTCATAATC+AGG 0.422373 2_3:+7437403 None:intergenic
GATTTGAAGATAGAGAGATT+AGG 0.426811 2_3:-7437481 Msa0275400:CDS
TGTAGAGGATGTAGGAAGAG+AGG 0.435172 2_3:+7437677 None:intergenic
GTTGAAGATGTAGAGGATGT+AGG 0.435475 2_3:+7437669 None:intergenic
GTGAATATGAGAAACTTCCT+TGG 0.438620 2_3:-7437447 Msa0275400:CDS
GGAGGAGGATGAGGAGGTCG+AGG 0.441658 2_3:+7437725 None:intergenic
GGAAAGCGTCAGAAGAGGTT+AGG 0.449218 2_3:-7437277 Msa0275400:CDS
GTGAGCGGAAAGGGTGTAAA+GGG 0.452025 2_3:-7437525 Msa0275400:CDS
GGAGAGAGAAGGAAGGGAGG+AGG 0.454349 2_3:+7437635 None:intergenic
AGAGGGAGTTGAAGATGTAG+AGG 0.456028 2_3:+7437662 None:intergenic
ATCCTGATTATGAGTGTTTG+AGG 0.464912 2_3:-7437405 Msa0275400:CDS
GAGGATGAGGAGGTCGAGGG+TGG 0.469592 2_3:+7437729 None:intergenic
AGGAGGTCGAGGGTGGCGGA+TGG 0.474368 2_3:+7437736 None:intergenic
GTAAGGGATGGGGAGAGAGA+AGG 0.474797 2_3:+7437624 None:intergenic
GGAAGGGAGGAGGAGAGAGA+GGG 0.479217 2_3:+7437645 None:intergenic
GGAGGTCGAGGGTGGCGGAT+GGG 0.479340 2_3:+7437737 None:intergenic
GAAGCTTCAAGCTTAGCAAC+AGG 0.479449 2_3:+7437313 None:intergenic
AGTGTTTGAGGTCTGAGTTA+AGG 0.480456 2_3:-7437393 Msa0275400:CDS
GCATTCATCATCTTCTCCAT+CGG 0.493706 2_3:-7437595 Msa0275400:CDS
CGGAGAAGAGAACGAGGAGG+AGG 0.502036 2_3:+7437710 None:intergenic
TGTGAGCGGAAAGGGTGTAA+AGG 0.504435 2_3:-7437526 Msa0275400:CDS
CTCCTCCTCGTTCTCTTCTC+CGG 0.508827 2_3:-7437709 Msa0275400:CDS
AGAGGATGTAGGAAGAGAGG+AGG 0.509455 2_3:+7437680 None:intergenic
CCTTGGAAAGGTGGGAGTGA+AGG 0.509828 2_3:-7437430 Msa0275400:CDS
CTTGGAAAGGTGGGAGTGAA+GGG 0.516479 2_3:-7437429 Msa0275400:CDS
AATGCGAGGATGTAAGGGAT+GGG 0.524206 2_3:+7437613 None:intergenic
GAGAAACTTCCTTGGAAAGG+TGG 0.532025 2_3:-7437439 Msa0275400:CDS
CCTTCACTCCCACCTTTCCA+AGG 0.533293 2_3:+7437430 None:intergenic
GAAGCTTCTGGTCCTAAGAA+AGG 0.534494 2_3:-7437298 Msa0275400:CDS
GGAAGAGAGGAGGAACGCGC+CGG 0.539333 2_3:+7437690 None:intergenic
AGAGGAAGATGAAGATGAAG+AGG 0.540483 2_3:+7437807 None:intergenic
GGATGGGGAGAGAGAAGGAA+GGG 0.553140 2_3:+7437629 None:intergenic
TTTAACATAAACATGCAAGA+AGG 0.554886 2_3:-7437853 None:intergenic
GAGGAGGATGAGGAGGTCGA+GGG 0.555296 2_3:+7437726 None:intergenic
GGGATGGGGAGAGAGAAGGA+AGG 0.558143 2_3:+7437628 None:intergenic
ATGCGAGGATGTAAGGGATG+GGG 0.563162 2_3:+7437614 None:intergenic
GAGGAAGATGAAGATGAAGA+GGG 0.563876 2_3:+7437808 None:intergenic
TATGTTGCGGTGCTCGATCG+AGG 0.567177 2_3:-7437552 Msa0275400:CDS
AGAAACTTCCTTGGAAAGGT+GGG 0.577982 2_3:-7437438 Msa0275400:CDS
TGCAGAGATTGTTGCAATGG+TGG 0.578137 2_3:+7437773 None:intergenic
TCGAGGAAGTGTGAGCGGAA+AGG 0.582933 2_3:-7437535 Msa0275400:CDS
TGATGAATGCGAGGATGTAA+GGG 0.585002 2_3:+7437608 None:intergenic
AGTTGCAGAGATTGTTGCAA+TGG 0.585063 2_3:+7437770 None:intergenic
GAATGCGAGGATGTAAGGGA+TGG 0.586112 2_3:+7437612 None:intergenic
TATGAGAAACTTCCTTGGAA+AGG 0.586994 2_3:-7437442 Msa0275400:CDS
GAACGAGGAGGAGGATGAGG+AGG 0.608762 2_3:+7437719 None:intergenic
ACGCGCCGGAGAAGAGAACG+AGG 0.608896 2_3:+7437704 None:intergenic
AGAAAGGAAAGCGTCAGAAG+AGG 0.610714 2_3:-7437282 Msa0275400:CDS
CTCGATCGAGGAAGTGTGAG+CGG 0.637391 2_3:-7437540 Msa0275400:CDS
CGCCGGAGAAGAGAACGAGG+AGG 0.649974 2_3:+7437707 None:intergenic
AAAACCGAAGACGAAACCGA+TGG 0.658416 2_3:+7437579 None:intergenic
ATGGTGGCGTAATGATGAAG+AGG 0.679254 2_3:+7437789 None:intergenic
TAAAGGGTTGAAGAAAGCGA+CGG 0.685657 2_3:-7437509 Msa0275400:CDS
TGGAGAAGATGATGAATGCG+AGG 0.698786 2_3:+7437599 None:intergenic
TTAGCAACAGGACAACCACA+AGG 0.706608 2_3:+7437325 None:intergenic
AGATGAAGAGGGCATTGCTG+TGG 0.719826 2_3:+7437819 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! ATTTGAAGATAGAGAGATTA+GGG - chr2_3:7437592-7437611 Msa0275400:CDS 25.0%
GATTTGAAGATAGAGAGATT+AGG - chr2_3:7437591-7437610 Msa0275400:CDS 30.0%
!!! TTCGGTTTTGAGATATGTTG+CGG - chr2_3:7437507-7437526 Msa0275400:CDS 35.0%
AAGATAGAGAGATTAGGGTT+AGG - chr2_3:7437597-7437616 Msa0275400:CDS 35.0%
AGATAGAGAGATTAGGGTTA+GGG - chr2_3:7437598-7437617 Msa0275400:CDS 35.0%
GTGAATATGAGAAACTTCCT+TGG - chr2_3:7437625-7437644 Msa0275400:CDS 35.0%
TATGAGAAACTTCCTTGGAA+AGG - chr2_3:7437630-7437649 Msa0275400:CDS 35.0%
ATCCTGATTATGAGTGTTTG+AGG - chr2_3:7437667-7437686 Msa0275400:CDS 35.0%
AAAAGAGCTTTCCCATTAAC+AGG + chr2_3:7437714-7437733 None:intergenic 35.0%
GAGGAAGATGAAGATGAAGA+GGG + chr2_3:7437267-7437286 None:intergenic 40.0%
AGAGGAAGATGAAGATGAAG+AGG + chr2_3:7437268-7437287 None:intergenic 40.0%
AGTTGCAGAGATTGTTGCAA+TGG + chr2_3:7437305-7437324 None:intergenic 40.0%
GTTGAAGATGTAGAGGATGT+AGG + chr2_3:7437406-7437425 None:intergenic 40.0%
TGATGAATGCGAGGATGTAA+GGG + chr2_3:7437467-7437486 None:intergenic 40.0%
ATGATGAATGCGAGGATGTA+AGG + chr2_3:7437468-7437487 None:intergenic 40.0%
GCATTCATCATCTTCTCCAT+CGG - chr2_3:7437477-7437496 Msa0275400:CDS 40.0%
TAAAGGGTTGAAGAAAGCGA+CGG - chr2_3:7437563-7437582 Msa0275400:CDS 40.0%
AGAAACTTCCTTGGAAAGGT+GGG - chr2_3:7437634-7437653 Msa0275400:CDS 40.0%
GACCTCAAACACTCATAATC+AGG + chr2_3:7437672-7437691 None:intergenic 40.0%
! AGTGTTTGAGGTCTGAGTTA+AGG - chr2_3:7437679-7437698 Msa0275400:CDS 40.0%
GAGGTCTGAGTTAAGGAAAA+TGG - chr2_3:7437686-7437705 Msa0275400:CDS 40.0%
AGGAAAATGGCTCCTGTTAA+TGG - chr2_3:7437699-7437718 Msa0275400:CDS 40.0%
GGAAAATGGCTCCTGTTAAT+GGG - chr2_3:7437700-7437719 Msa0275400:CDS 40.0%
!!! TTGCTTTTTAGAGCTCCTTG+TGG - chr2_3:7437732-7437751 Msa0275400:CDS 40.0%
TTCTGACGCTTTCCTTTCTT+AGG + chr2_3:7437789-7437808 None:intergenic 40.0%
! ATGGTGGCGTAATGATGAAG+AGG + chr2_3:7437286-7437305 None:intergenic 45.0%
TGCAGAGATTGTTGCAATGG+TGG + chr2_3:7437302-7437321 None:intergenic 45.0%
TGTAGAGGATGTAGGAAGAG+AGG + chr2_3:7437398-7437417 None:intergenic 45.0%
AGAGGGAGTTGAAGATGTAG+AGG + chr2_3:7437413-7437432 None:intergenic 45.0%
AATGCGAGGATGTAAGGGAT+GGG + chr2_3:7437462-7437481 None:intergenic 45.0%
TGGAGAAGATGATGAATGCG+AGG + chr2_3:7437476-7437495 None:intergenic 45.0%
!! TTCTCCATCGGTTTCGTCTT+CGG - chr2_3:7437489-7437508 Msa0275400:CDS 45.0%
AAAACCGAAGACGAAACCGA+TGG + chr2_3:7437496-7437515 None:intergenic 45.0%
GAGAGATTAGGGTTAGGGTT+TGG - chr2_3:7437603-7437622 Msa0275400:CDS 45.0%
GAGAAACTTCCTTGGAAAGG+TGG - chr2_3:7437633-7437652 Msa0275400:CDS 45.0%
TTAGCAACAGGACAACCACA+AGG + chr2_3:7437750-7437769 None:intergenic 45.0%
GAAGCTTCAAGCTTAGCAAC+AGG + chr2_3:7437762-7437781 None:intergenic 45.0%
GTTGCTAAGCTTGAAGCTTC+TGG - chr2_3:7437762-7437781 Msa0275400:CDS 45.0%
GAAGCTTCTGGTCCTAAGAA+AGG - chr2_3:7437774-7437793 Msa0275400:CDS 45.0%
!! AGAAAGGAAAGCGTCAGAAG+AGG - chr2_3:7437790-7437809 Msa0275400:CDS 45.0%
!! AGATGAAGAGGGCATTGCTG+TGG + chr2_3:7437256-7437275 None:intergenic 50.0%
AGAGGATGTAGGAAGAGAGG+AGG + chr2_3:7437395-7437414 None:intergenic 50.0%
ATGCGAGGATGTAAGGGATG+GGG + chr2_3:7437461-7437480 None:intergenic 50.0%
GAATGCGAGGATGTAAGGGA+TGG + chr2_3:7437463-7437482 None:intergenic 50.0%
! TGTGAGCGGAAAGGGTGTAA+AGG - chr2_3:7437546-7437565 Msa0275400:CDS 50.0%
! GTGAGCGGAAAGGGTGTAAA+GGG - chr2_3:7437547-7437566 Msa0275400:CDS 50.0%
CTTGGAAAGGTGGGAGTGAA+GGG - chr2_3:7437643-7437662 Msa0275400:CDS 50.0%
!! GGAAAGCGTCAGAAGAGGTT+AGG - chr2_3:7437795-7437814 Msa0275400:CDS 50.0%
AGAGAACGAGGAGGAGGATG+AGG + chr2_3:7437359-7437378 None:intergenic 55.0%
CTCCTCCTCGTTCTCTTCTC+CGG - chr2_3:7437363-7437382 Msa0275400:CDS 55.0%
GGATGGGGAGAGAGAAGGAA+GGG + chr2_3:7437446-7437465 None:intergenic 55.0%
GTAAGGGATGGGGAGAGAGA+AGG + chr2_3:7437451-7437470 None:intergenic 55.0%
TATGTTGCGGTGCTCGATCG+AGG - chr2_3:7437520-7437539 Msa0275400:CDS 55.0%
! CTCGATCGAGGAAGTGTGAG+CGG - chr2_3:7437532-7437551 Msa0275400:CDS 55.0%
! TCGAGGAAGTGTGAGCGGAA+AGG - chr2_3:7437537-7437556 Msa0275400:CDS 55.0%
! CGAGGAAGTGTGAGCGGAAA+GGG - chr2_3:7437538-7437557 Msa0275400:CDS 55.0%
CCTTCACTCCCACCTTTCCA+AGG + chr2_3:7437645-7437664 None:intergenic 55.0%
CCTTGGAAAGGTGGGAGTGA+AGG - chr2_3:7437642-7437661 Msa0275400:CDS 55.0%
GAGGAGGATGAGGAGGTCGA+GGG + chr2_3:7437349-7437368 None:intergenic 60.0%
GAACGAGGAGGAGGATGAGG+AGG + chr2_3:7437356-7437375 None:intergenic 60.0%
CGGAGAAGAGAACGAGGAGG+AGG + chr2_3:7437365-7437384 None:intergenic 60.0%
GGAAGGGAGGAGGAGAGAGA+GGG + chr2_3:7437430-7437449 None:intergenic 60.0%
AGGAAGGGAGGAGGAGAGAG+AGG + chr2_3:7437431-7437450 None:intergenic 60.0%
GGAGAGAGAAGGAAGGGAGG+AGG + chr2_3:7437440-7437459 None:intergenic 60.0%
TGGGGAGAGAGAAGGAAGGG+AGG + chr2_3:7437443-7437462 None:intergenic 60.0%
GGGATGGGGAGAGAGAAGGA+AGG + chr2_3:7437447-7437466 None:intergenic 60.0%
GATGAGGAGGTCGAGGGTGG+CGG + chr2_3:7437343-7437362 None:intergenic 65.0%
GAGGATGAGGAGGTCGAGGG+TGG + chr2_3:7437346-7437365 None:intergenic 65.0%
GGAGGAGGATGAGGAGGTCG+AGG + chr2_3:7437350-7437369 None:intergenic 65.0%
CGCCGGAGAAGAGAACGAGG+AGG + chr2_3:7437368-7437387 None:intergenic 65.0%
ACGCGCCGGAGAAGAGAACG+AGG + chr2_3:7437371-7437390 None:intergenic 65.0%
GGAAGAGAGGAGGAACGCGC+CGG + chr2_3:7437385-7437404 None:intergenic 65.0%
!! GAGGTCGAGGGTGGCGGATG+GGG + chr2_3:7437337-7437356 None:intergenic 70.0%
!! GGAGGTCGAGGGTGGCGGAT+GGG + chr2_3:7437338-7437357 None:intergenic 70.0%
!! AGGAGGTCGAGGGTGGCGGA+TGG + chr2_3:7437339-7437358 None:intergenic 70.0%
Chromosome Type Strat End Strand Name
chr2_3 gene 7437231 7437863 7437231 ID=Msa0275400;Name=Msa0275400
chr2_3 mRNA 7437231 7437863 7437231 ID=Msa0275400-mRNA-1;Parent=Msa0275400;Name=Msa0275400-mRNA-1;_AED=0.04;_eAED=0.04;_QI=0|-1|0|1|-1|1|1|0|210
chr2_3 exon 7437231 7437863 7437231 ID=Msa0275400-mRNA-1:exon:3441;Parent=Msa0275400-mRNA-1
chr2_3 CDS 7437231 7437863 7437231 ID=Msa0275400-mRNA-1:cds;Parent=Msa0275400-mRNA-1
Gene Sequence

>Msa0275400

ATGCAAGAAGGCATTGTATTAACCACAGCAATGCCCTCTTCATCTTCATCTTCCTCTTCATCATTACGCCACCATTGCAACAATCTCTGCAACTGCAAACATGCCCCATCCGCCACCCTCGACCTCCTCATCCTCCTCCTCGTTCTCTTCTCCGGCGCGTTCCTCCTCTCTTCCTACATCCTCTACATCTTCAACTCCCTCTCTCTCCTCCTCCCTTCCTTCTCTCTCCCCATCCCTTACATCCTCGCATTCATCATCTTCTCCATCGGTTTCGTCTTCGGTTTTGAGATATGTTGCGGTGCTCGATCGAGGAAGTGTGAGCGGAAAGGGTGTAAAGGGTTGAAGAAAGCGACGGAGTTTGATTTGAAGATAGAGAGATTAGGGTTAGGGTTTGGTGAATATGAGAAACTTCCTTGGAAAGGTGGGAGTGAAGGGAATCCTGATTATGAGTGTTTGAGGTCTGAGTTAAGGAAAATGGCTCCTGTTAATGGGAAAGCTCTTTTGCTTTTTAGAGCTCCTTGTGGTTGTCCTGTTGCTAAGCTTGAAGCTTCTGGTCCTAAGAAAGGAAAGCGTCAGAAGAGGTTAGGTTTTACTCGCTCACTCATAGTCAAAAGATTGATTCAATTTGTCTAA

Protein sequence

>Msa0275400

MQEGIVLTTAMPSSSSSSSSSLRHHCNNLCNCKHAPSATLDLLILLLVLFSGAFLLSSYILYIFNSLSLLLPSFSLPIPYILAFIIFSIGFVFGFEICCGARSRKCERKGCKGLKKATEFDLKIERLGLGFGEYEKLPWKGGSEGNPDYECLRSELRKMAPVNGKALLLFRAPCGCPVAKLEASGPKKGKRQKRLGFTRSLIVKRLIQFV*