AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene65896


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene65896.t1 MTR_5g062650 94.972 179 9 0 1 179 607 785 5.60e-109 328
MS.gene65896.t1 MTR_5g062430 94.972 179 9 0 1 179 604 782 4.49e-108 326
MS.gene65896.t1 MTR_5g062370 93.855 179 11 0 1 179 604 782 6.19e-107 323
MS.gene65896.t1 MTR_5g062320 92.737 179 13 0 1 179 602 780 2.15e-105 319
MS.gene65896.t1 MTR_3g074060 63.687 179 65 0 1 179 598 776 8.48e-81 254
MS.gene65896.t1 MTR_5g030860 38.172 186 106 2 1 179 599 782 1.33e-35 131
MS.gene65896.t1 MTR_2g034720 36.364 176 101 3 1 175 587 752 1.44e-30 117
MS.gene65896.t1 MTR_1g106860 35.385 195 101 4 1 180 591 775 5.13e-30 115
MS.gene65896.t1 MTR_2g008240 33.889 180 110 3 1 179 604 775 8.88e-30 115
MS.gene65896.t1 MTR_4g094285 34.054 185 103 4 1 179 603 774 2.67e-27 107
MS.gene65896.t1 MTR_1g087240 34.054 185 101 4 1 177 584 755 4.53e-27 107
MS.gene65896.t1 MTR_7g109390 35.135 185 100 6 1 177 589 761 1.51e-24 100
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene65896.t1 AT1G78060 51.934 181 80 4 1 179 592 767 2.36e-56 189
MS.gene65896.t1 AT5G10560 37.569 181 109 1 1 177 610 790 5.93e-36 132
MS.gene65896.t1 AT3G19620 37.356 174 96 4 1 169 593 758 3.17e-28 110
MS.gene65896.t1 AT5G09700 37.912 182 105 3 1 179 350 526 8.03e-28 108
MS.gene65896.t1 AT5G09730 36.957 184 104 4 1 179 597 773 3.17e-27 107
MS.gene65896.t1 AT1G02640 33.898 177 108 3 1 177 591 758 6.07e-26 103
MS.gene65896.t1 AT5G64570 36.757 185 104 3 1 179 449 626 1.69e-25 102
MS.gene65896.t1 AT5G64570 36.757 185 104 3 1 179 607 784 2.38e-25 102
MS.gene65896.t1 AT5G49360 35.326 184 100 7 1 175 595 768 2.74e-24 99.4

Find 53 sgRNAs with CRISPR-Local

Find 50 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTTCCATTTCTACCTTTCTT+TGG 0.223144 5.2:+71657318 None:intergenic
TTTGACTGAAATGAAGTTGT+AGG 0.288846 5.2:+71657527 None:intergenic
TTTGAGAGTGTGACGGTAGA+AGG 0.295260 5.2:-71657273 MS.gene65896:CDS
TACAAACTTGTTTCAGAGAT+AGG 0.351981 5.2:-71657438 MS.gene65896:CDS
AGCAAATGAGAGTGGTGTTA+AGG 0.359751 5.2:-71657196 MS.gene65896:CDS
GGAGGTGGAAAGGGTGAAGT+TGG 0.369858 5.2:-71657252 MS.gene65896:CDS
ACATTGGGAATTACAAATAC+TGG 0.373679 5.2:-71657381 MS.gene65896:CDS
GGTCCAAAGGTCTACGAATT+CGG 0.387773 5.2:-71657576 MS.gene65896:CDS
ACAAATACTGGAGGCATGGC+TGG 0.398922 5.2:-71657369 MS.gene65896:CDS
AGGAATAATTTGAGTAGCTT+AGG 0.401616 5.2:+71657547 None:intergenic
TAGCCGAATTCGTAGACCTT+TGG 0.407677 5.2:+71657573 None:intergenic
AACCCTACCAACTGTTTCAC+TGG 0.418928 5.2:+71657294 None:intergenic
AGGTGGTTATTTGTTGGTTG+TGG 0.420306 5.2:-71657163 MS.gene65896:CDS
TCTCTGAAACAAGTTTGTAA+TGG 0.433264 5.2:+71657442 None:intergenic
AAGCCAAAGAAAGGTAGAAA+TGG 0.439382 5.2:-71657321 MS.gene65896:CDS
AATTCCCAATGTGACAGAAA+TGG 0.462642 5.2:+71657392 None:intergenic
ATGTCCATTTCTGTCACATT+GGG 0.462961 5.2:-71657396 MS.gene65896:CDS
CTCATTCTCATGTCAGTCAT+TGG 0.465198 5.2:+71657648 None:intergenic
TTATTTGTTGGTTGTGGGAG+AGG 0.471909 5.2:-71657157 MS.gene65896:CDS
ACGGTAGAAGGAGGTGGAAA+GGG 0.488877 5.2:-71657261 MS.gene65896:CDS
GGTGGTTATTTGTTGGTTGT+GGG 0.491601 5.2:-71657162 MS.gene65896:CDS
CATGTCCATTTCTGTCACAT+TGG 0.509436 5.2:-71657397 MS.gene65896:CDS
ATGAGGGCTGATCCATCATC+AGG 0.511303 5.2:-71657630 MS.gene65896:CDS
GTAGAAACGGTAGGTTCTAC+CGG 0.511605 5.2:+71657602 None:intergenic
TACTCAATAAATATCACTGT+TGG 0.517582 5.2:-71657129 MS.gene65896:CDS
CTACCGGGATAGCCTGATGA+TGG 0.517596 5.2:+71657618 None:intergenic
GACGGTAGAAGGAGGTGGAA+AGG 0.524657 5.2:-71657262 MS.gene65896:CDS
TGAAGAAGGTGGTTATTTGT+TGG 0.528173 5.2:-71657169 MS.gene65896:CDS
AAGGTCTACGAATTCGGCTA+TGG 0.539382 5.2:-71657570 MS.gene65896:CDS
CCTTTGGACCTGTGTAGAAA+CGG 0.540578 5.2:+71657589 None:intergenic
GATCCATCATCAGGCTATCC+CGG 0.540808 5.2:-71657621 MS.gene65896:CDS
ATCCAGTGAAACAGTTGGTA+GGG 0.542668 5.2:-71657296 MS.gene65896:CDS
TTGTTTGTGAAGCCAAAGAA+AGG 0.545721 5.2:-71657330 MS.gene65896:CDS
AGTGTGACGGTAGAAGGAGG+TGG 0.547541 5.2:-71657267 MS.gene65896:CDS
AATCCAGTGAAACAGTTGGT+AGG 0.561271 5.2:-71657297 MS.gene65896:CDS
GAGAGTGTGACGGTAGAAGG+AGG 0.561859 5.2:-71657270 MS.gene65896:CDS
CAAATACTGGAGGCATGGCT+GGG 0.567905 5.2:-71657368 MS.gene65896:CDS
TTGTTGATTGATTGATGTGA+AGG 0.569073 5.2:+71657496 None:intergenic
CAATGACTGACATGAGAATG+AGG 0.574292 5.2:-71657647 MS.gene65896:CDS
GGTAGGGTTTGAGAGTGTGA+CGG 0.580407 5.2:-71657280 MS.gene65896:CDS
AATTACAAATACTGGAGGCA+TGG 0.594236 5.2:-71657373 MS.gene65896:CDS
CAATGTGACAGAAATGGACA+TGG 0.599069 5.2:+71657398 None:intergenic
GGTGTTAAGGTGATTGAAGA+AGG 0.603997 5.2:-71657183 MS.gene65896:CDS
CCGTTTCTACACAGGTCCAA+AGG 0.609130 5.2:-71657589 MS.gene65896:CDS
GGCTTCACAAACAACAACAC+AGG 0.609698 5.2:+71657339 None:intergenic
AGAACCTACCGTTTCTACAC+AGG 0.612051 5.2:-71657597 MS.gene65896:CDS
GTTAAGGTGATTGAAGAAGG+TGG 0.615321 5.2:-71657180 MS.gene65896:CDS
TGGAAATCCAGTGAAACAGT+TGG 0.620701 5.2:-71657301 MS.gene65896:CDS
TGGACCTGTGTAGAAACGGT+AGG 0.625209 5.2:+71657593 None:intergenic
TAGAAACGGTAGGTTCTACC+GGG 0.648311 5.2:+71657603 None:intergenic
CTTAGTAGAGCAAATGAGAG+TGG 0.648348 5.2:-71657204 MS.gene65896:CDS
AATGACTGACATGAGAATGA+GGG 0.678215 5.2:-71657646 MS.gene65896:CDS
TTGGGAATTACAAATACTGG+AGG 0.696508 5.2:-71657378 MS.gene65896:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! TACTCAATAAATATCACTGT+TGG - chr5.2:71657641-71657660 MS.gene65896:CDS 25.0%
ACATTGGGAATTACAAATAC+TGG - chr5.2:71657389-71657408 MS.gene65896:CDS 30.0%
AGGAATAATTTGAGTAGCTT+AGG + chr5.2:71657226-71657245 None:intergenic 30.0%
TTTCCATTTCTACCTTTCTT+TGG + chr5.2:71657455-71657474 None:intergenic 30.0%
TTTGACTGAAATGAAGTTGT+AGG + chr5.2:71657246-71657265 None:intergenic 30.0%
! TACAAACTTGTTTCAGAGAT+AGG - chr5.2:71657332-71657351 MS.gene65896:CDS 30.0%
! TTGTTGATTGATTGATGTGA+AGG + chr5.2:71657277-71657296 None:intergenic 30.0%
!! TCTCTGAAACAAGTTTGTAA+TGG + chr5.2:71657331-71657350 None:intergenic 30.0%
AAGCCAAAGAAAGGTAGAAA+TGG - chr5.2:71657449-71657468 MS.gene65896:CDS 35.0%
AATTACAAATACTGGAGGCA+TGG - chr5.2:71657397-71657416 MS.gene65896:CDS 35.0%
AATTCCCAATGTGACAGAAA+TGG + chr5.2:71657381-71657400 None:intergenic 35.0%
ATGTCCATTTCTGTCACATT+GGG - chr5.2:71657374-71657393 MS.gene65896:CDS 35.0%
TGAAGAAGGTGGTTATTTGT+TGG - chr5.2:71657601-71657620 MS.gene65896:CDS 35.0%
TTGGGAATTACAAATACTGG+AGG - chr5.2:71657392-71657411 MS.gene65896:CDS 35.0%
TTGTTTGTGAAGCCAAAGAA+AGG - chr5.2:71657440-71657459 MS.gene65896:CDS 35.0%
AATCCAGTGAAACAGTTGGT+AGG - chr5.2:71657473-71657492 MS.gene65896:CDS 40.0%
CAATGTGACAGAAATGGACA+TGG + chr5.2:71657375-71657394 None:intergenic 40.0%
CATGTCCATTTCTGTCACAT+TGG - chr5.2:71657373-71657392 MS.gene65896:CDS 40.0%
CTTAGTAGAGCAAATGAGAG+TGG - chr5.2:71657566-71657585 MS.gene65896:CDS 40.0%
GGTGTTAAGGTGATTGAAGA+AGG - chr5.2:71657587-71657606 MS.gene65896:CDS 40.0%
GTTAAGGTGATTGAAGAAGG+TGG - chr5.2:71657590-71657609 MS.gene65896:CDS 40.0%
TGGAAATCCAGTGAAACAGT+TGG - chr5.2:71657469-71657488 MS.gene65896:CDS 40.0%
! AGCAAATGAGAGTGGTGTTA+AGG - chr5.2:71657574-71657593 MS.gene65896:CDS 40.0%
! AGGTGGTTATTTGTTGGTTG+TGG - chr5.2:71657607-71657626 MS.gene65896:CDS 40.0%
! ATCCAGTGAAACAGTTGGTA+GGG - chr5.2:71657474-71657493 MS.gene65896:CDS 40.0%
! GGTGGTTATTTGTTGGTTGT+GGG - chr5.2:71657608-71657627 MS.gene65896:CDS 40.0%
! TTATTTGTTGGTTGTGGGAG+AGG - chr5.2:71657613-71657632 MS.gene65896:CDS 40.0%
AACCCTACCAACTGTTTCAC+TGG + chr5.2:71657479-71657498 None:intergenic 45.0%
AAGGTCTACGAATTCGGCTA+TGG - chr5.2:71657200-71657219 MS.gene65896:CDS 45.0%
AGAACCTACCGTTTCTACAC+AGG - chr5.2:71657173-71657192 MS.gene65896:CDS 45.0%
CCTTTGGACCTGTGTAGAAA+CGG + chr5.2:71657184-71657203 None:intergenic 45.0%
GGCTTCACAAACAACAACAC+AGG + chr5.2:71657434-71657453 None:intergenic 45.0%
GGTCCAAAGGTCTACGAATT+CGG - chr5.2:71657194-71657213 MS.gene65896:CDS 45.0%
GTAGAAACGGTAGGTTCTAC+CGG + chr5.2:71657171-71657190 None:intergenic 45.0%
TAGAAACGGTAGGTTCTACC+GGG + chr5.2:71657170-71657189 None:intergenic 45.0%
TAGCCGAATTCGTAGACCTT+TGG + chr5.2:71657200-71657219 None:intergenic 45.0%
! TTTGAGAGTGTGACGGTAGA+AGG - chr5.2:71657497-71657516 MS.gene65896:CDS 45.0%
ACGGTAGAAGGAGGTGGAAA+GGG - chr5.2:71657509-71657528 MS.gene65896:CDS 50.0%
ATGAGGGCTGATCCATCATC+AGG - chr5.2:71657140-71657159 MS.gene65896:CDS 50.0%
CCGTTTCTACACAGGTCCAA+AGG - chr5.2:71657181-71657200 MS.gene65896:CDS 50.0%
GATCCATCATCAGGCTATCC+CGG - chr5.2:71657149-71657168 MS.gene65896:CDS 50.0%
TGGACCTGTGTAGAAACGGT+AGG + chr5.2:71657180-71657199 None:intergenic 50.0%
! ACAAATACTGGAGGCATGGC+TGG - chr5.2:71657401-71657420 MS.gene65896:CDS 50.0%
! CAAATACTGGAGGCATGGCT+GGG - chr5.2:71657402-71657421 MS.gene65896:CDS 50.0%
! GGTAGGGTTTGAGAGTGTGA+CGG - chr5.2:71657490-71657509 MS.gene65896:CDS 50.0%
AGTGTGACGGTAGAAGGAGG+TGG - chr5.2:71657503-71657522 MS.gene65896:CDS 55.0%
CTACCGGGATAGCCTGATGA+TGG + chr5.2:71657155-71657174 None:intergenic 55.0%
GACGGTAGAAGGAGGTGGAA+AGG - chr5.2:71657508-71657527 MS.gene65896:CDS 55.0%
GGAGGTGGAAAGGGTGAAGT+TGG - chr5.2:71657518-71657537 MS.gene65896:CDS 55.0%
! GAGAGTGTGACGGTAGAAGG+AGG - chr5.2:71657500-71657519 MS.gene65896:CDS 55.0%


Chromosome Type Strat End Strand Name
chr5.2 gene 71657125 71657667 71657125 ID=MS.gene65896
chr5.2 mRNA 71657125 71657667 71657125 ID=MS.gene65896.t1;Parent=MS.gene65896
chr5.2 exon 71657125 71657667 71657125 ID=MS.gene65896.t1.exon1;Parent=MS.gene65896.t1
chr5.2 CDS 71657125 71657667 71657125 ID=cds.MS.gene65896.t1;Parent=MS.gene65896.t1
Gene Sequence

>MS.gene65896

ATGACTGACATGAGAATGAGGGCTGATCCATCATCAGGCTATCCCGGTAGAACCTACCGTTTCTACACAGGTCCAAAGGTCTACGAATTCGGCTATGGCCTAAGCTACTCAAATTATTCCTACAACTTCATTTCAGTCAAAAATAACAACCTTCACATCAATCAATCAACAACTTATTCGATACTCGAAAAATCTCATACAATCCATTACAAACTTGTTTCAGAGATAGGCGAAAAAACATGTAAAACCATGTCCATTTCTGTCACATTGGGAATTACAAATACTGGAGGCATGGCTGGGAAACATCCTGTGTTGTTGTTTGTGAAGCCAAAGAAAGGTAGAAATGGAAATCCAGTGAAACAGTTGGTAGGGTTTGAGAGTGTGACGGTAGAAGGAGGTGGAAAGGGTGAAGTTGGATTCGAAGTTAGTGTTTGTGAGCATCTTAGTAGAGCAAATGAGAGTGGTGTTAAGGTGATTGAAGAAGGTGGTTATTTGTTGGTTGTGGGAGAGGAAGAGTACTCAATAAATATCACTGTTGGATGA

Protein sequence

>MS.gene65896.t1

MTDMRMRADPSSGYPGRTYRFYTGPKVYEFGYGLSYSNYSYNFISVKNNNLHINQSTTYSILEKSHTIHYKLVSEIGEKTCKTMSISVTLGITNTGGMAGKHPVLLFVKPKKGRNGNPVKQLVGFESVTVEGGGKGEVGFEVSVCEHLSRANESGVKVIEEGGYLLVVGEEEYSINITVG