AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene015279

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene015279.t1 MTR_5g015090 94.904 157 8 0 1 157 1 157 2.19e-108 305
MS.gene015279.t1 MTR_4g097440 55.747 174 60 6 1 157 1 174 1.39e-53 167
MS.gene015279.t1 MTR_3g103360 41.860 129 59 3 11 136 16 131 1.35e-17 74.7
MS.gene015279.t1 MTR_1g017570 54.321 81 37 0 60 140 59 139 5.59e-16 70.9
MS.gene015279.t1 MTR_7g029400 41.667 96 49 1 58 153 81 169 2.96e-15 69.7
MS.gene015279.t1 MTR_4g070860 44.444 81 45 0 58 138 27 107 6.81e-15 68.2
MS.gene015279.t1 MTR_8g015250 40.625 96 50 1 58 153 71 159 2.80e-14 67.0
MS.gene015279.t1 MTR_3g117120 38.542 96 51 1 58 145 27 122 7.93e-13 62.8
MS.gene015279.t1 MTR_8g086020 38.462 78 48 0 59 136 33 110 1.98e-12 61.6
MS.gene015279.t1 MTR_1g022495 37.736 106 62 1 36 137 1 106 2.04e-12 61.6
MS.gene015279.t1 MTR_1g087040 36.667 90 42 2 36 125 8 82 7.11e-12 60.1
MS.gene015279.t1 MTR_6g016375 45.570 79 43 0 58 136 87 165 3.04e-11 59.3
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene015279.t1 AT3G49760 38.129 139 85 1 5 142 15 153 1.22e-27 101
MS.gene015279.t1 AT4G37730 40.580 138 74 2 7 136 135 272 5.40e-20 84.3
MS.gene015279.t1 AT2G22850 48.235 85 44 0 59 143 127 211 5.84e-19 80.5
MS.gene015279.t1 AT2G22850 48.235 85 44 0 59 143 127 211 5.84e-19 80.5
MS.gene015279.t1 AT3G30530 40.833 120 66 2 27 146 49 163 7.97e-16 70.9
MS.gene015279.t1 AT1G75390 36.667 120 75 1 31 149 10 129 3.39e-14 66.6
MS.gene015279.t1 AT2G18160 39.130 92 49 1 52 136 15 106 1.79e-13 64.7
MS.gene015279.t1 AT1G75390 39.394 99 59 1 31 128 10 108 2.74e-13 63.2
MS.gene015279.t1 AT4G34590 41.176 85 50 0 58 142 24 108 6.76e-13 63.2
MS.gene015279.t1 AT1G13600 49.367 79 40 0 58 136 83 161 1.81e-12 62.4
MS.gene015279.t1 AT4G36730 34.513 113 55 2 48 141 192 304 2.43e-12 63.5
MS.gene015279.t1 AT4G36730 34.513 113 55 2 48 141 194 306 2.63e-12 63.5
MS.gene015279.t1 AT2G04038 43.750 96 49 1 36 131 54 144 4.33e-12 60.8
MS.gene015279.t1 AT5G15830 39.423 104 57 1 33 136 52 149 1.39e-11 60.1
MS.gene015279.t1 AT5G38800 40.404 99 52 1 38 136 56 147 1.58e-11 59.3

Find 51 sgRNAs with CRISPR-Local

Find 60 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AAAGACATCTAGAGAATTTA+CGG 0.286559 5.4:-8833600 MS.gene015279:CDS
GTCAAACATAGGTCAAAATA+TGG 0.308208 5.4:-8833443 MS.gene015279:CDS
GGATGGCTCGAACCGGAATA+TGG 0.309967 5.4:-8833689 MS.gene015279:CDS
GGGCTGGTGGGTTGGAAGGG+TGG 0.313437 5.4:+8833763 None:intergenic
ATATCATTCTCCTCCGCTTT+CGG 0.329484 5.4:+8833662 None:intergenic
GCAACCCGTTGTTCAATTCC+CGG 0.358900 5.4:+8833548 None:intergenic
GTGACCTCCGTGCCGATTCC+CGG 0.363167 5.4:+8833635 None:intergenic
TTCGTCTAACTCCGTGAAAT+CGG 0.374640 5.4:+8833819 None:intergenic
GCTTTCGGTCCTCCATATTC+CGG 0.399400 5.4:+8833677 None:intergenic
CTTAGGGCTGGTGGGTTGGA+AGG 0.408872 5.4:+8833759 None:intergenic
ACCGGTTTAGAGTTGAAAAC+CGG 0.409929 5.4:-8833567 MS.gene015279:CDS
CCGGTTGGAACGAACCATGC+TGG 0.411515 5.4:-8833476 MS.gene015279:CDS
TCTCTATGCCTCCGATTTCA+CGG 0.417032 5.4:-8833830 MS.gene015279:CDS
CTCACTTCAAGCTCCGGTTC+AGG 0.426863 5.4:-8833736 MS.gene015279:CDS
CCGGAGCTTGAAGTGAGCTT+AGG 0.429061 5.4:+8833742 None:intergenic
AAAACCGGGAATTGAACAAC+GGG 0.452979 5.4:-8833552 MS.gene015279:CDS
ATTTACGGAACCAGGTGAAC+CGG 0.455271 5.4:-8833585 MS.gene015279:CDS
CCAGCATGGTTCGTTCCAAC+CGG 0.461195 5.4:+8833476 None:intergenic
TGAAGTGAGCTTAGGGCTGG+TGG 0.471435 5.4:+8833750 None:intergenic
CAACTCTAAACCGGTTCACC+TGG 0.478647 5.4:+8833575 None:intergenic
CGGAGCTTGAAGTGAGCTTA+GGG 0.479442 5.4:+8833743 None:intergenic
TTAGGGCTGGTGGGTTGGAA+GGG 0.484445 5.4:+8833760 None:intergenic
CGGTCATGGATGGCTCGAAC+CGG 0.489104 5.4:-8833696 MS.gene015279:CDS
CGGTTCGAGCCATCCATGAC+CGG 0.490515 5.4:+8833697 None:intergenic
TTCAACCTTTCTCATCTGCA+TGG 0.491200 5.4:-8833417 MS.gene015279:CDS
GGAGGAGAATGATATCAAAC+CGG 0.491685 5.4:-8833654 MS.gene015279:CDS
AATGATATCAAACCGGGAAT+CGG 0.493933 5.4:-8833647 MS.gene015279:CDS
TGAGCTTAGGGCTGGTGGGT+TGG 0.515513 5.4:+8833755 None:intergenic
CCTAAGCTCACTTCAAGCTC+CGG 0.518730 5.4:-8833742 MS.gene015279:CDS
CGGTTGGAACGAACCATGCT+GGG 0.526524 5.4:-8833475 MS.gene015279:CDS
GAACCGAAAATGAGTGGCTC+CGG 0.546667 5.4:-8833495 MS.gene015279:CDS
GAAGTGAGCTTAGGGCTGGT+GGG 0.547493 5.4:+8833751 None:intergenic
CGAAAATGAGTGGCTCCGGT+TGG 0.563412 5.4:-8833491 MS.gene015279:CDS
GGCATAGAGAGAAGAGAGCA+TGG 0.571054 5.4:+8833843 None:intergenic
CATGGCCATGCAGATGAGAA+AGG 0.571565 5.4:+8833412 None:intergenic
GCTTGAAGTGAGCTTAGGGC+TGG 0.571567 5.4:+8833747 None:intergenic
CCGGTTTAGAGTTGAAAACC+GGG 0.582456 5.4:-8833566 MS.gene015279:CDS
TCTAGAGAATTTACGGAACC+AGG 0.588686 5.4:-8833593 MS.gene015279:CDS
AGACGAAAGTTTAACGCCGT+GGG 0.596983 5.4:-8833803 MS.gene015279:CDS
TATCAAACCGGGAATCGGCA+CGG 0.599707 5.4:-8833642 MS.gene015279:CDS
TAGACGAAAGTTTAACGCCG+TGG 0.603199 5.4:-8833804 MS.gene015279:CDS
GTCTAACTCCGTGAAATCGG+AGG 0.604952 5.4:+8833822 None:intergenic
GGTCAAAAGTTGTCAAACAT+AGG 0.610074 5.4:-8833454 MS.gene015279:CDS
GGAATATGGAGGACCGAAAG+CGG 0.611264 5.4:-8833675 MS.gene015279:CDS
GAGGAGAATGATATCAAACC+GGG 0.616694 5.4:-8833653 MS.gene015279:CDS
TCAGCTGTGACAATATTGCA+TGG 0.636378 5.4:+8833394 None:intergenic
GAAAACCGGGAATTGAACAA+CGG 0.656607 5.4:-8833553 MS.gene015279:CDS
GCCTACGAACCGAAAATGAG+TGG 0.658730 5.4:-8833501 MS.gene015279:CDS
ATATGGAGGACCGAAAGCGG+AGG 0.670255 5.4:-8833672 MS.gene015279:CDS
TGGCTCGAACCGGAATATGG+AGG 0.676236 5.4:-8833686 MS.gene015279:CDS
CAAACCGGGAATCGGCACGG+AGG 0.765542 5.4:-8833639 MS.gene015279:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! AAAGACATCTAGAGAATTTA+CGG - chr5.4:8833631-8833650 MS.gene015279:CDS 25.0%
AGAATGTTAGAAAAATCCCA+CGG + chr5.4:8833447-8833466 None:intergenic 30.0%
GTCAAACATAGGTCAAAATA+TGG - chr5.4:8833788-8833807 MS.gene015279:CDS 30.0%
AATGATATCAAACCGGGAAT+CGG - chr5.4:8833584-8833603 MS.gene015279:CDS 35.0%
GGTCAAAAGTTGTCAAACAT+AGG - chr5.4:8833777-8833796 MS.gene015279:CDS 35.0%
AAAACCGGGAATTGAACAAC+GGG - chr5.4:8833679-8833698 MS.gene015279:CDS 40.0%
AAAGAAAAACCGGTCATGGA+TGG - chr5.4:8833525-8833544 MS.gene015279:CDS 40.0%
ACCAAAAGAAAAACCGGTCA+TGG - chr5.4:8833521-8833540 MS.gene015279:CDS 40.0%
AGGCGAACCAAAAGAAAAAC+CGG - chr5.4:8833515-8833534 MS.gene015279:CDS 40.0%
ATATCATTCTCCTCCGCTTT+CGG + chr5.4:8833572-8833591 None:intergenic 40.0%
GAAAACCGGGAATTGAACAA+CGG - chr5.4:8833678-8833697 MS.gene015279:CDS 40.0%
GAGGAGAATGATATCAAACC+GGG - chr5.4:8833578-8833597 MS.gene015279:CDS 40.0%
GGAGGAGAATGATATCAAAC+CGG - chr5.4:8833577-8833596 MS.gene015279:CDS 40.0%
TCAGCTGTGACAATATTGCA+TGG + chr5.4:8833840-8833859 None:intergenic 40.0%
TCTAGAGAATTTACGGAACC+AGG - chr5.4:8833638-8833657 MS.gene015279:CDS 40.0%
TTCAACCTTTCTCATCTGCA+TGG - chr5.4:8833814-8833833 MS.gene015279:CDS 40.0%
TTCGTCTAACTCCGTGAAAT+CGG + chr5.4:8833415-8833434 None:intergenic 40.0%
! ACCGGTTTAGAGTTGAAAAC+CGG - chr5.4:8833664-8833683 MS.gene015279:CDS 40.0%
!! TCCATGACCGGTTTTTCTTT+TGG + chr5.4:8833525-8833544 None:intergenic 40.0%
AGACGAAAGTTTAACGCCGT+GGG - chr5.4:8833428-8833447 MS.gene015279:CDS 45.0%
ATTTACGGAACCAGGTGAAC+CGG - chr5.4:8833646-8833665 MS.gene015279:CDS 45.0%
TAGACGAAAGTTTAACGCCG+TGG - chr5.4:8833427-8833446 MS.gene015279:CDS 45.0%
TCTCTATGCCTCCGATTTCA+CGG - chr5.4:8833401-8833420 MS.gene015279:CDS 45.0%
! CCCGGTTTTCAACTCTAAAC+CGG + chr5.4:8833668-8833687 None:intergenic 45.0%
! CCGGTTTAGAGTTGAAAACC+GGG - chr5.4:8833665-8833684 MS.gene015279:CDS 45.0%
! TGACAACTTTTGACCCAGCA+TGG + chr5.4:8833772-8833791 None:intergenic 45.0%
!!! TTCTTTTGGTTCGCCTGAAC+CGG + chr5.4:8833511-8833530 None:intergenic 45.0%
CATGGCCATGCAGATGAGAA+AGG + chr5.4:8833822-8833841 None:intergenic 50.0%
CCTAAGCTCACTTCAAGCTC+CGG - chr5.4:8833489-8833508 MS.gene015279:CDS 50.0%
CGGAGCTTGAAGTGAGCTTA+GGG + chr5.4:8833491-8833510 None:intergenic 50.0%
GAACCGAAAATGAGTGGCTC+CGG - chr5.4:8833736-8833755 MS.gene015279:CDS 50.0%
GCAACCCGTTGTTCAATTCC+CGG + chr5.4:8833686-8833705 None:intergenic 50.0%
GCCTACGAACCGAAAATGAG+TGG - chr5.4:8833730-8833749 MS.gene015279:CDS 50.0%
GCTTTCGGTCCTCCATATTC+CGG + chr5.4:8833557-8833576 None:intergenic 50.0%
GGAATATGGAGGACCGAAAG+CGG - chr5.4:8833556-8833575 MS.gene015279:CDS 50.0%
GTCTAACTCCGTGAAATCGG+AGG + chr5.4:8833412-8833431 None:intergenic 50.0%
TATCAAACCGGGAATCGGCA+CGG - chr5.4:8833589-8833608 MS.gene015279:CDS 50.0%
! CAACCGGAGCCACTCATTTT+CGG + chr5.4:8833742-8833761 None:intergenic 50.0%
! CAACTCTAAACCGGTTCACC+TGG + chr5.4:8833659-8833678 None:intergenic 50.0%
!! GCCACTCATTTTCGGTTCGT+AGG + chr5.4:8833734-8833753 None:intergenic 50.0%
ATATGGAGGACCGAAAGCGG+AGG - chr5.4:8833559-8833578 MS.gene015279:CDS 55.0%
CCAGCATGGTTCGTTCCAAC+CGG + chr5.4:8833758-8833777 None:intergenic 55.0%
CCGGAGCTTGAAGTGAGCTT+AGG + chr5.4:8833492-8833511 None:intergenic 55.0%
CGAAAATGAGTGGCTCCGGT+TGG - chr5.4:8833740-8833759 MS.gene015279:CDS 55.0%
CGGTTGGAACGAACCATGCT+GGG - chr5.4:8833756-8833775 MS.gene015279:CDS 55.0%
CTCACTTCAAGCTCCGGTTC+AGG - chr5.4:8833495-8833514 MS.gene015279:CDS 55.0%
GCTTGAAGTGAGCTTAGGGC+TGG + chr5.4:8833487-8833506 None:intergenic 55.0%
GGATGGCTCGAACCGGAATA+TGG - chr5.4:8833542-8833561 MS.gene015279:CDS 55.0%
TGAAGTGAGCTTAGGGCTGG+TGG + chr5.4:8833484-8833503 None:intergenic 55.0%
TGGCTCGAACCGGAATATGG+AGG - chr5.4:8833545-8833564 MS.gene015279:CDS 55.0%
! GAAGTGAGCTTAGGGCTGGT+GGG + chr5.4:8833483-8833502 None:intergenic 55.0%
!! TTAGGGCTGGTGGGTTGGAA+GGG + chr5.4:8833474-8833493 None:intergenic 55.0%
CCGGTTGGAACGAACCATGC+TGG - chr5.4:8833755-8833774 MS.gene015279:CDS 60.0%
CGGTCATGGATGGCTCGAAC+CGG - chr5.4:8833535-8833554 MS.gene015279:CDS 60.0%
CGGTTCGAGCCATCCATGAC+CGG + chr5.4:8833537-8833556 None:intergenic 60.0%
! TGAGCTTAGGGCTGGTGGGT+TGG + chr5.4:8833479-8833498 None:intergenic 60.0%
!! CTTAGGGCTGGTGGGTTGGA+AGG + chr5.4:8833475-8833494 None:intergenic 60.0%
CAAACCGGGAATCGGCACGG+AGG - chr5.4:8833592-8833611 MS.gene015279:CDS 65.0%
!! GTGACCTCCGTGCCGATTCC+CGG + chr5.4:8833599-8833618 None:intergenic 65.0%
!! GGGCTGGTGGGTTGGAAGGG+TGG + chr5.4:8833471-8833490 None:intergenic 70.0%


Chromosome Type Strat End Strand Name
chr5.4 gene 8833390 8833863 8833390 ID=MS.gene015279
chr5.4 mRNA 8833390 8833863 8833390 ID=MS.gene015279.t1;Parent=MS.gene015279
chr5.4 exon 8833390 8833863 8833390 ID=MS.gene015279.t1.exon1;Parent=MS.gene015279.t1
chr5.4 CDS 8833390 8833863 8833390 ID=cds.MS.gene015279.t1;Parent=MS.gene015279.t1
Gene Sequence

>MS.gene015279

ATGCTCTCTTCTCTCTATGCCTCCGATTTCACGGAGTTAGACGAAAGTTTAACGCCGTGGGATTTTTCTAACATTCTGCCACCCTTCCAACCCACCAGCCCTAAGCTCACTTCAAGCTCCGGTTCAGGCGAACCAAAAGAAAAACCGGTCATGGATGGCTCGAACCGGAATATGGAGGACCGAAAGCGGAGGAGAATGATATCAAACCGGGAATCGGCACGGAGGTCACGTATGAGAAAACAAAGACATCTAGAGAATTTACGGAACCAGGTGAACCGGTTTAGAGTTGAAAACCGGGAATTGAACAACGGGTTGCAGTTTTTGCTGTATCAATGCAATCGCCTACGAACCGAAAATGAGTGGCTCCGGTTGGAACGAACCATGCTGGGTCAAAAGTTGTCAAACATAGGTCAAAATATGGTTTTTCAACCTTTCTCATCTGCATGGCCATGCAATATTGTCACAGCTGAATAA
Protein sequence

>MS.gene015279.t1

MLSSLYASDFTELDESLTPWDFSNILPPFQPTSPKLTSSSGSGEPKEKPVMDGSNRNMEDRKRRRMISNRESARRSRMRKQRHLENLRNQVNRFRVENRELNNGLQFLLYQCNRLRTENEWLRLERTMLGQKLSNIGQNMVFQPFSSAWPCNIVTAE