AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene38308

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene38308.t1 MTR_4g008050 90.400 250 23 1 1 249 1 250 3.83e-160 444
MS.gene38308.t1 MTR_4g046640 50.000 66 33 0 8 73 36 101 2.14e-15 70.9
MS.gene38308.t1 MTR_2g089310 50.000 66 33 0 6 71 3 68 3.48e-12 64.7
MS.gene38308.t1 MTR_2g011450 48.276 58 30 0 6 63 3 60 4.99e-12 61.6
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene38308.t1 AT3G21150 32.051 234 128 5 8 240 5 208 5.95e-25 99.0
MS.gene38308.t1 AT4G27310 47.500 80 41 1 6 85 3 81 2.04e-15 73.2
MS.gene38308.t1 AT3G21890 51.613 62 30 0 7 68 30 91 5.08e-15 69.7
MS.gene38308.t1 AT5G54470 52.000 75 35 1 3 77 1 74 6.75e-15 71.6
MS.gene38308.t1 AT4G15248 44.156 77 43 0 8 84 32 108 1.56e-14 68.6

Find 61 sgRNAs with CRISPR-Local

Find 71 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ATGAGGTTGGAGAAAATATC+AGG 0.281886 4.3:+87515584 MS.gene38308:CDS
TTCGGTGAAACCGTCGCATT+TGG 0.282536 4.3:-87515102 None:intergenic
CGCACCCTTCTTGCAATTCA+AGG 0.341656 4.3:-87515667 None:intergenic
CCGATTCCGCCTTTCTCTGC+CGG 0.365012 4.3:+87515012 MS.gene38308:CDS
TTGTTATTGTTCTCCGGTGC+CGG 0.383054 4.3:-87515323 None:intergenic
TGGCTGCTGCGACGTCGTTT+TGG 0.398824 4.3:+87515510 MS.gene38308:CDS
TTCCTCTTGTTATTGTTCTC+CGG 0.408628 4.3:-87515329 None:intergenic
AACAAGAGGAAGAAGATGAT+TGG 0.414945 4.3:+87515341 MS.gene38308:CDS
AGCTGCGACGACGCCGTTCA+CGG 0.441391 4.3:+87515035 MS.gene38308:CDS
CGGAGGAGATATTTGCGAAA+TGG 0.441862 4.3:+87515387 MS.gene38308:CDS
ACAAGAGGAAGAAGATGATT+GGG 0.446433 4.3:+87515342 MS.gene38308:CDS
CCGGCAGAGAAAGGCGGAAT+CGG 0.453844 4.3:-87515012 None:intergenic
TTCCGGTGAGCAAGAGCGGC+AGG 0.464761 4.3:-87515168 None:intergenic
GAACGGCGTCGTCGCAGCTC+CGG 0.476153 4.3:-87515031 None:intergenic
GTCGCAGCAGCCACCTTCAC+CGG 0.482296 4.3:-87515500 None:intergenic
AGTGCCGGAGATATGAATTT+CGG 0.485587 4.3:-87515120 None:intergenic
GAGAACGTGGAAGTTACTTC+CGG 0.494776 4.3:+87515481 MS.gene38308:CDS
GTGGCTAAAATAAGCTTAGC+TGG 0.495492 4.3:-87515611 None:intergenic
GTCGCAGCTCCGGCAGAGAA+AGG 0.496029 4.3:-87515021 None:intergenic
TTCACCGAAATTCATATCTC+CGG 0.509514 4.3:+87515116 MS.gene38308:CDS
GTGTCGTAATTTGATGAGGT+TGG 0.531412 4.3:+87515571 MS.gene38308:CDS
GCCACACGATCACCGTTCAC+CGG 0.535889 4.3:-87515434 None:intergenic
AACCTGCCGCTCTTGCTCAC+CGG 0.536391 4.3:+87515166 MS.gene38308:CDS
CGATGATACATCTCCGGCAC+CGG 0.539008 4.3:+87515310 MS.gene38308:CDS
GAACGGTGATCGTGTGGCGG+TGG 0.541705 4.3:+87515439 MS.gene38308:CDS
TGAGGTTGGAGAAAATATCA+GGG 0.543347 4.3:+87515585 MS.gene38308:CDS
TCGTGTGGCGGTGGAAGCTA+TGG 0.543504 4.3:+87515448 MS.gene38308:CDS
CAGAGAAAGGCGGAATCGGA+AGG 0.554491 4.3:-87515008 None:intergenic
ACGGTGGTGTAGTGTAGTGC+CGG 0.554858 4.3:-87515135 None:intergenic
AACACCTTGAATTGCAAGAA+GGG 0.556767 4.3:+87515663 MS.gene38308:CDS
TCACCGGAAAATCATTCCTC+CGG 0.557681 4.3:+87515182 MS.gene38308:CDS
TGAAAGTGTTGGATCGGTGG+CGG 0.559970 4.3:+87515367 MS.gene38308:CDS
AAGTGTTGGATCGGTGGCGG+AGG 0.560614 4.3:+87515370 MS.gene38308:CDS
AGATTGAGAACTCGCCTCAC+CGG 0.561454 4.3:-87515201 None:intergenic
GACTGAAAGTGTTGGATCGG+TGG 0.563595 4.3:+87515364 MS.gene38308:CDS
TCCGGTGAACGGTGATCGTG+TGG 0.570131 4.3:+87515433 MS.gene38308:CDS
CAACACCTTGAATTGCAAGA+AGG 0.572050 4.3:+87515662 MS.gene38308:CDS
GTGGAAGTTACTTCCGGTGA+AGG 0.577957 4.3:+87515487 MS.gene38308:CDS
ATGATTGGGACTGAAAGTGT+TGG 0.593930 4.3:+87515356 MS.gene38308:CDS
TGTTACCGATGATACATCTC+CGG 0.594095 4.3:+87515304 MS.gene38308:CDS
GAAGTTACTTCCGGTGAAGG+TGG 0.596707 4.3:+87515490 MS.gene38308:CDS
CCACGTGTCGTAATTTGATG+AGG 0.597307 4.3:+87515567 MS.gene38308:CDS
GAGGAAGTTAGCGCCGTGAA+CGG 0.601829 4.3:-87515048 None:intergenic
ATCTTGTGCTCCAAATGCGA+CGG 0.602290 4.3:+87515092 MS.gene38308:CDS
AGCGGCAGGTTGATGAGAGA+CGG 0.602586 4.3:-87515154 None:intergenic
CACCGGAGAACAATAACAAG+AGG 0.613856 4.3:+87515327 MS.gene38308:CDS
CCTCATCAAATTACGACACG+TGG 0.625412 4.3:-87515567 None:intergenic
TGGGACTGAAAGTGTTGGAT+CGG 0.630097 4.3:+87515361 MS.gene38308:CDS
ATTTGGAGCACAAGATGTGA+CGG 0.631824 4.3:-87515085 None:intergenic
GCAGCTCCGGCAGAGAAAGG+CGG 0.638220 4.3:-87515018 None:intergenic
TGTGGCGGTGGAAGCTATGG+CGG 0.643579 4.3:+87515451 MS.gene38308:CDS
TTGAGAACTCGCCTCACCGG+AGG 0.643923 4.3:-87515198 None:intergenic
CGGTGCCGGAGATGTATCAT+CGG 0.645343 4.3:-87515309 None:intergenic
GGTGAACGGTGATCGTGTGG+CGG 0.678941 4.3:+87515436 MS.gene38308:CDS
GGAAAATCATTCCTCCGGTG+AGG 0.685941 4.3:+87515187 MS.gene38308:CDS
ACGTGCGAGTTTCACATGTG+TGG 0.691088 4.3:-87515630 None:intergenic
GGCAGGTTGATGAGAGACGG+TGG 0.691500 4.3:-87515151 None:intergenic
TGGCGGTGTGTATGAGAACG+TGG 0.692845 4.3:+87515468 MS.gene38308:CDS
GAGGTTGGAGAAAATATCAG+GGG 0.723090 4.3:+87515586 MS.gene38308:CDS
TGGAGCACAAGATGTGACGG+AGG 0.724489 4.3:-87515082 None:intergenic
GACGGAGGTGACGAGCGACG+AGG 0.727759 4.3:-87515067 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! AGAGTTAGAGTTAGATTTTC+CGG + chr4.3:87515415-87515434 MS.gene38308:CDS 30.0%
AACAAGAGGAAGAAGATGAT+TGG + chr4.3:87515341-87515360 MS.gene38308:CDS 35.0%
AACACCTTGAATTGCAAGAA+GGG + chr4.3:87515663-87515682 MS.gene38308:CDS 35.0%
ACAAGAGGAAGAAGATGATT+GGG + chr4.3:87515342-87515361 MS.gene38308:CDS 35.0%
ATGAGGTTGGAGAAAATATC+AGG + chr4.3:87515584-87515603 MS.gene38308:CDS 35.0%
TGAGGTTGGAGAAAATATCA+GGG + chr4.3:87515585-87515604 MS.gene38308:CDS 35.0%
TTCACCGAAATTCATATCTC+CGG + chr4.3:87515116-87515135 MS.gene38308:CDS 35.0%
!! TTCCTCTTGTTATTGTTCTC+CGG - chr4.3:87515332-87515351 None:intergenic 35.0%
CAACACCTTGAATTGCAAGA+AGG + chr4.3:87515662-87515681 MS.gene38308:CDS 40.0%
GAGGTTGGAGAAAATATCAG+GGG + chr4.3:87515586-87515605 MS.gene38308:CDS 40.0%
GTGGCTAAAATAAGCTTAGC+TGG - chr4.3:87515614-87515633 None:intergenic 40.0%
GTGTCGTAATTTGATGAGGT+TGG + chr4.3:87515571-87515590 MS.gene38308:CDS 40.0%
TGTTACCGATGATACATCTC+CGG + chr4.3:87515304-87515323 MS.gene38308:CDS 40.0%
! AGTGCCGGAGATATGAATTT+CGG - chr4.3:87515123-87515142 None:intergenic 40.0%
! ATGATTGGGACTGAAAGTGT+TGG + chr4.3:87515356-87515375 MS.gene38308:CDS 40.0%
! ATTTGGAGCACAAGATGTGA+CGG - chr4.3:87515088-87515107 None:intergenic 40.0%
! GAGTTAGATTTTCCGGTGAA+CGG + chr4.3:87515422-87515441 MS.gene38308:CDS 40.0%
! GGTTGGGGTTAAGATTTTGT+GGG + chr4.3:87515531-87515550 MS.gene38308:CDS 40.0%
! GTTGGGGTTAAGATTTTGTG+GGG + chr4.3:87515532-87515551 MS.gene38308:CDS 40.0%
! TGGTTGGGGTTAAGATTTTG+TGG + chr4.3:87515530-87515549 MS.gene38308:CDS 40.0%
ATCTTGTGCTCCAAATGCGA+CGG + chr4.3:87515092-87515111 MS.gene38308:CDS 45.0%
CACCGGAGAACAATAACAAG+AGG + chr4.3:87515327-87515346 MS.gene38308:CDS 45.0%
CCACGTGTCGTAATTTGATG+AGG + chr4.3:87515567-87515586 MS.gene38308:CDS 45.0%
CCTCATCAAATTACGACACG+TGG - chr4.3:87515570-87515589 None:intergenic 45.0%
CGGAGGAGATATTTGCGAAA+TGG + chr4.3:87515387-87515406 MS.gene38308:CDS 45.0%
GAGAACGTGGAAGTTACTTC+CGG + chr4.3:87515481-87515500 MS.gene38308:CDS 45.0%
TCACCGGAAAATCATTCCTC+CGG + chr4.3:87515182-87515201 MS.gene38308:CDS 45.0%
! TCACCGGAGGAATGATTTTC+CGG - chr4.3:87515188-87515207 None:intergenic 45.0%
! TTGTTATTGTTCTCCGGTGC+CGG - chr4.3:87515326-87515345 None:intergenic 45.0%
!! TGGGACTGAAAGTGTTGGAT+CGG + chr4.3:87515361-87515380 MS.gene38308:CDS 45.0%
ACGTGCGAGTTTCACATGTG+TGG - chr4.3:87515633-87515652 None:intergenic 50.0%
AGATTGAGAACTCGCCTCAC+CGG - chr4.3:87515204-87515223 None:intergenic 50.0%
CGCACCCTTCTTGCAATTCA+AGG - chr4.3:87515670-87515689 None:intergenic 50.0%
GAAGTTACTTCCGGTGAAGG+TGG + chr4.3:87515490-87515509 MS.gene38308:CDS 50.0%
GGAAAATCATTCCTCCGGTG+AGG + chr4.3:87515187-87515206 MS.gene38308:CDS 50.0%
GTGGAAGTTACTTCCGGTGA+AGG + chr4.3:87515487-87515506 MS.gene38308:CDS 50.0%
TTCGGTGAAACCGTCGCATT+TGG - chr4.3:87515105-87515124 None:intergenic 50.0%
! GATTTTCCGGTGAGCAAGAG+CGG - chr4.3:87515175-87515194 None:intergenic 50.0%
!! GACTGAAAGTGTTGGATCGG+TGG + chr4.3:87515364-87515383 MS.gene38308:CDS 50.0%
!! TGAAAGTGTTGGATCGGTGG+CGG + chr4.3:87515367-87515386 MS.gene38308:CDS 50.0%
ACGGTGGTGTAGTGTAGTGC+CGG - chr4.3:87515138-87515157 None:intergenic 55.0%
CAGAGAAAGGCGGAATCGGA+AGG - chr4.3:87515011-87515030 None:intergenic 55.0%
CGATGATACATCTCCGGCAC+CGG + chr4.3:87515310-87515329 MS.gene38308:CDS 55.0%
GAGGAAGTTAGCGCCGTGAA+CGG - chr4.3:87515051-87515070 None:intergenic 55.0%
TGGAGCACAAGATGTGACGG+AGG - chr4.3:87515085-87515104 None:intergenic 55.0%
TGGCGGTGTGTATGAGAACG+TGG + chr4.3:87515468-87515487 MS.gene38308:CDS 55.0%
! CGGTGCCGGAGATGTATCAT+CGG - chr4.3:87515312-87515331 None:intergenic 55.0%
!! AGCGGCAGGTTGATGAGAGA+CGG - chr4.3:87515157-87515176 None:intergenic 55.0%
!! TGCTGCGACGTCGTTTTGGT+TGG + chr4.3:87515514-87515533 MS.gene38308:CDS 55.0%
!!! CTGCGACGTCGTTTTGGTTG+GGG + chr4.3:87515516-87515535 MS.gene38308:CDS 55.0%
!!! GCTGCGACGTCGTTTTGGTT+GGG + chr4.3:87515515-87515534 MS.gene38308:CDS 55.0%
AACCTGCCGCTCTTGCTCAC+CGG + chr4.3:87515166-87515185 MS.gene38308:CDS 60.0%
CCGATTCCGCCTTTCTCTGC+CGG + chr4.3:87515012-87515031 MS.gene38308:CDS 60.0%
CCGGCAGAGAAAGGCGGAAT+CGG - chr4.3:87515015-87515034 None:intergenic 60.0%
GCCACACGATCACCGTTCAC+CGG - chr4.3:87515437-87515456 None:intergenic 60.0%
GGTGAACGGTGATCGTGTGG+CGG + chr4.3:87515436-87515455 MS.gene38308:CDS 60.0%
TCCGGTGAACGGTGATCGTG+TGG + chr4.3:87515433-87515452 MS.gene38308:CDS 60.0%
TCGTGTGGCGGTGGAAGCTA+TGG + chr4.3:87515448-87515467 MS.gene38308:CDS 60.0%
TGTGGCGGTGGAAGCTATGG+CGG + chr4.3:87515451-87515470 MS.gene38308:CDS 60.0%
TTGAGAACTCGCCTCACCGG+AGG - chr4.3:87515201-87515220 None:intergenic 60.0%
! TGGCTGCTGCGACGTCGTTT+TGG + chr4.3:87515510-87515529 MS.gene38308:CDS 60.0%
!! AAGTGTTGGATCGGTGGCGG+AGG + chr4.3:87515370-87515389 MS.gene38308:CDS 60.0%
!! GGCAGGTTGATGAGAGACGG+TGG - chr4.3:87515154-87515173 None:intergenic 60.0%
AGCTGCGACGACGCCGTTCA+CGG + chr4.3:87515035-87515054 MS.gene38308:CDS 65.0%
GAACGGTGATCGTGTGGCGG+TGG + chr4.3:87515439-87515458 MS.gene38308:CDS 65.0%
GCAGCTCCGGCAGAGAAAGG+CGG - chr4.3:87515021-87515040 None:intergenic 65.0%
GTCGCAGCAGCCACCTTCAC+CGG - chr4.3:87515503-87515522 None:intergenic 65.0%
GTCGCAGCTCCGGCAGAGAA+AGG - chr4.3:87515024-87515043 None:intergenic 65.0%
TTCCGGTGAGCAAGAGCGGC+AGG - chr4.3:87515171-87515190 None:intergenic 65.0%
GAACGGCGTCGTCGCAGCTC+CGG - chr4.3:87515034-87515053 None:intergenic 70.0%
GACGGAGGTGACGAGCGACG+AGG - chr4.3:87515070-87515089 None:intergenic 70.0%


Chromosome Type Strat End Strand Name
chr4.3 gene 87514951 87515700 87514951 ID=MS.gene38308
chr4.3 mRNA 87514951 87515700 87514951 ID=MS.gene38308.t1;Parent=MS.gene38308
chr4.3 exon 87514951 87515700 87514951 ID=MS.gene38308.t1.exon1;Parent=MS.gene38308.t1
chr4.3 CDS 87514951 87515700 87514951 ID=cds.MS.gene38308.t1;Parent=MS.gene38308.t1
Gene Sequence

>MS.gene38308

ATGAAGATGAAGTGCAAACAATGCGAACTTTGTAATCAACAAGCTTCTTTCTATTGTCCTTCCGATTCCGCCTTTCTCTGCCGGAGCTGCGACGACGCCGTTCACGGCGCTAACTTCCTCGTCGCTCGTCACCTCCGTCACATCTTGTGCTCCAAATGCGACGGTTTCACCGAAATTCATATCTCCGGCACTACACTACACCACCGTCTCTCATCAACCTGCCGCTCTTGCTCACCGGAAAATCATTCCTCCGGTGAGGCGAGTTCTCAATCTTCTTCTTGCGAGTCTTGCGTTACAGAAAAGAAGAAAACAAAATCTCGAAAGATAATGAAGAGTTTTACAATTTCGAATTCTGTTACCGATGATACATCTCCGGCACCGGAGAACAATAACAAGAGGAAGAAGATGATTGGGACTGAAAGTGTTGGATCGGTGGCGGAGGAGATATTTGCGAAATGGAGAAGAGAGTTAGAGTTAGATTTTCCGGTGAACGGTGATCGTGTGGCGGTGGAAGCTATGGCGGTGTGTATGAGAACGTGGAAGTTACTTCCGGTGAAGGTGGCTGCTGCGACGTCGTTTTGGTTGGGGTTAAGATTTTGTGGGGACAATAGTTTTGCCACGTGTCGTAATTTGATGAGGTTGGAGAAAATATCAGGGGTGCCAGCTAAGCTTATTTTAGCCACACATGTGAAACTCGCACGTGTCTTTACTCAACACCTTGAATTGCAAGAAGGGTGCGATGAGTCCTAA
Protein sequence

>MS.gene38308.t1

MKMKCKQCELCNQQASFYCPSDSAFLCRSCDDAVHGANFLVARHLRHILCSKCDGFTEIHISGTTLHHRLSSTCRSCSPENHSSGEASSQSSSCESCVTEKKKTKSRKIMKSFTISNSVTDDTSPAPENNNKRKKMIGTESVGSVAEEIFAKWRRELELDFPVNGDRVAVEAMAVCMRTWKLLPVKVAAATSFWLGLRFCGDNSFATCRNLMRLEKISGVPAKLILATHVKLARVFTQHLELQEGCDES