AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene37911

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene37911.t1 MTR_5g085810 77.286 339 72 3 1 337 398 733 8.56e-169 488
MS.gene37911.t1 MTR_5g085830 72.189 338 89 2 1 337 372 705 1.03e-163 474
MS.gene37911.t1 MTR_5g085480 57.143 357 123 7 1 335 179 527 2.21e-112 337
MS.gene37911.t1 MTR_5g085480 57.143 357 123 7 1 335 339 687 1.25e-110 337
MS.gene37911.t1 MTR_5g085500 51.157 389 132 9 1 333 68 454 1.27e-107 322
MS.gene37911.t1 MTR_2g033045 64.615 195 56 3 142 333 30 214 1.55e-75 234
MS.gene37911.t1 MTR_5g085440 58.019 212 79 3 125 333 145 349 2.11e-70 223
MS.gene37911.t1 MTR_2g033050 64.444 90 28 2 1 88 295 382 2.21e-28 114
MS.gene37911.t1 MTR_1g115575 27.299 348 206 15 5 322 232 562 6.40e-13 70.1
MS.gene37911.t1 MTR_1g032100 23.684 342 200 12 11 328 197 501 3.87e-12 67.4
MS.gene37911.t1 MTR_8g105260 24.333 300 170 9 11 289 204 467 3.64e-11 64.3
MS.gene37911.t1 MTR_5g085560 40.517 116 54 4 105 205 1 116 8.41e-11 59.7
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene37911.t1 AT4G03460 34.328 335 167 5 8 336 302 589 2.12e-39 147
MS.gene37911.t1 AT4G03460 34.328 335 167 5 8 336 334 621 2.25e-39 147
MS.gene37911.t1 AT4G03500 33.030 330 169 5 8 331 326 609 3.01e-38 144
MS.gene37911.t1 AT4G03500 33.030 330 169 5 8 331 326 609 3.01e-38 144
MS.gene37911.t1 AT4G03500 33.030 330 169 5 8 331 349 632 4.03e-38 144
MS.gene37911.t1 AT1G03670 30.631 333 172 7 8 332 322 603 1.28e-35 136
MS.gene37911.t1 AT4G03490 28.698 338 190 6 5 336 300 592 1.40e-30 122
MS.gene37911.t1 AT4G03490 28.698 338 190 6 5 336 310 602 1.58e-30 122
MS.gene37911.t1 AT4G03490 29.560 318 169 8 5 316 310 578 3.26e-28 115
MS.gene37911.t1 AT4G03450 27.241 290 158 6 8 288 326 571 6.68e-17 82.0
MS.gene37911.t1 AT4G03450 26.852 324 176 8 8 322 326 597 1.04e-16 81.6
MS.gene37911.t1 AT4G03440 25.962 312 179 9 8 310 409 677 8.42e-16 79.0
MS.gene37911.t1 AT4G03440 25.962 312 179 9 8 310 409 677 8.42e-16 79.0
MS.gene37911.t1 AT4G03440 25.962 312 179 9 8 310 416 684 9.02e-16 79.0
MS.gene37911.t1 AT3G12360 25.648 347 213 11 5 322 230 560 2.03e-13 71.6
MS.gene37911.t1 AT3G12360 25.648 347 213 11 5 322 218 548 2.16e-13 71.2
MS.gene37911.t1 AT4G03490 31.944 144 88 4 179 316 381 520 5.67e-13 70.1
MS.gene37911.t1 AT4G03490 31.944 144 88 4 179 316 391 530 7.99e-13 69.7

Find 51 sgRNAs with CRISPR-Local

Find 83 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CTCACTGTCTTTGGCTTTCA+TGG 0.097564 5.3:-69431102 MS.gene37911:CDS
TGCTCTCATCTCACTGTCTT+TGG 0.207336 5.3:-69431111 MS.gene37911:CDS
GTGCTACAATCCTCCTCTTT+TGG 0.218883 5.3:-69431199 MS.gene37911:CDS
TTGGTTGGCCTATCTATTTA+TGG 0.227074 5.3:-69431048 MS.gene37911:CDS
CTACTGAAGCAGTGATTATA+AGG 0.264237 5.3:+69431333 None:intergenic
CTGTCTTTGGCTTTCATGGC+TGG 0.281772 5.3:-69431098 MS.gene37911:CDS
AGGAAATACTCCTTTGCTTC+TGG 0.312272 5.3:-69431936 MS.gene37911:CDS
AAAATAGTAATGCCAATTCT+TGG 0.318642 5.3:-69431137 MS.gene37911:CDS
CTGTTATCAGTGAACTTACT+TGG 0.359026 5.3:-69431067 MS.gene37911:CDS
TTTATCATCCTATCAAGTTC+AGG 0.370811 5.3:+69431974 None:intergenic
GAGGAGGATTGTAGCACTAA+TGG 0.394706 5.3:+69431205 None:intergenic
ATGAGAGCAATTCCAAGAAT+TGG 0.406320 5.3:+69431125 None:intergenic
TCTGACACCAAACGACCTAT+AGG 0.432161 5.3:-69431482 MS.gene37911:CDS
CAACTAATCTTCTAAAACTC+AGG 0.435810 5.3:+69431567 None:intergenic
ACTTGGATTAACTGACTTGG+CGG 0.440496 5.3:-69431171 MS.gene37911:CDS
TTATAATGTTCTTCGGAGCC+TGG 0.444014 5.3:+69431389 None:intergenic
ACTTTGTCCTATAGGTCGTT+TGG 0.445352 5.3:+69431475 None:intergenic
TGACAACTTCAAGAGCTGTT+TGG 0.453693 5.3:+69431831 None:intergenic
AGTTACAACCATAAATAGAT+AGG 0.459512 5.3:+69431040 None:intergenic
TCCCCTTTCTTATACTAGCA+TGG 0.460875 5.3:-69430926 MS.gene37911:CDS
TTCGAGTCACTTTGTCCTAT+AGG 0.471538 5.3:+69431467 None:intergenic
TTGATGATGAGGGGAGGAAA+AGG 0.474134 5.3:+69430979 None:intergenic
TATCAGTGAACTTACTTGGT+TGG 0.481569 5.3:-69431063 MS.gene37911:CDS
TGATAGGATGATAAATCAAA+AGG 0.490334 5.3:-69431966 MS.gene37911:CDS
GTCGAATTCCTGAACTTGAT+AGG 0.496981 5.3:-69431982 MS.gene37911:CDS
TAGTATAAGAAAGGGGAAGT+AGG 0.498465 5.3:+69430932 None:intergenic
ATCCAAGTGTTGCCCAAAAG+AGG 0.511836 5.3:+69431186 None:intergenic
AGCCATGCTAGTATAAGAAA+GGG 0.515852 5.3:+69430924 None:intergenic
GAGCCATGCTAGTATAAGAA+AGG 0.533660 5.3:+69430923 None:intergenic
TGATGAAGATAATGAAAGCT+TGG 0.535914 5.3:+69431246 None:intergenic
AACACTTGGATTAACTGACT+TGG 0.536609 5.3:-69431174 MS.gene37911:CDS
GAATATTACGCTTAAATGAA+AGG 0.539847 5.3:+69432065 None:intergenic
TACTGAAGCAGTGATTATAA+GGG 0.546627 5.3:+69431334 None:intergenic
TTCTAGTTGATGATGAGGGG+AGG 0.549260 5.3:+69430973 None:intergenic
TTTAACATGGGATGAAAGAG+TGG 0.555233 5.3:-69431879 MS.gene37911:CDS
CTACTTACCCTTCTCGTGGG+TGG 0.556353 5.3:+69431788 None:intergenic
TATAGGTCGTTTGGTGTCAG+AGG 0.559162 5.3:+69431484 None:intergenic
GCATTACTCTGCTCTAATTG+TGG 0.561826 5.3:+69431512 None:intergenic
AATTCTACTTACCCTTCTCG+TGG 0.564631 5.3:+69431784 None:intergenic
CTTGTAGCACTGAATTCTGC+TGG 0.570512 5.3:-69431596 MS.gene37911:CDS
TTCGTAATCCACCCACGAGA+AGG 0.570876 5.3:-69431796 MS.gene37911:CDS
GCTGTTCCAGGTGAAGCGGA+TGG 0.571638 5.3:-69431299 MS.gene37911:CDS
CTTGGAACATTGCATGACAT+AGG 0.575152 5.3:+69431264 None:intergenic
TCGTAATCCACCCACGAGAA+GGG 0.592425 5.3:-69431795 MS.gene37911:intron
ATTCTACTTACCCTTCTCGT+GGG 0.603839 5.3:+69431785 None:intergenic
GAAGTAGGAAATGTATCGCA+AGG 0.625002 5.3:+69430947 None:intergenic
CAAGTGTTGCCCAAAAGAGG+AGG 0.636685 5.3:+69431189 None:intergenic
ATAAATCAAAAGGATTACAA+AGG 0.638699 5.3:-69431956 MS.gene37911:CDS
CATGGTGCAGACACTCACAT+TGG 0.643071 5.3:-69431363 MS.gene37911:CDS
TGAAAGAGTGGATCTTCATG+TGG 0.669289 5.3:-69431867 MS.gene37911:CDS
GCCATGCTAGTATAAGAAAG+GGG 0.679151 5.3:+69430925 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAAATTAAAGATTGTAAATA+TGG + chr5.3:69431278-69431297 None:intergenic 10.0%
!! AAATTAAAGATTGTAAATAT+GGG + chr5.3:69431277-69431296 None:intergenic 10.0%
!!! TATTTACAATCTTTAATTTT+AGG - chr5.3:69431278-69431297 MS.gene37911:CDS 10.0%
!! ATCTATTTGTCATATATAAA+AGG + chr5.3:69431349-69431368 None:intergenic 15.0%
!! TCTATTTGTCATATATAAAA+GGG + chr5.3:69431348-69431367 None:intergenic 15.0%
!! ATAAATCAAAAGGATTACAA+AGG - chr5.3:69431031-69431050 MS.gene37911:CDS 20.0%
!! GTTAAATAAAAAACAGTCTT+GGG + chr5.3:69431094-69431113 None:intergenic 20.0%
!! TGTTAAATAAAAAACAGTCT+TGG + chr5.3:69431095-69431114 None:intergenic 20.0%
!!! AGACTGTTTTTTATTTAACA+TGG - chr5.3:69431095-69431114 MS.gene37911:CDS 20.0%
!!! CATGTTTTTATAATGTTCTT+CGG + chr5.3:69431608-69431627 None:intergenic 20.0%
!!! GACTGTTTTTTATTTAACAT+GGG - chr5.3:69431096-69431115 MS.gene37911:CDS 20.0%
!!! TAGAATTCATTTTGAATGTT+AGG - chr5.3:69431219-69431238 MS.gene37911:CDS 20.0%
! AAAAAAAATGTGTAGTGTTG+TGG + chr5.3:69431573-69431592 None:intergenic 25.0%
! AAAAAAATGTGTAGTGTTGT+GGG + chr5.3:69431572-69431591 None:intergenic 25.0%
! AAAATAGTAATGCCAATTCT+TGG - chr5.3:69431850-69431869 MS.gene37911:CDS 25.0%
! AAAGATTGTAAATATGGGAA+GGG + chr5.3:69431272-69431291 None:intergenic 25.0%
! AGTTACAACCATAAATAGAT+AGG + chr5.3:69431950-69431969 None:intergenic 25.0%
! CGAAGAACATTATAAAAACA+TGG - chr5.3:69431606-69431625 MS.gene37911:CDS 25.0%
! GAATATTACGCTTAAATGAA+AGG + chr5.3:69430925-69430944 None:intergenic 25.0%
! TAAAGATTGTAAATATGGGA+AGG + chr5.3:69431273-69431292 None:intergenic 25.0%
! TGATAGGATGATAAATCAAA+AGG - chr5.3:69431021-69431040 MS.gene37911:CDS 25.0%
!! ATTCATTTTGAATGTTAGGA+TGG - chr5.3:69431223-69431242 MS.gene37911:CDS 25.0%
!!! ACACATTTTTTTTTTTTGCC+AGG - chr5.3:69431580-69431599 MS.gene37911:CDS 25.0%
AACACAACCACAACAAAAAT+CGG + chr5.3:69431973-69431992 None:intergenic 30.0%
CAAATAGATGTAATGTTTGC+AGG - chr5.3:69431360-69431379 MS.gene37911:CDS 30.0%
TACTGAAGCAGTGATTATAA+GGG + chr5.3:69431656-69431675 None:intergenic 30.0%
TGATGAAGATAATGAAAGCT+TGG + chr5.3:69431744-69431763 None:intergenic 30.0%
TTTATCATCCTATCAAGTTC+AGG + chr5.3:69431016-69431035 None:intergenic 30.0%
!! CAACTAATCTTCTAAAACTC+AGG + chr5.3:69431423-69431442 None:intergenic 30.0%
!!! ATTTTCTAGTTGATGATGAG+GGG + chr5.3:69432020-69432039 None:intergenic 30.0%
!!! GATTTTCTAGTTGATGATGA+GGG + chr5.3:69432021-69432040 None:intergenic 30.0%
AACACTTGGATTAACTGACT+TGG - chr5.3:69431813-69431832 MS.gene37911:CDS 35.0%
AATGTTAGGATGGATGTTTC+AGG - chr5.3:69431233-69431252 MS.gene37911:CDS 35.0%
AGCCATGCTAGTATAAGAAA+GGG + chr5.3:69432066-69432085 None:intergenic 35.0%
ATGAGAGCAATTCCAAGAAT+TGG + chr5.3:69431865-69431884 None:intergenic 35.0%
CTACTGAAGCAGTGATTATA+AGG + chr5.3:69431657-69431676 None:intergenic 35.0%
CTGTTATCAGTGAACTTACT+TGG - chr5.3:69431920-69431939 MS.gene37911:CDS 35.0%
CTTCATGTTGCAGCAAAAAA+TGG - chr5.3:69430944-69430963 MS.gene37911:CDS 35.0%
TAGTATAAGAAAGGGGAAGT+AGG + chr5.3:69432058-69432077 None:intergenic 35.0%
TATCAGTGAACTTACTTGGT+TGG - chr5.3:69431924-69431943 MS.gene37911:CDS 35.0%
TTTAACATGGGATGAAAGAG+TGG - chr5.3:69431108-69431127 MS.gene37911:CDS 35.0%
! TGTAACTCCGATTTTTGTTG+TGG - chr5.3:69431963-69431982 MS.gene37911:CDS 35.0%
!! TTGGTTGGCCTATCTATTTA+TGG - chr5.3:69431939-69431958 MS.gene37911:CDS 35.0%
!!! GGATTTTCTAGTTGATGATG+AGG + chr5.3:69432022-69432041 None:intergenic 35.0%
AATTCTACTTACCCTTCTCG+TGG + chr5.3:69431206-69431225 None:intergenic 40.0%
ACTTTGTCCTATAGGTCGTT+TGG + chr5.3:69431515-69431534 None:intergenic 40.0%
AGGAAATACTCCTTTGCTTC+TGG - chr5.3:69431051-69431070 MS.gene37911:CDS 40.0%
ATTCTACTTACCCTTCTCGT+GGG + chr5.3:69431205-69431224 None:intergenic 40.0%
CTTGGAACATTGCATGACAT+AGG + chr5.3:69431726-69431745 None:intergenic 40.0%
GAAGTAGGAAATGTATCGCA+AGG + chr5.3:69432043-69432062 None:intergenic 40.0%
GAGCCATGCTAGTATAAGAA+AGG + chr5.3:69432067-69432086 None:intergenic 40.0%
GCATTACTCTGCTCTAATTG+TGG + chr5.3:69431478-69431497 None:intergenic 40.0%
GCCATGCTAGTATAAGAAAG+GGG + chr5.3:69432065-69432084 None:intergenic 40.0%
GTCGAATTCCTGAACTTGAT+AGG - chr5.3:69431005-69431024 MS.gene37911:CDS 40.0%
TCCCCTTTCTTATACTAGCA+TGG - chr5.3:69432061-69432080 MS.gene37911:CDS 40.0%
TGAAAGAGTGGATCTTCATG+TGG - chr5.3:69431120-69431139 MS.gene37911:CDS 40.0%
TGACAACTTCAAGAGCTGTT+TGG + chr5.3:69431159-69431178 None:intergenic 40.0%
TTATAATGTTCTTCGGAGCC+TGG + chr5.3:69431601-69431620 None:intergenic 40.0%
! TGCTACAATCCTCCTCTTTT+GGG - chr5.3:69431789-69431808 MS.gene37911:intron 40.0%
! TTCGAGTCACTTTGTCCTAT+AGG + chr5.3:69431523-69431542 None:intergenic 40.0%
!! ACTTGGATTAACTGACTTGG+CGG - chr5.3:69431816-69431835 MS.gene37911:CDS 40.0%
GAGGAGGATTGTAGCACTAA+TGG + chr5.3:69431785-69431804 None:intergenic 45.0%
TCTGACACCAAACGACCTAT+AGG - chr5.3:69431505-69431524 MS.gene37911:CDS 45.0%
TGCTCTCATCTCACTGTCTT+TGG - chr5.3:69431876-69431895 MS.gene37911:CDS 45.0%
! ATCCAAGTGTTGCCCAAAAG+AGG + chr5.3:69431804-69431823 None:intergenic 45.0%
! CTTGTAGCACTGAATTCTGC+TGG - chr5.3:69431391-69431410 MS.gene37911:CDS 45.0%
! GATTTTGCAGCCAGAAGCAA+AGG + chr5.3:69431064-69431083 None:intergenic 45.0%
! GTGCTACAATCCTCCTCTTT+TGG - chr5.3:69431788-69431807 MS.gene37911:intron 45.0%
!! CTCACTGTCTTTGGCTTTCA+TGG - chr5.3:69431885-69431904 MS.gene37911:CDS 45.0%
!! TATAGGTCGTTTGGTGTCAG+AGG + chr5.3:69431506-69431525 None:intergenic 45.0%
!! TTCTAGTTGATGATGAGGGG+AGG + chr5.3:69432017-69432036 None:intergenic 45.0%
!! TTGATGATGAGGGGAGGAAA+AGG + chr5.3:69432011-69432030 None:intergenic 45.0%
!!! TTTTGCTGTTCCAGGTGAAG+CGG - chr5.3:69431684-69431703 MS.gene37911:intron 45.0%
CATGGTGCAGACACTCACAT+TGG - chr5.3:69431624-69431643 MS.gene37911:intron 50.0%
TCGTAATCCACCCACGAGAA+GGG - chr5.3:69431192-69431211 MS.gene37911:CDS 50.0%
TTCGTAATCCACCCACGAGA+AGG - chr5.3:69431191-69431210 MS.gene37911:CDS 50.0%
! CAAGTGTTGCCCAAAAGAGG+AGG + chr5.3:69431801-69431820 None:intergenic 50.0%
! CTCCTCTTTTGGGCAACACT+TGG - chr5.3:69431799-69431818 MS.gene37911:CDS 50.0%
!! CTGTCTTTGGCTTTCATGGC+TGG - chr5.3:69431889-69431908 MS.gene37911:CDS 50.0%
!!! GCAGCATGTTTTGCTGTTCC+AGG - chr5.3:69431676-69431695 MS.gene37911:intron 50.0%
CTACTTACCCTTCTCGTGGG+TGG + chr5.3:69431202-69431221 None:intergenic 55.0%
! GCTTTTCCATCCGCTTCACC+TGG + chr5.3:69431697-69431716 None:intergenic 55.0%
GCTGTTCCAGGTGAAGCGGA+TGG - chr5.3:69431688-69431707 MS.gene37911:intron 60.0%


Chromosome Type Strat End Strand Name
chr5.3 gene 69430914 69432095 69430914 ID=MS.gene37911
chr5.3 mRNA 69430914 69432095 69430914 ID=MS.gene37911.t1;Parent=MS.gene37911
chr5.3 exon 69431796 69432095 69431796 ID=MS.gene37911.t1.exon1;Parent=MS.gene37911.t1
chr5.3 CDS 69431796 69432095 69431796 ID=cds.MS.gene37911.t1;Parent=MS.gene37911.t1
chr5.3 exon 69430914 69431627 69430914 ID=MS.gene37911.t1.exon2;Parent=MS.gene37911.t1
chr5.3 CDS 69430914 69431627 69430914 ID=cds.MS.gene37911.t1;Parent=MS.gene37911.t1
Gene Sequence

>MS.gene37911

ATGCTTGACCTTTCATTTAAGCGTAATATTCTTCATGTTGCAGCAAAAAATGGAAAGCATGACGTAGTAAAATACATATTACTGCAAAGTCGTCGAATTCCTGAACTTGATAGGATGATAAATCAAAAGGATTACAAAGGAAATACTCCTTTGCTTCTGGCTGCAAAATCGTGTCATCCCAAGACTGTTTTTTATTTAACATGGGATGAAAGAGTGGATCTTCATGTGGTTAACAAAAACAACCAAACAGCTCTTGAAGTTGTCAACGCATCTCAACTTCGTAATCCACCCACGAGAAGGGTAAGTAGAATTCATTTTGAATGTTAGGATGGATGTTTCAGGATAGAGTTGATTTCCCTTCCCATATTTACAATCTTTAATTTTAGGCTATTATTTTGTCAAAAATGAAAGATTTGTTCGATTATCTTTTTCCCTTTTATATATGACAAATAGATGTAATGTTTGCAGGAACTTACACTTGTAGCACTGAATTCTGCTGGTGCAAACCTGAGTTTTAGAAGATTAGTTGATGATAAATCGAGACAAAGTGACTCAAACTTGCCACAATTAGAGCAGAGTAATGCTGAATCCTCTGACACCAAACGACCTATAGGACAAAGTGACTCGAAGTCGAATGAGAATAACAAAAATGTCTCCCACAACACTACACATTTTTTTTTTTTGCCAGGCTCCGAAGAACATTATAAAAACATGGTGCAGACACTCACATTGGTTTCAACCCTTATAATCACTGCTTCAGTAGCAGCATGTTTTGCTGTTCCAGGTGAAGCGGATGGAAAAGCAAACAACCTATGTCATGCAATGTTCCAAGCTTTCATTATCTTCATCACAATATCATTGTTCAGCTCCATTAGTGCTACAATCCTCCTCTTTTGGGCAACACTTGGATTAACTGACTTGGCGGCTTTCTCTCTCAAAATAGTAATGCCAATTCTTGGAATTGCTCTCATCTCACTGTCTTTGGCTTTCATGGCTGGTCTCTACACTGTTATCAGTGAACTTACTTGGTTGGCCTATCTATTTATGGTTGTAACTCCGATTTTTGTTGTGGTTGTGTTTTTGTTATATATGCTCCTTTTCCTCCCCTCATCATCAACTAGAAAATCCTTGCGATACATTTCCTACTTCCCCTTTCTTATACTAGCATGGCTCGCAGAGTAA
Protein sequence

>MS.gene37911.t1

MLDLSFKRNILHVAAKNGKHDVVKYILLQSRRIPELDRMINQKDYKGNTPLLLAAKSCHPKTVFYLTWDERVDLHVVNKNNQTALEVVNASQLRNPPTRRELTLVALNSAGANLSFRRLVDDKSRQSDSNLPQLEQSNAESSDTKRPIGQSDSKSNENNKNVSHNTTHFFFLPGSEEHYKNMVQTLTLVSTLIITASVAACFAVPGEADGKANNLCHAMFQAFIIFITISLFSSISATILLFWATLGLTDLAAFSLKIVMPILGIALISLSLAFMAGLYTVISELTWLAYLFMVVTPIFVVVVFLLYMLLFLPSSSTRKSLRYISYFPFLILAWLAE