AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene35330

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene35330.t1 MTR_2g084510 83.884 242 38 1 5 245 1 242 4.01e-149 416
MS.gene35330.t1 MTR_2g084525 89.300 243 25 1 4 245 1 243 6.80e-147 410
MS.gene35330.t1 MTR_2g084495 59.917 242 85 3 4 245 1 230 5.17e-95 278
MS.gene35330.t1 MTR_2g060540 76.923 143 33 0 3 145 6 148 2.27e-78 233
MS.gene35330.t1 MTR_2g060500 77.857 140 31 0 3 142 6 145 3.22e-78 233
MS.gene35330.t1 MTR_1g062160 38.057 247 101 9 3 244 2 201 4.11e-40 137
MS.gene35330.t1 MTR_7g102790 37.398 246 108 7 1 244 1 202 4.24e-39 135
MS.gene35330.t1 MTR_4g078170 47.794 136 61 3 8 143 16 141 4.97e-36 127
MS.gene35330.t1 MTR_5g030130 45.070 142 68 3 8 149 36 167 1.93e-35 126
MS.gene35330.t1 MTR_5g030130 45.652 138 65 3 8 145 36 163 5.47e-35 124
MS.gene35330.t1 MTR_5g007230 44.853 136 65 3 8 143 22 147 2.15e-33 120
MS.gene35330.t1 MTR_8g066820 44.853 136 65 3 8 143 34 159 2.52e-32 118
MS.gene35330.t1 MTR_4g094680 30.645 248 127 8 9 245 24 237 2.74e-27 105
MS.gene35330.t1 MTR_4g116300 37.589 141 78 4 8 148 6 136 1.68e-23 95.5
MS.gene35330.t1 MTR_2g083710 63.934 61 22 0 3 63 2 62 3.78e-23 89.4
MS.gene35330.t1 MTR_2g055210 28.346 254 151 10 7 244 101 339 4.03e-22 93.6
MS.gene35330.t1 MTR_2g083720 39.669 121 35 2 3 123 2 84 1.71e-17 75.1
MS.gene35330.t1 MTR_2g036170 26.295 251 132 9 9 244 39 251 4.43e-16 75.5
MS.gene35330.t1 MTR_8g105930 30.968 155 90 5 9 150 15 165 8.88e-14 68.9
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene35330.t1 AT1G43000 37.190 242 122 7 3 244 5 216 6.75e-40 137
MS.gene35330.t1 AT1G43000 37.190 242 122 7 3 244 12 223 6.96e-40 137
MS.gene35330.t1 AT1G21000 34.959 246 145 8 3 244 9 243 3.55e-36 128
MS.gene35330.t1 AT1G21000 34.959 246 145 8 3 244 12 246 3.75e-36 128
MS.gene35330.t1 AT1G76590 33.473 239 145 7 8 244 19 245 1.63e-35 127
MS.gene35330.t1 AT4G17900 47.445 137 61 4 8 143 35 161 2.08e-34 123
MS.gene35330.t1 AT4G17900 47.445 137 61 4 8 143 21 147 4.68e-34 122
MS.gene35330.t1 AT1G32700 45.714 140 66 3 9 148 14 143 7.86e-33 119
MS.gene35330.t1 AT2G27930 48.201 139 66 3 9 144 6 141 2.29e-32 117
MS.gene35330.t1 AT2G27930 48.201 139 66 3 9 144 6 141 2.29e-32 117
MS.gene35330.t1 AT2G27930 47.857 140 67 3 9 145 6 142 3.22e-32 116
MS.gene35330.t1 AT2G27930 47.857 140 67 3 9 145 6 142 3.22e-32 116
MS.gene35330.t1 AT1G32700 48.214 112 49 2 37 148 2 104 1.55e-27 104
MS.gene35330.t1 AT5G46710 43.704 135 65 4 9 142 30 154 6.54e-26 99.8
MS.gene35330.t1 AT5G46710 43.704 135 65 4 9 142 30 154 9.55e-26 100
MS.gene35330.t1 AT5G46710 43.704 135 65 4 9 142 14 138 9.79e-26 100
MS.gene35330.t1 AT2G12646 39.583 144 76 5 5 148 1 133 4.77e-25 99.8
MS.gene35330.t1 AT2G12646 40.000 140 73 5 9 148 8 136 9.18e-25 99.0
MS.gene35330.t1 AT2G12646 40.000 140 73 5 9 148 8 136 9.18e-25 99.0
MS.gene35330.t1 AT1G31040 29.167 240 148 7 9 244 21 242 4.09e-24 97.1
MS.gene35330.t1 AT3G60670 35.862 145 81 5 9 152 9 142 5.04e-19 83.6
MS.gene35330.t1 AT2G01818 28.631 241 137 8 9 245 13 222 6.32e-19 82.8
MS.gene35330.t1 AT2G27930 51.163 86 37 2 62 144 61 144 1.44e-17 78.6
MS.gene35330.t1 AT2G27930 51.163 86 37 2 62 144 61 144 1.44e-17 78.6

Find 43 sgRNAs with CRISPR-Local

Find 77 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CGCTCATTTCTGAACTTGTT+TGG 0.226434 2.1:-17012631 None:intergenic
TCCATTTCTTCCATCTCTCT+TGG 0.271024 2.1:-17013436 None:intergenic
CCAGTTTGAGTTTATCAAAA+AGG 0.273252 2.1:+17013393 MS.gene35330:intron
AAAGAAAGGGAATAGCTTAT+AGG 0.288773 2.1:+17013671 MS.gene35330:CDS
TTTCCAATGTTGAACCTCTT+AGG 0.309596 2.1:-17013032 None:intergenic
CCATTTCTTCCATCTCTCTT+GGG 0.325447 2.1:-17013435 None:intergenic
TCTATACAAAATTCACATAA+TGG 0.333459 2.1:-17012685 None:intergenic
CCCAAGAGAGATGGAAGAAA+TGG 0.347606 2.1:+17013435 MS.gene35330:CDS
AAGAAAGGGAATAGCTTATA+GGG 0.348822 2.1:+17013672 MS.gene35330:CDS
CATTTCTGAACTTGTTTGGA+TGG 0.368188 2.1:-17012627 None:intergenic
ACCTTGGCTTGTAAACTTGC+TGG 0.395128 2.1:+17012573 MS.gene35330:CDS
TTAGAAGACGTAAGAATTGA+TGG 0.404655 2.1:+17013541 MS.gene35330:CDS
AATGTTGAACCTCTTAGGTT+GGG 0.427697 2.1:-17013027 None:intergenic
CAAAGGTCATAGAGTAATAC+AGG 0.450961 2.1:+17012717 MS.gene35330:CDS
ATTTCTGAACTTGTTTGGAT+GGG 0.453864 2.1:-17012626 None:intergenic
CGGAATGCTTTCTTTGTCAT+CGG 0.464171 2.1:-17013608 None:intergenic
CAATGTTGAACCTCTTAGGT+TGG 0.476236 2.1:-17013028 None:intergenic
CGTAAGAATTGATGGGAAAG+AGG 0.477127 2.1:+17013549 MS.gene35330:CDS
GAAGCCGATGAACGATTAAC+CGG 0.479886 2.1:-17013628 None:intergenic
AATTGATGGGAAAGAGGAAG+AGG 0.481751 2.1:+17013555 MS.gene35330:CDS
GAGCTCATGCCCAACCTAAG+AGG 0.493266 2.1:+17013018 MS.gene35330:CDS
CACATGTTTGTAAATTTCGA+TGG 0.514074 2.1:-17012934 None:intergenic
GCCAGCAAGTTTACAAGCCA+AGG 0.514131 2.1:-17012574 None:intergenic
CGATGACAAAGAAAGCATTC+CGG 0.540471 2.1:+17013609 MS.gene35330:CDS
AAAAGAGTCCCTATTGTGAC+CGG 0.541668 2.1:-17013057 None:intergenic
ATATCTAGATCAATCAATCA+AGG 0.554194 2.1:+17013462 MS.gene35330:CDS
CATTCCGGTTAATCGTTCAT+CGG 0.555156 2.1:+17013624 MS.gene35330:CDS
TACAAACATGTGGATATCCT+CGG 0.556715 2.1:+17012945 MS.gene35330:CDS
CCAAAGAGCAAAAGTAGGTA+GGG 0.559658 2.1:-17013109 None:intergenic
AGGATATGATGAGTGTACCT+TGG 0.561440 2.1:+17012557 MS.gene35330:intron
TTTCGTAAACCCAAGAGAGA+TGG 0.562278 2.1:+17013426 MS.gene35330:CDS
TAGAAGACGTAAGAATTGAT+GGG 0.577498 2.1:+17013542 MS.gene35330:CDS
TCACGTAGGTTTGAATTCCG+AGG 0.586677 2.1:-17012962 None:intergenic
GCCAAAGAGCAAAAGTAGGT+AGG 0.587378 2.1:-17013110 None:intergenic
AAGAAGATCATCATATAATG+AGG 0.589252 2.1:+17012902 MS.gene35330:CDS
CATCGAAATTTACAAACATG+TGG 0.610863 2.1:+17012935 MS.gene35330:CDS
CAACCTAAGAGGTTCAACAT+TGG 0.618975 2.1:+17013029 MS.gene35330:CDS
GCATGCCAAAGAGCAAAAGT+AGG 0.621061 2.1:-17013114 None:intergenic
TGTATAGAATCTCGTCACAA+AGG 0.625069 2.1:+17012700 MS.gene35330:CDS
GGCATCGCCTAGAAAAGAGA+AGG 0.632887 2.1:+17013483 MS.gene35330:CDS
AAGATCATCATATAATGAGG+TGG 0.649716 2.1:+17012905 MS.gene35330:CDS
ACTAGAGCTATTAATCACGT+AGG 0.680389 2.1:-17012976 None:intergenic
CAAACAAGTTCAGAAATGAG+CGG 0.722844 2.1:+17012632 MS.gene35330:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ATATAAAAAAAAATAATAAT+AGG - chr2.1:17013158-17013177 None:intergenic 0.0%
!! AAGAAAAAATACAAAGAATT+AGG - chr2.1:17012511-17012530 None:intergenic 15.0%
!!! TTTTTCTTAATGCAATTTTT+GGG + chr2.1:17012523-17012542 MS.gene35330:intron 15.0%
!!! TTTTTTCTTAATGCAATTTT+TGG + chr2.1:17012522-17012541 MS.gene35330:intron 15.0%
!! ATTAATAGTAATAAAAGGAG+TGG - chr2.1:17013236-17013255 None:intergenic 20.0%
!! TCTATACAAAATTCACATAA+TGG - chr2.1:17012688-17012707 None:intergenic 20.0%
!!! ATAATATTTTGCAATGATCT+AGG + chr2.1:17012772-17012791 MS.gene35330:intron 20.0%
!!! ATGTTTTAAACGGTAAAAAA+TGG + chr2.1:17013179-17013198 MS.gene35330:intron 20.0%
!!! TCCTTTTATTACTATTAATC+CGG + chr2.1:17013237-17013256 MS.gene35330:intron 20.0%
! AAGAAGATCATCATATAATG+AGG + chr2.1:17012902-17012921 MS.gene35330:CDS 25.0%
! AAGCCAAATTCAAAAAGAAA+GGG + chr2.1:17013658-17013677 MS.gene35330:CDS 25.0%
! ATATCTAGATCAATCAATCA+AGG + chr2.1:17013462-17013481 MS.gene35330:CDS 25.0%
! ATCAACATAAGTACAATAAC+CGG - chr2.1:17013324-17013343 None:intergenic 25.0%
! GTAGAAAAAGAAAAGAAAGA+AGG + chr2.1:17013583-17013602 MS.gene35330:CDS 25.0%
! TCCGGATTAATAGTAATAAA+AGG - chr2.1:17013241-17013260 None:intergenic 25.0%
!! ATTCCCTTTCTTTTTGAATT+TGG - chr2.1:17013664-17013683 None:intergenic 25.0%
!! TTTGAGTTTATCAAAAAGGA+TGG + chr2.1:17013397-17013416 MS.gene35330:CDS 25.0%
!!! ATTTTTGGGTTTTGTTTCTT+AGG + chr2.1:17012537-17012556 MS.gene35330:intron 25.0%
AAAGAAAGGGAATAGCTTAT+AGG + chr2.1:17013671-17013690 MS.gene35330:CDS 30.0%
AAGAAAGGGAATAGCTTATA+GGG + chr2.1:17013672-17013691 MS.gene35330:CDS 30.0%
AAGATCATCATATAATGAGG+TGG + chr2.1:17012905-17012924 MS.gene35330:CDS 30.0%
AGGAGTGGAATAAAATATAC+TGG - chr2.1:17013221-17013240 None:intergenic 30.0%
CAAGCCAAATTCAAAAAGAA+AGG + chr2.1:17013657-17013676 MS.gene35330:CDS 30.0%
CACATGTTTGTAAATTTCGA+TGG - chr2.1:17012937-17012956 None:intergenic 30.0%
CATCGAAATTTACAAACATG+TGG + chr2.1:17012935-17012954 MS.gene35330:CDS 30.0%
TAGAAGACGTAAGAATTGAT+GGG + chr2.1:17013542-17013561 MS.gene35330:CDS 30.0%
TTAGAAGACGTAAGAATTGA+TGG + chr2.1:17013541-17013560 MS.gene35330:CDS 30.0%
! ACTTTTCTTTCAACCATTAC+CGG + chr2.1:17013294-17013313 MS.gene35330:intron 30.0%
! ATTTCTGAACTTGTTTGGAT+GGG - chr2.1:17012629-17012648 None:intergenic 30.0%
! CCAGTTTGAGTTTATCAAAA+AGG + chr2.1:17013393-17013412 MS.gene35330:intron 30.0%
! CCTTTTTGATAAACTCAAAC+TGG - chr2.1:17013396-17013415 None:intergenic 30.0%
!!! TTTTTTGCCTTCTCTTTTCT+AGG - chr2.1:17013493-17013512 None:intergenic 30.0%
AAGTACAATAACCGGTATTC+CGG - chr2.1:17013316-17013335 None:intergenic 35.0%
AATGTTGAACCTCTTAGGTT+GGG - chr2.1:17013030-17013049 None:intergenic 35.0%
ACTAGAGCTATTAATCACGT+AGG - chr2.1:17012979-17012998 None:intergenic 35.0%
ACTATTAATCCGGAGATTGA+AGG + chr2.1:17013247-17013266 MS.gene35330:intron 35.0%
AGGTTCAACATTGGAAAAAC+CGG + chr2.1:17013038-17013057 MS.gene35330:CDS 35.0%
CAAACAAGTTCAGAAATGAG+CGG + chr2.1:17012632-17012651 MS.gene35330:CDS 35.0%
CAAAGGTCATAGAGTAATAC+AGG + chr2.1:17012717-17012736 MS.gene35330:CDS 35.0%
GAGTTTATCAAAAAGGATGG+TGG + chr2.1:17013400-17013419 MS.gene35330:CDS 35.0%
TACAAACATGTGGATATCCT+CGG + chr2.1:17012945-17012964 MS.gene35330:CDS 35.0%
TGTATAGAATCTCGTCACAA+AGG + chr2.1:17012700-17012719 MS.gene35330:CDS 35.0%
TTTCCAATGTTGAACCTCTT+AGG - chr2.1:17013035-17013054 None:intergenic 35.0%
! CATTTCTGAACTTGTTTGGA+TGG - chr2.1:17012630-17012649 None:intergenic 35.0%
AAAAGAGTCCCTATTGTGAC+CGG - chr2.1:17013060-17013079 None:intergenic 40.0%
AATAACCGGTATTCCGGTAA+TGG - chr2.1:17013310-17013329 None:intergenic 40.0%
AATTGATGGGAAAGAGGAAG+AGG + chr2.1:17013555-17013574 MS.gene35330:CDS 40.0%
AGGATATGATGAGTGTACCT+TGG + chr2.1:17012557-17012576 MS.gene35330:intron 40.0%
CAACCTAAGAGGTTCAACAT+TGG + chr2.1:17013029-17013048 MS.gene35330:CDS 40.0%
CAATGTTGAACCTCTTAGGT+TGG - chr2.1:17013031-17013050 None:intergenic 40.0%
CATCATATGCCTTCAATCTC+CGG - chr2.1:17013259-17013278 None:intergenic 40.0%
CATTCCGGTTAATCGTTCAT+CGG + chr2.1:17013624-17013643 MS.gene35330:CDS 40.0%
CCAAAGAGCAAAAGTAGGTA+GGG - chr2.1:17013112-17013131 None:intergenic 40.0%
CCATTTCTTCCATCTCTCTT+GGG - chr2.1:17013438-17013457 None:intergenic 40.0%
CGGAATGCTTTCTTTGTCAT+CGG - chr2.1:17013611-17013630 None:intergenic 40.0%
CGTAAGAATTGATGGGAAAG+AGG + chr2.1:17013549-17013568 MS.gene35330:CDS 40.0%
TCCATTTCTTCCATCTCTCT+TGG - chr2.1:17013439-17013458 None:intergenic 40.0%
TGGAAAAACCGGTCACAATA+GGG + chr2.1:17013049-17013068 MS.gene35330:CDS 40.0%
TTCAACCATTACCGGAATAC+CGG + chr2.1:17013302-17013321 MS.gene35330:intron 40.0%
TTGGAAAAACCGGTCACAAT+AGG + chr2.1:17013048-17013067 MS.gene35330:CDS 40.0%
TTTCGTAAACCCAAGAGAGA+TGG + chr2.1:17013426-17013445 MS.gene35330:CDS 40.0%
! ATGGATTTTCATTGCAGTCG+AGG - chr2.1:17012669-17012688 None:intergenic 40.0%
! CGCTCATTTCTGAACTTGTT+TGG - chr2.1:17012634-17012653 None:intergenic 40.0%
! TGGCATGCAAGGTGAAATTT+TGG + chr2.1:17013129-17013148 MS.gene35330:intron 40.0%
!! CGATGACAAAGAAAGCATTC+CGG + chr2.1:17013609-17013628 MS.gene35330:CDS 40.0%
CCCAAGAGAGATGGAAGAAA+TGG + chr2.1:17013435-17013454 MS.gene35330:CDS 45.0%
GAAGCCGATGAACGATTAAC+CGG - chr2.1:17013631-17013650 None:intergenic 45.0%
GCATGCCAAAGAGCAAAAGT+AGG - chr2.1:17013117-17013136 None:intergenic 45.0%
GCCAAAGAGCAAAAGTAGGT+AGG - chr2.1:17013113-17013132 None:intergenic 45.0%
TCACGTAGGTTTGAATTCCG+AGG - chr2.1:17012965-17012984 None:intergenic 45.0%
! CTTTTGCTCTTTGGCATGCA+AGG + chr2.1:17013118-17013137 MS.gene35330:CDS 45.0%
!! ACCTTGGCTTGTAAACTTGC+TGG + chr2.1:17012573-17012592 MS.gene35330:CDS 45.0%
!! CCCTACCTACTTTTGCTCTT+TGG + chr2.1:17013109-17013128 MS.gene35330:CDS 45.0%
!!! TTTTTATATTATGTTTTAAA+CGG + chr2.1:17013169-17013188 MS.gene35330:intron 5.0%
GCCAGCAAGTTTACAAGCCA+AGG - chr2.1:17012577-17012596 None:intergenic 50.0%
GGCATCGCCTAGAAAAGAGA+AGG + chr2.1:17013483-17013502 MS.gene35330:CDS 50.0%
GAGCTCATGCCCAACCTAAG+AGG + chr2.1:17013018-17013037 MS.gene35330:CDS 55.0%


Chromosome Type Strat End Strand Name
chr2.1 gene 17012467 17013708 17012467 ID=MS.gene35330
chr2.1 mRNA 17012467 17013708 17012467 ID=MS.gene35330.t1;Parent=MS.gene35330
chr2.1 exon 17012467 17012472 17012467 ID=MS.gene35330.t1.exon1;Parent=MS.gene35330.t1
chr2.1 CDS 17012467 17012472 17012467 ID=cds.MS.gene35330.t1;Parent=MS.gene35330.t1
chr2.1 exon 17012559 17012738 17012559 ID=MS.gene35330.t1.exon2;Parent=MS.gene35330.t1
chr2.1 CDS 17012559 17012738 17012559 ID=cds.MS.gene35330.t1;Parent=MS.gene35330.t1
chr2.1 exon 17012900 17013139 17012900 ID=MS.gene35330.t1.exon3;Parent=MS.gene35330.t1
chr2.1 CDS 17012900 17013139 17012900 ID=cds.MS.gene35330.t1;Parent=MS.gene35330.t1
chr2.1 exon 17013397 17013708 17013397 ID=MS.gene35330.t1.exon4;Parent=MS.gene35330.t1
chr2.1 CDS 17013397 17013708 17013397 ID=cds.MS.gene35330.t1;Parent=MS.gene35330.t1
Gene Sequence

>MS.gene35330

ATGACGGTAATGTGTCTATGCATTTTAATTATAATGTCAAGCCTAATTCTTTGTATTTTTTCTTAATGCAATTTTTGGGTTTTGTTTCTTAGGATATGATGAGTGTACCTTGGCTTGTAAACTTGCTGGCAATCACTTCGTTTTTCACAACATGTGAAGCCCATCCAAACAAGTTCAGAAATGAGCGGAACAAGTTCTGCCTCGACTGCAATGAAAATCCATTATGTGAATTTTGTATAGAATCTCGTCACAAAGGTCATAGAGTAATACAGGTGAGTGTTGTTTAATTTGATTACTAGATCTGTATAATATTTTGCAATGATCTAGGTATCTGTGTCATATCTATTTCTCTTCGCTTTGTTTTTATTACACTTAAGCAATTTTAATTGATTTTTTTAACTATGTTATGTAAATATTTGCAATGATAAATCAGATAAGAAGATCATCATATAATGAGGTGGTTAAGACCATCGAAATTTACAAACATGTGGATATCCTCGGAATTCAAACCTACGTGATTAATAGCTCTAGTGTTGTATTCTTAAGCAAGAGAGCTCATGCCCAACCTAAGAGGTTCAACATTGGAAAAACCGGTCACAATAGGGACTCTTTTTGTAAGAGATGTGATAGAAATCTTGCAGACCCTACCTACTTTTGCTCTTTGGCATGCAAGGTGAAATTTTGGTCTCCTATTATTATTTTTTTTTATATTATGTTTTAAACGGTAAAAAATGGTTCAATATATGAAAAACCAGTATATTTTATTCCACTCCTTTTATTACTATTAATCCGGAGATTGAAGGCATATGATGAAGATTATAACTTATACTTTTCTTTCAACCATTACCGGAATACCGGTTATTGTACTTATGTTGATTTTGTTTTCTTTTTGAAAGAATGATTAATTAATGTTGCATTATATGATACCAGTTTGAGTTTATCAAAAAGGATGGTGGCTTTTTCGTAAACCCAAGAGAGATGGAAGAAATGGAAAGATATCTAGATCAATCAATCAAGGCATCGCCTAGAAAAGAGAAGGCAAAAAAATGTTGCAAACAAAATCTGAAACGAAAATTAGAAGACGTAAGAATTGATGGGAAAGAGGAAGAGGAAGACGTAGAAAAAGAAAAGAAAGAAGGCGCCGATGACAAAGAAAGCATTCCGGTTAATCGTTCATCGGCTTCACTTCGCAAGCCAAATTCAAAAAGAAAGGGAATAGCTTATAGGGCACCTTTTTTTTAA
Protein sequence

>MS.gene35330.t1

MTDMMSVPWLVNLLAITSFFTTCEAHPNKFRNERNKFCLDCNENPLCEFCIESRHKGHRVIQIRRSSYNEVVKTIEIYKHVDILGIQTYVINSSSVVFLSKRAHAQPKRFNIGKTGHNRDSFCKRCDRNLADPTYFCSLACKFEFIKKDGGFFVNPREMEEMERYLDQSIKASPRKEKAKKCCKQNLKRKLEDVRIDGKEEEEDVEKEKKEGADDKESIPVNRSSASLRKPNSKRKGIAYRAPFF