AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene023281

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene023281.t1 MTR_1g033340 51.765 255 80 8 1 217 2 251 4.69e-78 234
MS.gene023281.t1 MTR_3g065020 48.000 200 93 6 21 217 47 238 4.57e-57 181
MS.gene023281.t1 MTR_5g077370 45.588 204 92 6 23 217 44 237 1.78e-50 164
MS.gene023281.t1 MTR_2g104900 45.333 150 63 6 2 133 10 158 5.04e-30 111
MS.gene023281.t1 MTR_1g107055 45.763 118 58 3 62 179 64 175 7.07e-25 97.1
MS.gene023281.t1 MTR_1g013130 40.278 144 60 4 15 132 37 180 3.11e-24 97.1
MS.gene023281.t1 MTR_4g006575 40.876 137 63 4 2 132 6 130 2.43e-23 93.6
MS.gene023281.t1 MTR_4g006600 40.876 137 63 4 2 132 6 130 2.43e-23 93.6
MS.gene023281.t1 MTR_3g106230 50.562 89 26 4 61 132 71 158 9.68e-20 84.3
MS.gene023281.t1 MTR_4g128340 62.295 61 21 1 59 119 42 100 5.45e-18 78.2
MS.gene023281.t1 MTR_8g466760 43.038 79 36 3 62 134 98 173 4.06e-12 64.3
MS.gene023281.t1 MTR_7g083210 75.758 33 8 0 62 94 39 71 4.47e-12 62.8
MS.gene023281.t1 MTR_7g086860 61.905 42 16 0 57 98 25 66 5.02e-12 62.0
MS.gene023281.t1 MTR_3g011990 43.421 76 36 2 62 132 98 171 3.83e-11 61.6
MS.gene023281.t1 MTR_5g008280 46.753 77 35 4 62 132 46 122 5.12e-11 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.gene023281.t1 AT1G66140 47.059 187 69 7 57 217 78 260 2.64e-45 151
MS.gene023281.t1 AT1G24625 44.970 169 66 7 61 217 56 209 8.89e-33 117
MS.gene023281.t1 AT1G80730 42.484 153 66 4 2 132 1 153 9.63e-26 100
MS.gene023281.t1 AT5G25160 46.226 106 49 3 32 132 32 134 1.06e-22 92.4
MS.gene023281.t1 AT5G10970 42.105 133 67 6 9 132 44 175 1.85e-22 92.4
MS.gene023281.t1 AT5G57520 76.923 39 9 0 61 99 49 87 1.08e-16 74.3
MS.gene023281.t1 AT5G14010 72.222 36 10 0 62 97 36 71 3.77e-13 65.1
MS.gene023281.t1 AT5G01860 57.500 40 17 0 62 101 65 104 2.34e-11 61.2
MS.gene023281.t1 AT5G27880 44.928 69 36 1 33 99 47 115 7.94e-11 60.5

Find 54 sgRNAs with CRISPR-Local

Find 63 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AAATTTGATAGAAACCATTT+TGG 0.216847 4.3:+17383401 MS.gene023281:CDS
TTCGAGTGAGGCCGAGTTAA+TGG 0.228364 4.3:+17383046 MS.gene023281:CDS
GTCCACCTGTCTAAAACTTC+CGG 0.315216 4.3:-17383468 None:intergenic
TTCGCAGCAGCTCTCATATC+TGG 0.318459 4.3:-17383380 None:intergenic
CTTGCATCTCTACCTCTTCA+TGG 0.342785 4.3:+17383275 MS.gene023281:CDS
TCAGGTTCCAAGTTCAAGTT+TGG 0.345240 4.3:-17382960 None:intergenic
ATGATGATGCAGGTAGCTTT+TGG 0.346841 4.3:+17383444 MS.gene023281:CDS
CGAAAACTAGCGATCCAAAA+TGG 0.355731 4.3:-17383415 None:intergenic
TGCAAGGCTTGTATACCTTT+CGG 0.407124 4.3:-17383258 None:intergenic
TCCACCTGTCTAAAACTTCC+GGG 0.407344 4.3:-17383467 None:intergenic
AAACTCGAATTTGAAGTTTG+AGG 0.421800 4.3:-17383518 None:intergenic
GATGCAGATGCTTGAGGTGG+AGG 0.428693 4.3:-17383557 None:intergenic
TCGAGTGAGGCCGAGTTAAT+GGG 0.432246 4.3:+17383047 MS.gene023281:CDS
GTCATCAGAACGCTCACAAA+AGG 0.433204 4.3:+17383192 MS.gene023281:CDS
GGTCATAGGATCTAGATCTT+GGG 0.441405 4.3:-17383000 None:intergenic
CTATATTAACACTTCCTCCT+TGG 0.445595 4.3:-17383490 None:intergenic
GGGTCATAGGATCTAGATCT+TGG 0.448749 4.3:-17383001 None:intergenic
GGCTAAACGTGCAATGCGAA+TGG 0.452909 4.3:+17383226 MS.gene023281:CDS
TTCTATAGCTCGCAAGCATT+AGG 0.456033 4.3:+17383167 MS.gene023281:CDS
CAAGGAGGAAGTGTTAATAT+AGG 0.461179 4.3:+17383491 MS.gene023281:CDS
GATGACTCCAAACTTGAACT+TGG 0.465674 4.3:+17382953 MS.gene023281:CDS
AGTGATGCTAGTAGTGAAGT+AGG 0.485652 4.3:+17383074 MS.gene023281:CDS
TAATTACAAGAGAATATCCT+TGG 0.504702 4.3:-17383131 None:intergenic
AGTGTCAAGTCAAGGGTCAT+AGG 0.518887 4.3:-17383014 None:intergenic
TGAGGTGGAGGAGGTGCCAT+TGG 0.521384 4.3:-17383545 None:intergenic
TATAGCTTCAGTGTAAGATC+AGG 0.526650 4.3:-17383581 None:intergenic
TCTCTTGTAATTACTGCAAG+AGG 0.530679 4.3:+17383141 MS.gene023281:CDS
GCTAAACGTGCAATGCGAAT+GGG 0.536618 4.3:+17383227 MS.gene023281:CDS
TGAAATTGAGTGTCAAGTCA+AGG 0.555713 4.3:-17383022 None:intergenic
TCATCAGAACGCTCACAAAA+GGG 0.564572 4.3:+17383193 MS.gene023281:CDS
TCAACACCAAGGGACCGAAA+AGG 0.568839 4.3:-17383302 None:intergenic
GCAGATGCTTGAGGTGGAGG+AGG 0.582836 4.3:-17383554 None:intergenic
TTCGTGGAAGATGATGATGC+AGG 0.588719 4.3:+17383434 MS.gene023281:CDS
GAAATTGAGTGTCAAGTCAA+GGG 0.590766 4.3:-17383021 None:intergenic
GTCATAGGATCTAGATCTTG+GGG 0.590838 4.3:-17382999 None:intergenic
CTTCGCCATCGGTAACTCCA+AGG 0.598331 4.3:+17383114 MS.gene023281:CDS
TGCAACCATCGTCAACAATG+AGG 0.600965 4.3:+17383354 MS.gene023281:CDS
GCAACCATCGTCAACAATGA+GGG 0.605847 4.3:+17383355 MS.gene023281:CDS
TCAGGAGATGCAGATGCTTG+AGG 0.608142 4.3:-17383563 None:intergenic
ACTCAATTTCAGTTCGAGTG+AGG 0.611871 4.3:+17383034 MS.gene023281:CDS
TGAAGTTCATGCTTCGCCAT+CGG 0.612721 4.3:+17383103 MS.gene023281:CDS
ATCACTTGAACCCATTAACT+CGG 0.613671 4.3:-17383057 None:intergenic
GGAGATGCAGATGCTTGAGG+TGG 0.634898 4.3:-17383560 None:intergenic
AGAACGCTCACAAAAGGGAG+AGG 0.635123 4.3:+17383198 MS.gene023281:CDS
CAGAATGAGCTTCAACACCA+AGG 0.638470 4.3:-17383313 None:intergenic
CATGAAGAGGTAGAGATGCA+AGG 0.640521 4.3:-17383274 None:intergenic
AATATCCTTGGAGTTACCGA+TGG 0.642699 4.3:-17383119 None:intergenic
GAATGGGAATGTTCACCGAA+AGG 0.647190 4.3:+17383243 MS.gene023281:CDS
CGAAAAGGCGAACCATGAAG+AGG 0.651068 4.3:-17383287 None:intergenic
AGAATGAGCTTCAACACCAA+GGG 0.655962 4.3:-17383312 None:intergenic
TATAGCTCGCAAGCATTAGG+CGG 0.663928 4.3:+17383170 MS.gene023281:CDS
GGAGCCCTCATTGTTGACGA+TGG 0.667173 4.3:-17383359 None:intergenic
TTTAGACAGGTGGACCAAGG+AGG 0.688046 4.3:+17383476 MS.gene023281:CDS
TCACAAAAGGGAGAGGACGA+TGG 0.689083 4.3:+17383205 MS.gene023281:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! AAATTTGATAGAAACCATTT+TGG + chr4.3:17383401-17383420 MS.gene023281:CDS 20.0%
! TAATTACAAGAGAATATCCT+TGG - chr4.3:17383134-17383153 None:intergenic 25.0%
! AAACTCGAATTTGAAGTTTG+AGG - chr4.3:17383521-17383540 None:intergenic 30.0%
!!! AAATTCGAGTTTTGTTCCAA+TGG + chr4.3:17383529-17383548 MS.gene023281:CDS 30.0%
ATCACTTGAACCCATTAACT+CGG - chr4.3:17383060-17383079 None:intergenic 35.0%
CTATATTAACACTTCCTCCT+TGG - chr4.3:17383493-17383512 None:intergenic 35.0%
GAAATTGAGTGTCAAGTCAA+GGG - chr4.3:17383024-17383043 None:intergenic 35.0%
TATAGCTTCAGTGTAAGATC+AGG - chr4.3:17383584-17383603 None:intergenic 35.0%
TCTCTTGTAATTACTGCAAG+AGG + chr4.3:17383141-17383160 MS.gene023281:CDS 35.0%
TGAAATTGAGTGTCAAGTCA+AGG - chr4.3:17383025-17383044 None:intergenic 35.0%
!! CAAGGAGGAAGTGTTAATAT+AGG + chr4.3:17383491-17383510 MS.gene023281:CDS 35.0%
AATATCCTTGGAGTTACCGA+TGG - chr4.3:17383122-17383141 None:intergenic 40.0%
ACTCAATTTCAGTTCGAGTG+AGG + chr4.3:17383034-17383053 MS.gene023281:CDS 40.0%
AGAATGAGCTTCAACACCAA+GGG - chr4.3:17383315-17383334 None:intergenic 40.0%
AGTGATGCTAGTAGTGAAGT+AGG + chr4.3:17383074-17383093 MS.gene023281:CDS 40.0%
CGAAAACTAGCGATCCAAAA+TGG - chr4.3:17383418-17383437 None:intergenic 40.0%
GATGACTCCAAACTTGAACT+TGG + chr4.3:17382953-17382972 MS.gene023281:CDS 40.0%
GGTCATAGGATCTAGATCTT+GGG - chr4.3:17383003-17383022 None:intergenic 40.0%
GTCATAGGATCTAGATCTTG+GGG - chr4.3:17383002-17383021 None:intergenic 40.0%
TCATCAGAACGCTCACAAAA+GGG + chr4.3:17383193-17383212 MS.gene023281:CDS 40.0%
TGCAAGGCTTGTATACCTTT+CGG - chr4.3:17383261-17383280 None:intergenic 40.0%
TTCTATAGCTCGCAAGCATT+AGG + chr4.3:17383167-17383186 MS.gene023281:CDS 40.0%
! TCAGGTTCCAAGTTCAAGTT+TGG - chr4.3:17382963-17382982 None:intergenic 40.0%
!! ATGATGATGCAGGTAGCTTT+TGG + chr4.3:17383444-17383463 MS.gene023281:CDS 40.0%
!!! TTTTGGATCGCTAGTTTTCG+TGG + chr4.3:17383418-17383437 MS.gene023281:CDS 40.0%
AGTGTCAAGTCAAGGGTCAT+AGG - chr4.3:17383017-17383036 None:intergenic 45.0%
CAGAATGAGCTTCAACACCA+AGG - chr4.3:17383316-17383335 None:intergenic 45.0%
CATGAAGAGGTAGAGATGCA+AGG - chr4.3:17383277-17383296 None:intergenic 45.0%
CTTGCATCTCTACCTCTTCA+TGG + chr4.3:17383275-17383294 MS.gene023281:CDS 45.0%
GAATGGGAATGTTCACCGAA+AGG + chr4.3:17383243-17383262 MS.gene023281:CDS 45.0%
GCAACCATCGTCAACAATGA+GGG + chr4.3:17383355-17383374 MS.gene023281:CDS 45.0%
GCTAAACGTGCAATGCGAAT+GGG + chr4.3:17383227-17383246 MS.gene023281:CDS 45.0%
GGGTCATAGGATCTAGATCT+TGG - chr4.3:17383004-17383023 None:intergenic 45.0%
GTCATCAGAACGCTCACAAA+AGG + chr4.3:17383192-17383211 MS.gene023281:CDS 45.0%
TATAGCTCGCAAGCATTAGG+CGG + chr4.3:17383170-17383189 MS.gene023281:CDS 45.0%
TGAAGTTCATGCTTCGCCAT+CGG + chr4.3:17383103-17383122 MS.gene023281:CDS 45.0%
TGCAACCATCGTCAACAATG+AGG + chr4.3:17383354-17383373 MS.gene023281:CDS 45.0%
! CTCTTCATGGTTCGCCTTTT+CGG + chr4.3:17383288-17383307 MS.gene023281:CDS 45.0%
! GTCCACCTGTCTAAAACTTC+CGG - chr4.3:17383471-17383490 None:intergenic 45.0%
! TCCACCTGTCTAAAACTTCC+GGG - chr4.3:17383470-17383489 None:intergenic 45.0%
! TTCGTGGAAGATGATGATGC+AGG + chr4.3:17383434-17383453 MS.gene023281:CDS 45.0%
!! GGTGCTTCTGACTGATTTTC+AGG - chr4.3:17382981-17383000 None:intergenic 45.0%
!!! AGTTTTAGACAGGTGGACCA+AGG + chr4.3:17383473-17383492 MS.gene023281:CDS 45.0%
AGAACGCTCACAAAAGGGAG+AGG + chr4.3:17383198-17383217 MS.gene023281:CDS 50.0%
CGAAAAGGCGAACCATGAAG+AGG - chr4.3:17383290-17383309 None:intergenic 50.0%
GGCTAAACGTGCAATGCGAA+TGG + chr4.3:17383226-17383245 MS.gene023281:CDS 50.0%
TCAACACCAAGGGACCGAAA+AGG - chr4.3:17383305-17383324 None:intergenic 50.0%
TCACAAAAGGGAGAGGACGA+TGG + chr4.3:17383205-17383224 MS.gene023281:CDS 50.0%
TCAGGAGATGCAGATGCTTG+AGG - chr4.3:17383566-17383585 None:intergenic 50.0%
TCGAGTGAGGCCGAGTTAAT+GGG + chr4.3:17383047-17383066 MS.gene023281:CDS 50.0%
TTCGAGTGAGGCCGAGTTAA+TGG + chr4.3:17383046-17383065 MS.gene023281:CDS 50.0%
TTCGCAGCAGCTCTCATATC+TGG - chr4.3:17383383-17383402 None:intergenic 50.0%
TTTAGACAGGTGGACCAAGG+AGG + chr4.3:17383476-17383495 MS.gene023281:CDS 50.0%
!!! TTGGCCCGGAAGTTTTAGAC+AGG + chr4.3:17383463-17383482 MS.gene023281:CDS 50.0%
CTTCGCCATCGGTAACTCCA+AGG + chr4.3:17383114-17383133 MS.gene023281:CDS 55.0%
GATGCAGATGCTTGAGGTGG+AGG - chr4.3:17383560-17383579 None:intergenic 55.0%
GGAGATGCAGATGCTTGAGG+TGG - chr4.3:17383563-17383582 None:intergenic 55.0%
GGAGCCCTCATTGTTGACGA+TGG - chr4.3:17383362-17383381 None:intergenic 55.0%
! GATGCAGGTAGCTTTTGGCC+CGG + chr4.3:17383449-17383468 MS.gene023281:CDS 55.0%
!!! GCCCGGAAGTTTTAGACAGG+TGG + chr4.3:17383466-17383485 MS.gene023281:CDS 55.0%
GCAGATGCTTGAGGTGGAGG+AGG - chr4.3:17383557-17383576 None:intergenic 60.0%
! GGTTCGCCTTTTCGGTCCCT+TGG + chr4.3:17383296-17383315 MS.gene023281:CDS 60.0%
!! TGAGGTGGAGGAGGTGCCAT+TGG - chr4.3:17383548-17383567 None:intergenic 60.0%


Chromosome Type Strat End Strand Name
chr4.3 gene 17382951 17383604 17382951 ID=MS.gene023281
chr4.3 mRNA 17382951 17383604 17382951 ID=MS.gene023281.t1;Parent=MS.gene023281
chr4.3 exon 17382951 17383604 17382951 ID=MS.gene023281.t1.exon1;Parent=MS.gene023281.t1
chr4.3 CDS 17382951 17383604 17382951 ID=cds.MS.gene023281.t1;Parent=MS.gene023281.t1
Gene Sequence

>MS.gene023281

ATGATGACTCCAAACTTGAACTTGGAACCTGAAAATCAGTCAGAAGCACCCCAAGATCTAGATCCTATGACCCTTGACTTGACACTCAATTTCAGTTCGAGTGAGGCCGAGTTAATGGGTTCAAGTGATGCTAGTAGTGAAGTAGGAGCTGCTGAAGTTCATGCTTCGCCATCGGTAACTCCAAGGATATTCTCTTGTAATTACTGCAAGAGGAAGTTCTATAGCTCGCAAGCATTAGGCGGTCATCAGAACGCTCACAAAAGGGAGAGGACGATGGCTAAACGTGCAATGCGAATGGGAATGTTCACCGAAAGGTATACAAGCCTTGCATCTCTACCTCTTCATGGTTCGCCTTTTCGGTCCCTTGGTGTTGAAGCTCATTCTGCAATGCATCAAAGACATATGCAACCATCGTCAACAATGAGGGCTCCAGATATGAGAGCTGCTGCGAAATTTGATAGAAACCATTTTGGATCGCTAGTTTTCGTGGAAGATGATGATGCAGGTAGCTTTTGGCCCGGAAGTTTTAGACAGGTGGACCAAGGAGGAAGTGTTAATATAGGATATCCTCAAACTTCAAATTCGAGTTTTGTTCCAATGGCACCTCCTCCACCTCAAGCATCTGCATCTCCTGATCTTACACTGAAGCTATAA
Protein sequence

>MS.gene023281.t1

MMTPNLNLEPENQSEAPQDLDPMTLDLTLNFSSSEAELMGSSDASSEVGAAEVHASPSVTPRIFSCNYCKRKFYSSQALGGHQNAHKRERTMAKRAMRMGMFTERYTSLASLPLHGSPFRSLGVEAHSAMHQRHMQPSSTMRAPDMRAAAKFDRNHFGSLVFVEDDDAGSFWPGSFRQVDQGGSVNIGYPQTSNSSFVPMAPPPPQASASPDLTLKL