AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene003535

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene003535.t1 MTR_4g073590 100.000 143 0 0 1 143 1 143 1.06e-105 297
MS.gene003535.t1 MTR_7g096890 68.889 135 42 0 8 142 11 145 6.70e-71 209
MS.gene003535.t1 MTR_4g073590 100.000 94 0 0 1 94 1 94 1.10e-67 200
MS.gene003535.t1 MTR_1g076170 62.329 146 49 1 3 142 1 146 7.95e-62 187
MS.gene003535.t1 MTR_1g068950 61.194 134 52 0 8 141 4 137 2.21e-60 183
MS.gene003535.t1 MTR_5g010430 60.000 135 52 1 8 142 6 138 8.30e-60 181
MS.gene003535.t1 MTR_8g088210 57.778 135 57 0 8 142 4 138 2.44e-57 175
MS.gene003535.t1 MTR_2g028670 55.556 135 60 0 8 142 4 138 1.29e-56 173
MS.gene003535.t1 MTR_8g098470 57.037 135 56 1 8 142 4 136 1.00e-55 171
MS.gene003535.t1 MTR_8g088210 58.015 131 55 0 12 142 1 131 2.47e-55 170
MS.gene003535.t1 MTR_1g101190 59.259 135 53 1 8 142 465 597 7.22e-54 178
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene003535.t1 AT2G16700 86.014 143 20 0 1 143 1 143 1.19e-89 257
MS.gene003535.t1 AT4G34970 80.851 141 27 0 3 143 1 141 2.31e-86 248
MS.gene003535.t1 AT2G16700 84.848 132 20 0 12 143 1 132 4.82e-81 235
MS.gene003535.t1 AT2G16700 84.848 132 20 0 12 143 1 132 4.82e-81 235
MS.gene003535.t1 AT2G31200 62.222 135 51 0 8 142 11 145 2.61e-62 188
MS.gene003535.t1 AT4G00680 59.701 134 54 0 8 141 4 137 2.19e-61 185
MS.gene003535.t1 AT4G00680 59.701 134 54 0 8 141 14 147 4.15e-61 185
MS.gene003535.t1 AT1G01750 59.701 134 54 0 8 141 4 137 1.94e-60 183
MS.gene003535.t1 AT1G01750 59.701 134 54 0 8 141 9 142 2.51e-60 183
MS.gene003535.t1 AT5G59890 59.701 134 54 0 8 141 4 137 1.46e-59 181
MS.gene003535.t1 AT3G46010 58.519 135 56 0 8 142 15 149 2.49e-59 181
MS.gene003535.t1 AT3G46010 58.519 135 56 0 8 142 4 138 3.17e-59 180
MS.gene003535.t1 AT4G25590 60.741 135 51 1 8 142 4 136 4.36e-59 179
MS.gene003535.t1 AT5G59880 57.037 135 58 0 8 142 4 138 3.34e-58 177
MS.gene003535.t1 AT3G46000 60.448 134 51 1 8 141 4 135 1.14e-57 176
MS.gene003535.t1 AT5G59890 60.000 130 52 0 12 141 1 130 1.44e-57 176
MS.gene003535.t1 AT5G59890 60.000 130 52 0 12 141 1 130 1.44e-57 176
MS.gene003535.t1 AT3G46000 60.448 134 51 1 8 141 23 154 1.50e-57 176
MS.gene003535.t1 AT4G25590 61.069 131 49 1 12 142 1 129 4.18e-57 174
MS.gene003535.t1 AT2G16700 77.982 109 24 0 1 109 1 109 4.89e-56 171
MS.gene003535.t1 AT5G52360 57.778 135 55 1 8 142 4 136 7.97e-56 171
MS.gene003535.t1 AT3G46000 60.769 130 49 1 12 141 1 128 1.17e-55 171
MS.gene003535.t1 AT5G59880 52.593 135 49 1 8 142 4 123 1.96e-48 152
MS.gene003535.t1 AT3G45990 40.000 135 72 3 12 141 1 131 1.76e-31 109

Find 30 sgRNAs with CRISPR-Local

Find 52 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AATTAAGAGGGGCATCTATT+TGG 0.279597 4.1:+30226850 None:intergenic
AATGGCGATGGCTTTCAAAA+TGG 0.335809 4.1:-30227829 MS.gene003535:intron
GTTGACAAGGTTGGTGGTCC+TGG 0.380021 4.1:-30227533 MS.gene003535:CDS
TCTCTTATTCTTGATGCTGT+TGG 0.381519 4.1:+30226989 None:intergenic
GGATGGGTTAAGAAGAGCTT+TGG 0.389969 4.1:-30226942 MS.gene003535:CDS
GAATCTGAACAGGCTACTAC+TGG 0.427593 4.1:-30227662 MS.gene003535:intron
TGAGTGCAAGAACTCTTTCA+TGG 0.435498 4.1:-30227624 MS.gene003535:CDS
TCTCAGTTGGATCGGTTGCT+TGG 0.449998 4.1:+30226900 None:intergenic
GCATATCTACAATCATCATT+AGG 0.474554 4.1:+30227479 None:intergenic
AACAGGCTACTACTGGGATG+TGG 0.527418 4.1:-30227655 MS.gene003535:intron
AGCAACCGATCCAACTGAGA+TGG 0.533493 4.1:-30226897 MS.gene003535:CDS
ACATCGAATCCCATCTCAGT+TGG 0.534338 4.1:+30226887 None:intergenic
ACTCTTTCATGGAGATGAAG+TGG 0.542716 4.1:-30227613 MS.gene003535:CDS
CATGGAGATGAAGTGGAAGA+AGG 0.543453 4.1:-30227606 MS.gene003535:CDS
GCAACCGATCCAACTGAGAT+GGG 0.549755 4.1:-30226896 MS.gene003535:CDS
GCAAGATCTTCTTCATTGCA+TGG 0.552818 4.1:-30227412 MS.gene003535:intron
TGAAGAAGATCTTGCTCTTG+CGG 0.553047 4.1:+30227420 None:intergenic
GATACTATACGCAACATCAA+AGG 0.562150 4.1:-30226963 MS.gene003535:CDS
GGGTTAAGAAGAGCTTTGGA+TGG 0.582337 4.1:-30226938 MS.gene003535:CDS
GTGACCGTTGACAAGGTTGG+TGG 0.590709 4.1:-30227539 MS.gene003535:CDS
GAATCCCATCTCAGTTGGAT+CGG 0.598606 4.1:+30226892 None:intergenic
TGAAGTGGAAGAAGGTGCAT+AGG 0.607407 4.1:-30227598 MS.gene003535:CDS
CTATACGCAACATCAAAGGA+TGG 0.610779 4.1:-30226959 MS.gene003535:CDS
AAGGCTTGTGACCGTTGACA+AGG 0.611864 4.1:-30227546 MS.gene003535:CDS
ACAGGCTACTACTGGGATGT+GGG 0.613046 4.1:-30227654 MS.gene003535:intron
TCATCAGATAACAATGGCGA+TGG 0.623350 4.1:-30227841 None:intergenic
TATACGCAACATCAAAGGAT+GGG 0.626471 4.1:-30226958 MS.gene003535:CDS
AATCTGAACAGGCTACTACT+GGG 0.632062 4.1:-30227661 MS.gene003535:intron
AGGACCACCAACCTTGTCAA+CGG 0.633960 4.1:+30227535 None:intergenic
CTTGTGACCGTTGACAAGGT+TGG 0.653631 4.1:-30227542 MS.gene003535:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAAAAAAGTCAATTTAGTAT+AGG + chr4.1:30227487-30227506 None:intergenic 15.0%
!!! CTTTTTTTTTTACTTTTACT+TGG - chr4.1:30227499-30227518 MS.gene003535:CDS 15.0%
!! TTTAATCCAACAATTGAAAT+TGG - chr4.1:30227375-30227394 MS.gene003535:intron 20.0%
!! TTTGTTTATACACATGTTTA+TGG - chr4.1:30226978-30226997 MS.gene003535:CDS 20.0%
!!! TATTTTTGGGTAAAATTTTC+AGG - chr4.1:30227678-30227697 MS.gene003535:intron 20.0%
! CATATAATATGAATCTGAAC+AGG - chr4.1:30227021-30227040 MS.gene003535:intron 25.0%
! TATGAGTGAGATGATTTAAA+AGG + chr4.1:30226900-30226919 None:intergenic 25.0%
! TCAATTGTTGGATTAAACAA+AGG + chr4.1:30227372-30227391 None:intergenic 25.0%
! TCACATCATATGGTATTATT+TGG + chr4.1:30227581-30227600 None:intergenic 25.0%
CATTGAGCAAACATTGTTAT+TGG + chr4.1:30227348-30227367 None:intergenic 30.0%
GCATATCTACAATCATCATT+AGG + chr4.1:30227217-30227236 None:intergenic 30.0%
TAAATTGTACTACTAGTACC+TGG + chr4.1:30227531-30227550 None:intergenic 30.0%
TAGAGTCCAATTTCAATTGT+TGG + chr4.1:30227384-30227403 None:intergenic 30.0%
TATATGAGTCTAATACAAGC+TGG - chr4.1:30227555-30227574 MS.gene003535:CDS 30.0%
TCAAGATCGATGAAAAAACA+AGG - chr4.1:30227128-30227147 MS.gene003535:intron 30.0%
TGTACATTCATCACATCATA+TGG + chr4.1:30227591-30227610 None:intergenic 30.0%
! TGAATGTGAGGGATATTTTT+GGG - chr4.1:30227665-30227684 MS.gene003535:intron 30.0%
GATACTATACGCAACATCAA+AGG - chr4.1:30227730-30227749 MS.gene003535:intron 35.0%
GATGATGAATGTGAATGTGA+GGG - chr4.1:30227654-30227673 MS.gene003535:intron 35.0%
TATACGCAACATCAAAGGAT+GGG - chr4.1:30227735-30227754 MS.gene003535:intron 35.0%
TCAATCCAAACACACACAAT+TGG + chr4.1:30227431-30227450 None:intergenic 35.0%
TCTCTTATTCTTGATGCTGT+TGG + chr4.1:30227707-30227726 None:intergenic 35.0%
! ACTTTTACTTGGTAAGTACC+AGG - chr4.1:30227510-30227529 MS.gene003535:CDS 35.0%
! AGATCATCATAGTTTTCTCC+AGG + chr4.1:30227181-30227200 None:intergenic 35.0%
! GTGAATGTGAGGGATATTTT+TGG - chr4.1:30227664-30227683 MS.gene003535:intron 35.0%
! TGATGATGAATGTGAATGTG+AGG - chr4.1:30227653-30227672 MS.gene003535:CDS 35.0%
AATCTGAACAGGCTACTACT+GGG - chr4.1:30227032-30227051 MS.gene003535:intron 40.0%
AATTGGACTCTACAAAGCTG+TGG - chr4.1:30227392-30227411 MS.gene003535:intron 40.0%
ACACACAATTGGATCGTCTA+TGG + chr4.1:30227420-30227439 None:intergenic 40.0%
ACGATCCAATTGTGTGTGTT+TGG - chr4.1:30227423-30227442 MS.gene003535:CDS 40.0%
ACTCTTTCATGGAGATGAAG+TGG - chr4.1:30227080-30227099 MS.gene003535:intron 40.0%
CTATACGCAACATCAAAGGA+TGG - chr4.1:30227734-30227753 MS.gene003535:intron 40.0%
GCAAGATCTTCTTCATTGCA+TGG - chr4.1:30227281-30227300 MS.gene003535:intron 40.0%
TGAAGAAGATCTTGCTCTTG+CGG + chr4.1:30227276-30227295 None:intergenic 40.0%
TGAGTGCAAGAACTCTTTCA+TGG - chr4.1:30227069-30227088 MS.gene003535:intron 40.0%
ACATCGAATCCCATCTCAGT+TGG + chr4.1:30227809-30227828 None:intergenic 45.0%
CATGGAGATGAAGTGGAAGA+AGG - chr4.1:30227087-30227106 MS.gene003535:intron 45.0%
GAATCCCATCTCAGTTGGAT+CGG + chr4.1:30227804-30227823 None:intergenic 45.0%
GAATCTGAACAGGCTACTAC+TGG - chr4.1:30227031-30227050 MS.gene003535:intron 45.0%
! TGAAGTGGAAGAAGGTGCAT+AGG - chr4.1:30227095-30227114 MS.gene003535:intron 45.0%
!! GGATGGGTTAAGAAGAGCTT+TGG - chr4.1:30227751-30227770 MS.gene003535:intron 45.0%
!! GGGTTAAGAAGAGCTTTGGA+TGG - chr4.1:30227755-30227774 MS.gene003535:intron 45.0%
AACAGGCTACTACTGGGATG+TGG - chr4.1:30227038-30227057 MS.gene003535:intron 50.0%
AAGGCTTGTGACCGTTGACA+AGG - chr4.1:30227147-30227166 MS.gene003535:intron 50.0%
ACAGGCTACTACTGGGATGT+GGG - chr4.1:30227039-30227058 MS.gene003535:intron 50.0%
AGCAACCGATCCAACTGAGA+TGG - chr4.1:30227796-30227815 MS.gene003535:intron 50.0%
AGGACCACCAACCTTGTCAA+CGG + chr4.1:30227161-30227180 None:intergenic 50.0%
CTTGTGACCGTTGACAAGGT+TGG - chr4.1:30227151-30227170 MS.gene003535:intron 50.0%
GCAACCGATCCAACTGAGAT+GGG - chr4.1:30227797-30227816 MS.gene003535:intron 50.0%
TCTCAGTTGGATCGGTTGCT+TGG + chr4.1:30227796-30227815 None:intergenic 50.0%
GTGACCGTTGACAAGGTTGG+TGG - chr4.1:30227154-30227173 MS.gene003535:intron 55.0%
!! GTTGACAAGGTTGGTGGTCC+TGG - chr4.1:30227160-30227179 MS.gene003535:intron 55.0%


Chromosome Type Strat End Strand Name
chr4.1 gene 30226865 30227850 30226865 ID=MS.gene003535
chr4.1 mRNA 30226865 30227850 30226865 ID=MS.gene003535.t1;Parent=MS.gene003535
chr4.1 exon 30227830 30227850 30227830 ID=MS.gene003535.t1.exon1;Parent=MS.gene003535.t1
chr4.1 CDS 30227830 30227850 30227830 ID=cds.MS.gene003535.t1;Parent=MS.gene003535.t1
chr4.1 exon 30227413 30227672 30227413 ID=MS.gene003535.t1.exon2;Parent=MS.gene003535.t1
chr4.1 CDS 30227413 30227672 30227413 ID=cds.MS.gene003535.t1;Parent=MS.gene003535.t1
chr4.1 exon 30226865 30227015 30226865 ID=MS.gene003535.t1.exon3;Parent=MS.gene003535.t1
chr4.1 CDS 30226865 30227015 30226865 ID=cds.MS.gene003535.t1;Parent=MS.gene003535.t1
Gene Sequence

>MS.gene003535

ATGGCGATGGCTTTCAAAATGGTACTTCTTTACCTTTTAAATCATCTCACTCATATTAGAGTGTGTGTGATTTTACTTTGTTCTATATATTATTATATATTGATGAATTTTGCTTTGTTTATACACATGTTTATGGTAGATAAAATTATGAATTAACATATAATATGAATCTGAACAGGCTACTACTGGGATGTGGGTAACAGATGAGTGCAAGAACTCTTTCATGGAGATGAAGTGGAAGAAGGTGCATAGGTACATAGTTTTCAAGATCGATGAAAAAACAAGGCTTGTGACCGTTGACAAGGTTGGTGGTCCTGGAGAAAACTATGATGATCTTGCTGCTTCTTTGCCTAATGATGATTGTAGATATGCTGTCTTTGATTTTGATTTTGTCACTGTTGACAACTGCCGCAAGAGCAAGATCTTCTTCATTGCATGGTATAGTTCTCATTTCTCATCAATCTCAATTGTTAGATTAATCCAATAACAATGTTTGCTCAATGTCCTTTGTTTAATCCAACAATTGAAATTGGACTCTACAAAGCTGTGGCGCCATAGACGATCCAATTGTGTGTGTTTGGATTGACGATGAGTTTGTCAGAATTACTGTCAATCTAGACCTATACTAAATTGACTTTTTTTTTTACTTTTACTTGGTAAGTACCAGGTACTAGTAGTACAATTTAATGATATATGAGTCTAATACAAGCTGGCCAAATAATACCATATGATGTGATGAATGTACAATTTTAATTTCAATTATTATAAGATGATGATGATGATGATGATGATGATGAATGTGAATGTGAGGGATATTTTTGGGTAAAATTTTCAGGTCACCAACAGCATCAAGAATAAGAGAAAAGATACTATACGCAACATCAAAGGATGGGTTAAGAAGAGCTTTGGATGGAATCTCATATGAACTCCAAGCAACCGATCCAACTGAGATGGGATTCGATGTAATTCAAGACAGAGCCAAATAG
Protein sequence

>MS.gene003535.t1

MAMAFKMATTGMWVTDECKNSFMEMKWKKVHRYIVFKIDEKTRLVTVDKVGGPGENYDDLAASLPNDDCRYAVFDFDFVTVDNCRKSKIFFIAWSPTASRIREKILYATSKDGLRRALDGISYELQATDPTEMGFDVIQDRAK