AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene55239

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene55239.t1 MTR_5g041095 91.228 228 19 1 1 227 1 228 2.30e-146 407
MS.gene55239.t1 MTR_5g041040 73.684 228 59 1 1 227 1 228 1.89e-117 334
MS.gene55239.t1 MTR_5g041080 70.742 229 65 2 1 227 1 229 5.79e-117 333
MS.gene55239.t1 MTR_5g041010 66.228 228 75 2 1 227 1 227 1.79e-110 316
MS.gene55239.t1 MTR_5g040940 56.195 226 97 2 4 227 3 228 9.25e-88 259
MS.gene55239.t1 MTR_5g040960 55.111 225 97 3 7 227 6 230 1.59e-85 253
MS.gene55239.t1 MTR_0129s0080 30.837 227 140 9 1 218 1 219 2.29e-23 94.4
MS.gene55239.t1 MTR_2g021750 33.673 196 114 9 34 224 163 347 5.93e-23 95.5
MS.gene55239.t1 MTR_8g028080 34.946 186 97 6 26 188 41 225 3.42e-22 92.4
MS.gene55239.t1 MTR_5g086410 27.602 221 149 8 9 225 1 214 2.78e-19 83.2
MS.gene55239.t1 MTR_2g021830 27.586 203 132 6 23 224 1 189 2.47e-18 80.1
MS.gene55239.t1 MTR_3g030660 30.049 203 129 8 28 225 79 273 3.48e-18 81.3
MS.gene55239.t1 MTR_3g030640 29.557 203 130 8 28 225 74 268 5.68e-18 80.5
MS.gene55239.t1 MTR_4g057825 27.861 201 126 8 27 225 20 203 7.39e-18 79.0
MS.gene55239.t1 MTR_6g071425 28.708 209 131 8 28 224 78 280 8.18e-18 80.5
MS.gene55239.t1 MTR_2g021910 30.457 197 117 9 12 207 233 410 1.12e-16 79.0
MS.gene55239.t1 MTR_5g086770 32.258 155 94 4 59 211 62 207 1.87e-16 75.5
MS.gene55239.t1 MTR_6g090200 26.396 197 127 7 28 221 22 203 1.33e-15 73.2
MS.gene55239.t1 MTR_2g104370 30.189 159 94 5 64 211 34 186 5.94e-14 68.6
MS.gene55239.t1 MTR_6g071505 28.910 211 126 11 27 224 70 269 1.10e-12 65.9
MS.gene55239.t1 MTR_5g022810 27.805 205 128 11 35 225 31 229 1.97e-12 64.7
MS.gene55239.t1 MTR_1g048200 26.733 202 114 9 28 211 104 289 6.65e-12 63.9
MS.gene55239.t1 MTR_2g104300 27.869 122 71 3 25 141 24 133 1.46e-11 60.5
MS.gene55239.t1 MTR_0002s1200 27.941 204 133 9 28 225 104 299 2.67e-11 62.4
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene55239.t1 AT1G26820 53.456 217 99 2 12 227 7 222 2.24e-87 258
MS.gene55239.t1 AT1G14220 52.466 223 104 2 6 227 7 228 3.42e-85 252
MS.gene55239.t1 AT2G02990 50.000 226 112 1 3 227 5 230 4.02e-81 242
MS.gene55239.t1 AT1G14210 45.740 223 115 4 8 225 5 226 3.22e-65 202
MS.gene55239.t1 AT2G39780 36.264 182 104 5 24 194 28 208 7.39e-31 114
MS.gene55239.t1 AT2G39780 28.177 181 88 5 24 194 28 176 1.09e-15 73.6

Find 42 sgRNAs with CRISPR-Local

Find 58 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TGCCGCCGGTTTACCGGTTT+TGG 0.140961 5.2:-30819338 None:intergenic
TACATGTGCGTGGACATTTC+TGG 0.212476 5.2:+30820027 MS.gene55239:CDS
TTGAGAACTTGGAAATAAAT+TGG 0.220567 5.2:+30819586 MS.gene55239:CDS
GCTTCTTCTATAATACTTAA+AGG 0.225424 5.2:-30819937 None:intergenic
AAATGTCTTTCATAAATCTA+AGG 0.308390 5.2:+30819429 MS.gene55239:CDS
CCACAGTTGTCCACCAGATT+AGG 0.339955 5.2:-30820069 None:intergenic
AAAATCTGCCGCCGGTTTAC+CGG 0.341226 5.2:-30819344 None:intergenic
TCTCGATTACATTCTATTCC+TGG 0.351859 5.2:-30819973 None:intergenic
TTTCATTCAGTGCCCTAATC+TGG 0.357501 5.2:+30820056 MS.gene55239:CDS
ATGTCGTAAAATTGATCATT+TGG 0.360780 5.2:-30819907 None:intergenic
CTCAGACCTAATTGAGAACT+TGG 0.365073 5.2:+30819575 MS.gene55239:CDS
TTATTTCCAAGTTCTCAATT+AGG 0.365773 5.2:-30819581 None:intergenic
ACCATGTTCTGCTTAAAACT+TGG 0.376740 5.2:-30820109 None:intergenic
CTTCTTCTATAATACTTAAA+GGG 0.377238 5.2:-30819936 None:intergenic
GTCTCAACAATATTAAAATA+TGG 0.390023 5.2:+30819628 MS.gene55239:CDS
CACAGTTGTCCACCAGATTA+GGG 0.403167 5.2:-30820068 None:intergenic
GCTAGGCCTGAGTCCATATA+TGG 0.406091 5.2:-30819368 None:intergenic
TTAAAATATGGTCACATGAA+TGG 0.407215 5.2:+30819640 MS.gene55239:CDS
AAACTTGGGGAATTGTACTT+TGG 0.428810 5.2:-30820094 None:intergenic
AAATAAATTGGCCATCTTTG+AGG 0.430194 5.2:+30819598 MS.gene55239:CDS
CCATGTTCTGCTTAAAACTT+GGG 0.431272 5.2:-30820108 None:intergenic
AGTATTATAGAAGAAGCTAC+AGG 0.442254 5.2:+30819943 MS.gene55239:CDS
CTCGATTACATTCTATTCCT+GGG 0.468968 5.2:-30819972 None:intergenic
TTATCCCAAAACCGGTAAAC+CGG 0.471137 5.2:+30819333 MS.gene55239:CDS
GGCTGCTGTTATCCCAAAAC+CGG 0.481409 5.2:+30819325 MS.gene55239:CDS
CGTCCTCAAGAATTTGAAGA+AGG 0.510322 5.2:-30819746 None:intergenic
GAACCTTCTTCAAATTCTTG+AGG 0.516731 5.2:+30819743 MS.gene55239:CDS
TTTGAGTCACAGTATGATCC+TGG 0.517780 5.2:-30819298 None:intergenic
AATCAAAATCTTGAGCAGAA+AGG 0.530770 5.2:-30819153 None:intergenic
ATATTGTAGTATCAAAAGCT+TGG 0.539152 5.2:-30819116 None:intergenic
AGACGTGGACACCTCAAAGA+TGG 0.566148 5.2:-30819609 None:intergenic
TTTAAAAGTTTACATGTGCG+TGG 0.582503 5.2:+30820017 MS.gene55239:CDS
TCATACTGTGACTCAAAACT+AGG 0.585017 5.2:+30819304 MS.gene55239:CDS
CATTCAGTGCCCTAATCTGG+TGG 0.593616 5.2:+30820059 MS.gene55239:CDS
GAAGCTACAGGGTTTCTCCC+AGG 0.599536 5.2:+30819955 MS.gene55239:CDS
CTTCAAATTCTTGAGGACGC+AGG 0.604968 5.2:+30819750 MS.gene55239:CDS
CATGTTCTGCTTAAAACTTG+GGG 0.614034 5.2:-30820107 None:intergenic
GTATTATAGAAGAAGCTACA+GGG 0.644202 5.2:+30819944 MS.gene55239:CDS
TCCCAAAACCGGTAAACCGG+CGG 0.665182 5.2:+30819336 MS.gene55239:CDS
CCTAATCTGGTGGACAACTG+TGG 0.668218 5.2:+30820069 MS.gene55239:CDS
TATATGGTAAAATCTGCCGC+CGG 0.691290 5.2:-30819352 None:intergenic
TCACATGAATGGATGAAACA+TGG 0.720853 5.2:+30819651 MS.gene55239:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TCAAAAAAAAAAACTTAATT+TGG + chr5.2:30819545-30819564 MS.gene55239:intron 10.0%
!!! TAGTATTTCTAATCATTTAA+AGG + chr5.2:30819863-30819882 MS.gene55239:intron 15.0%
!! AAATGTCTTTCATAAATCTA+AGG + chr5.2:30819429-30819448 MS.gene55239:CDS 20.0%
!! ATTTAAAGGTAATGAATTTC+AGG + chr5.2:30819877-30819896 MS.gene55239:intron 20.0%
!! CTTCTTCTATAATACTTAAA+GGG - chr5.2:30819939-30819958 None:intergenic 20.0%
!! GTCTCAACAATATTAAAATA+TGG + chr5.2:30819628-30819647 MS.gene55239:CDS 20.0%
! ATATTGTAGTATCAAAAGCT+TGG - chr5.2:30819119-30819138 None:intergenic 25.0%
! ATGTCGTAAAATTGATCATT+TGG - chr5.2:30819910-30819929 None:intergenic 25.0%
! GCTTCTTCTATAATACTTAA+AGG - chr5.2:30819940-30819959 None:intergenic 25.0%
! TCAATGAGTCAAACTTAATT+TGG + chr5.2:30819514-30819533 MS.gene55239:intron 25.0%
! TTAAAATATGGTCACATGAA+TGG + chr5.2:30819640-30819659 MS.gene55239:CDS 25.0%
! TTATTTCCAAGTTCTCAATT+AGG - chr5.2:30819584-30819603 None:intergenic 25.0%
! TTGAGAACTTGGAAATAAAT+TGG + chr5.2:30819586-30819605 MS.gene55239:CDS 25.0%
!! AATGATCAATTTTACGACAT+AGG + chr5.2:30819910-30819929 MS.gene55239:CDS 25.0%
!! ATTTTGAATATCACAGTTTG+TGG - chr5.2:30819413-30819432 None:intergenic 25.0%
!! TTTTGAATATCACAGTTTGT+GGG - chr5.2:30819412-30819431 None:intergenic 25.0%
!!! ATTTTAATATTGTTGAGACG+TGG - chr5.2:30819627-30819646 None:intergenic 25.0%
AAATAAATTGGCCATCTTTG+AGG + chr5.2:30819598-30819617 MS.gene55239:CDS 30.0%
AATCAAAATCTTGAGCAGAA+AGG - chr5.2:30819156-30819175 None:intergenic 30.0%
AGTATTATAGAAGAAGCTAC+AGG + chr5.2:30819943-30819962 MS.gene55239:CDS 30.0%
GTATTATAGAAGAAGCTACA+GGG + chr5.2:30819944-30819963 MS.gene55239:CDS 30.0%
TTTAAAAGTTTACATGTGCG+TGG + chr5.2:30820017-30820036 MS.gene55239:CDS 30.0%
! AGACATGATTTTGAATCATC+TGG + chr5.2:30819778-30819797 MS.gene55239:intron 30.0%
! ATTTTACCATATATGGACTC+AGG + chr5.2:30819362-30819381 MS.gene55239:CDS 30.0%
!! TTTCTTCACTTTTATTCTGC+AGG + chr5.2:30819174-30819193 MS.gene55239:CDS 30.0%
!!! CATTGTTTTTAATGATGCAG+TGG + chr5.2:30819275-30819294 MS.gene55239:intron 30.0%
AAACTTGGGGAATTGTACTT+TGG - chr5.2:30820097-30820116 None:intergenic 35.0%
CTCGATTACATTCTATTCCT+GGG - chr5.2:30819975-30819994 None:intergenic 35.0%
GAACCTTCTTCAAATTCTTG+AGG + chr5.2:30819743-30819762 MS.gene55239:CDS 35.0%
TCACATGAATGGATGAAACA+TGG + chr5.2:30819651-30819670 MS.gene55239:CDS 35.0%
TCATACTGTGACTCAAAACT+AGG + chr5.2:30819304-30819323 MS.gene55239:CDS 35.0%
TCTCGATTACATTCTATTCC+TGG - chr5.2:30819976-30819995 None:intergenic 35.0%
!!! GATGATCCATTTTTGAAGCT+AGG - chr5.2:30819388-30819407 None:intergenic 35.0%
CGTCCTCAAGAATTTGAAGA+AGG - chr5.2:30819749-30819768 None:intergenic 40.0%
CTCAGACCTAATTGAGAACT+TGG + chr5.2:30819575-30819594 MS.gene55239:CDS 40.0%
TATATGGTAAAATCTGCCGC+CGG - chr5.2:30819355-30819374 None:intergenic 40.0%
TTATCCCAAAACCGGTAAAC+CGG + chr5.2:30819333-30819352 MS.gene55239:CDS 40.0%
TTTCATTCAGTGCCCTAATC+TGG + chr5.2:30820056-30820075 MS.gene55239:CDS 40.0%
TTTGAGTCACAGTATGATCC+TGG - chr5.2:30819301-30819320 None:intergenic 40.0%
! GCGGCAGATTTTACCATATA+TGG + chr5.2:30819355-30819374 MS.gene55239:CDS 40.0%
! TTTTTAATGATGCAGTGGCC+AGG + chr5.2:30819280-30819299 MS.gene55239:intron 40.0%
CACAGTTGTCCACCAGATTA+GGG - chr5.2:30820071-30820090 None:intergenic 45.0%
CTCAGGCCTAGCTTCAAAAA+TGG + chr5.2:30819379-30819398 MS.gene55239:CDS 45.0%
CTTCAAATTCTTGAGGACGC+AGG + chr5.2:30819750-30819769 MS.gene55239:CDS 45.0%
TACATGTGCGTGGACATTTC+TGG + chr5.2:30820027-30820046 MS.gene55239:CDS 45.0%
AATACTCACACACATGCGCG+CGG + chr5.2:30819811-30819830 MS.gene55239:intron 50.0%
AGACGTGGACACCTCAAAGA+TGG - chr5.2:30819612-30819631 None:intergenic 50.0%
CATTCAGTGCCCTAATCTGG+TGG + chr5.2:30820059-30820078 MS.gene55239:CDS 50.0%
CCACAGTTGTCCACCAGATT+AGG - chr5.2:30820072-30820091 None:intergenic 50.0%
GCTAGGCCTGAGTCCATATA+TGG - chr5.2:30819371-30819390 None:intergenic 50.0%
GGCTGCTGTTATCCCAAAAC+CGG + chr5.2:30819325-30819344 MS.gene55239:CDS 50.0%
! CCTAATCTGGTGGACAACTG+TGG + chr5.2:30820069-30820088 MS.gene55239:CDS 50.0%
!! AAAATCTGCCGCCGGTTTAC+CGG - chr5.2:30819347-30819366 None:intergenic 50.0%
ATACTCACACACATGCGCGC+GGG + chr5.2:30819812-30819831 MS.gene55239:intron 55.0%
GAAGCTACAGGGTTTCTCCC+AGG + chr5.2:30819955-30819974 MS.gene55239:CDS 55.0%
TCCCAAAACCGGTAAACCGG+CGG + chr5.2:30819336-30819355 MS.gene55239:CDS 55.0%
!!! GCCGCCGGTTTACCGGTTTT+GGG - chr5.2:30819340-30819359 None:intergenic 60.0%
!!! TGCCGCCGGTTTACCGGTTT+TGG - chr5.2:30819341-30819360 None:intergenic 60.0%


Chromosome Type Strat End Strand Name
chr5.2 gene 30819088 30820119 30819088 ID=MS.gene55239
chr5.2 mRNA 30819088 30820119 30819088 ID=MS.gene55239.t1;Parent=MS.gene55239
chr5.2 exon 30819088 30819195 30819088 ID=MS.gene55239.t1.exon1;Parent=MS.gene55239.t1
chr5.2 CDS 30819088 30819195 30819088 ID=cds.MS.gene55239.t1;Parent=MS.gene55239.t1
chr5.2 exon 30819295 30819450 30819295 ID=MS.gene55239.t1.exon2;Parent=MS.gene55239.t1
chr5.2 CDS 30819295 30819450 30819295 ID=cds.MS.gene55239.t1;Parent=MS.gene55239.t1
chr5.2 exon 30819573 30819771 30819573 ID=MS.gene55239.t1.exon3;Parent=MS.gene55239.t1
chr5.2 CDS 30819573 30819771 30819573 ID=cds.MS.gene55239.t1;Parent=MS.gene55239.t1
chr5.2 exon 30819899 30820119 30819899 ID=MS.gene55239.t1.exon4;Parent=MS.gene55239.t1
chr5.2 CDS 30819899 30820119 30819899 ID=cds.MS.gene55239.t1;Parent=MS.gene55239.t1
Gene Sequence

>MS.gene55239

ATGAAACTAAGCAGCATTTCAGTACTGTCCAAGCTTTTGATACTACAATATCTATCTGTTCAATGCCTTTCTGCTCAAGATTTTGATTTCTTCACTTTTATTCTGCAGGTAATTACAAATATTGTTGATAGTTTATATTTATATTTTTACACTTTATTAATCTGATTATTCAGTATTGCATTATTGACATTGTTTTTAATGATGCAGTGGCCAGGATCATACTGTGACTCAAAACTAGGCTGCTGTTATCCCAAAACCGGTAAACCGGCGGCAGATTTTACCATATATGGACTCAGGCCTAGCTTCAAAAATGGATCATCTCCCACAAACTGTGATATTCAAAATGTCTTTCATAAATCTAAGGTATTCATGTTATTTAAATTGTCTTTATGTTTTTATTAGTGTATTTCTCTACTGAAAAACTCATCAATGAGTCAAACTTAATTTGGTGTATGTTTCAAAAAAAAAAACTTAATTTGGTGTAGATCTCAGACCTAATTGAGAACTTGGAAATAAATTGGCCATCTTTGAGGTGTCCACGTCTCAACAATATTAAAATATGGTCACATGAATGGATGAAACATGGTACTTGTTCAGAATCTAAGTTTACTCAACATGACTACTTTCAAACAGCTCTCAAACTAAAAGAAAAACTGAACCTTCTTCAAATTCTTGAGGACGCAGGTAACAAGACATGATTTTGAATCATCTGGTGACTTCAAAAATACTCACACACATGCGCGCGGGCGCACACACATATATATTTGCAAATTAATAGTATTTCTAATCATTTAAAGGTAATGAATTTCAGGATTTGAACCAAATGATCAATTTTACGACATAGGAAACCCTTTAAGTATTATAGAAGAAGCTACAGGGTTTCTCCCAGGAATAGAATGTAATCGAGATTCAGCAAGTAACGATCAGATTTTAAAAGTTTACATGTGCGTGGACATTTCTGGATCAAATTTCATTCAGTGCCCTAATCTGGTGGACAACTGTGGTGCCAAAGTACAATTCCCCAAGTTTTAA
Protein sequence

>MS.gene55239.t1

MKLSSISVLSKLLILQYLSVQCLSAQDFDFFTFILQWPGSYCDSKLGCCYPKTGKPAADFTIYGLRPSFKNGSSPTNCDIQNVFHKSKISDLIENLEINWPSLRCPRLNNIKIWSHEWMKHGTCSESKFTQHDYFQTALKLKEKLNLLQILEDAGFEPNDQFYDIGNPLSIIEEATGFLPGIECNRDSASNDQILKVYMCVDISGSNFIQCPNLVDNCGAKVQFPKF