AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene071096


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene071096.t1 MTR_5g047050 98.729 236 3 0 1 236 1 236 1.01e-177 487
MS.gene071096.t1 MTR_4g109880 47.598 229 109 4 9 236 4 222 9.18e-66 203
MS.gene071096.t1 MTR_3g072390 35.976 164 92 4 74 236 73 224 2.54e-24 97.1
MS.gene071096.t1 MTR_8g088230 27.803 223 104 7 66 236 17 234 1.59e-19 84.3
MS.gene071096.t1 MTR_2g055760 32.143 140 84 3 79 216 16 146 2.64e-14 69.7
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene071096.t1 AT1G69080 44.309 246 104 5 1 236 1 223 1.70e-64 200
MS.gene071096.t1 AT2G03720 54.913 173 72 5 66 236 64 232 5.66e-59 186
MS.gene071096.t1 AT2G03720 55.030 169 70 5 70 236 1 165 1.25e-57 181
MS.gene071096.t1 AT1G69080 41.463 246 97 6 1 236 1 209 3.67e-55 176
MS.gene071096.t1 AT5G17390 49.133 173 79 4 68 236 118 285 1.64e-51 169
MS.gene071096.t1 AT3G03290 46.243 173 84 4 68 236 107 274 7.95e-48 159
MS.gene071096.t1 AT1G44760 38.012 171 87 4 66 236 62 213 9.00e-31 113
MS.gene071096.t1 AT1G44760 38.012 171 87 4 66 236 133 284 4.17e-30 113
MS.gene071096.t1 AT4G13450 27.885 208 111 6 66 236 14 219 1.41e-17 79.0
MS.gene071096.t1 AT1G48960 30.488 164 99 6 67 230 5 153 1.76e-14 70.5

Find 41 sgRNAs with CRISPR-Local

Find 76 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTGCCATACAATGTGCATTT+TGG 0.179754 5.1:-34911930 None:intergenic
AGAAGAAAGAGTAAGAAAAT+TGG 0.268808 5.1:+34911961 MS.gene071096:CDS
AAGACAAGGCGTGGCACTTT+TGG 0.275641 5.1:+34911816 MS.gene071096:CDS
TGCCCATTGCAAAGCACCTT+TGG 0.367782 5.1:-34911025 None:intergenic
TACTCACACTGTTCAGAATC+AGG 0.397968 5.1:+34911050 MS.gene071096:CDS
TATCCAAAATGCACATTGTA+TGG 0.401167 5.1:+34911927 MS.gene071096:CDS
TCATGCTTGGCTTGTATAGT+TGG 0.420901 5.1:-34910862 None:intergenic
AAGAGAGGAGCAAGGTTACC+AGG 0.459111 5.1:+34910796 MS.gene071096:CDS
CTGGCAATAGAGTCACTGGT+GGG 0.465505 5.1:+34911890 MS.gene071096:CDS
AGCCAAAGGTGCTTTGCAAT+GGG 0.470225 5.1:+34911023 MS.gene071096:CDS
AAGCCAAAGGTGCTTTGCAA+TGG 0.482336 5.1:+34911022 MS.gene071096:CDS
AGAAAGAGTAAGAAAATTGG+AGG 0.492506 5.1:+34911964 MS.gene071096:CDS
TGATGATGAAGCTACTAGTA+AGG 0.513401 5.1:+34911224 MS.gene071096:CDS
AGTAACAGAAGGGAAAGAAA+AGG 0.525585 5.1:+34911768 MS.gene071096:CDS
AACAAGGGTCAGTAGTTAGT+AGG 0.536437 5.1:+34910968 MS.gene071096:CDS
GTAACAGAAGGGAAAGAAAA+GGG 0.538384 5.1:+34911769 MS.gene071096:CDS
TGGGCTGGCAATAGAGTCAC+TGG 0.549351 5.1:+34911886 MS.gene071096:CDS
GGCGAACGCACCCTCGCATG+TGG 0.550940 5.1:-34910841 None:intergenic
AAACCTTGTTTAGAATTCGA+AGG 0.560200 5.1:-34911102 None:intergenic
TCGAATTAGGCCACATGCGA+GGG 0.562880 5.1:+34910831 MS.gene071096:CDS
TTTGACGATGGTGTGAAACA+AGG 0.566437 5.1:+34910952 MS.gene071096:CDS
GAAGCAAGTTCATAAGCCCT+TGG 0.570979 5.1:-34911255 None:intergenic
TTCCAAAACATGGGCAAGAG+AGG 0.576269 5.1:+34910781 None:intergenic
CGTCTTCTAATGATGTGGGC+TGG 0.577564 5.1:+34911871 MS.gene071096:CDS
CATTAGAAGACGCCATGTTG+TGG 0.577627 5.1:-34911860 None:intergenic
ATTGAGATTGCAGTAACAGA+AGG 0.585136 5.1:+34911757 MS.gene071096:CDS
CAATAGAGTCACTGGTGGGG+TGG 0.587431 5.1:+34911894 MS.gene071096:CDS
CATGGCGTCTTCTAATGATG+TGG 0.588320 5.1:+34911866 MS.gene071096:CDS
GAAAGAGTAAGAAAATTGGA+GGG 0.591657 5.1:+34911965 MS.gene071096:CDS
ATCGAATTAGGCCACATGCG+AGG 0.593025 5.1:+34910830 MS.gene071096:CDS
TTGACGATGGTGTGAAACAA+GGG 0.607583 5.1:+34910953 MS.gene071096:CDS
TTGAGATTGCAGTAACAGAA+GGG 0.610661 5.1:+34911758 MS.gene071096:CDS
GCTGGCAATAGAGTCACTGG+TGG 0.614214 5.1:+34911889 MS.gene071096:CDS
AAGCCTTCGAATTCTAAACA+AGG 0.615497 5.1:+34911099 MS.gene071096:CDS
TGGCAATAGAGTCACTGGTG+GGG 0.616318 5.1:+34911891 MS.gene071096:CDS
ATGGCGTCTTCTAATGATGT+GGG 0.632260 5.1:+34911867 MS.gene071096:CDS
CTAGTAAGGAGACAGATCCA+AGG 0.637212 5.1:+34911238 MS.gene071096:CDS
TAGTAAGGAGACAGATCCAA+GGG 0.640856 5.1:+34911239 MS.gene071096:CDS
TGCGAAGAGAAATTTGACGA+TGG 0.691085 5.1:+34910940 MS.gene071096:CDS
ACATGGGCAAGAGAGGAGCA+AGG 0.696922 5.1:+34910788 None:intergenic
TTGTAATCTGAAAATGCCTG+AGG 0.734520 5.1:+34911293 MS.gene071096:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TTTACTTAAAATTATTTCAA+AGG - chr5.1:34911524-34911543 None:intergenic 10.0%
!! CAATATAATGTAAATAAACA+AGG + chr5.1:34911622-34911641 MS.gene071096:intron 15.0%
!!! TATAAATCTAAATTTTCAGA+TGG - chr5.1:34911345-34911364 None:intergenic 15.0%
!! AAGGTTAAATGTTAAAATCT+CGG - chr5.1:34911505-34911524 None:intergenic 20.0%
!! ATCATCATACAAAGAATTTA+AGG - chr5.1:34911595-34911614 None:intergenic 20.0%
! AAAACATACAATGATATCAG+TGG - chr5.1:34911134-34911153 None:intergenic 25.0%
! AGAAGAAAGAGTAAGAAAAT+TGG + chr5.1:34911961-34911980 MS.gene071096:CDS 25.0%
! CAAGTATGATTCATTCAATA+TGG + chr5.1:34911194-34911213 MS.gene071096:intron 25.0%
! TGGATGGAATTTATTACATT+TGG - chr5.1:34911652-34911671 None:intergenic 25.0%
!! GTATGTTTTCTCTTCAAATT+TGG + chr5.1:34911145-34911164 MS.gene071096:intron 25.0%
!! TATATTGTCACTTACTTACA+TGG - chr5.1:34911672-34911691 None:intergenic 25.0%
AATCTCAATTTGTACCTATC+AGG - chr5.1:34911746-34911765 None:intergenic 30.0%
ACTGTATATATGATCCTGAT+AGG + chr5.1:34911729-34911748 MS.gene071096:intron 30.0%
AGAAAGAGTAAGAAAATTGG+AGG + chr5.1:34911964-34911983 MS.gene071096:CDS 30.0%
GAAAGAGTAAGAAAATTGGA+GGG + chr5.1:34911965-34911984 MS.gene071096:CDS 30.0%
TATCCAAAATGCACATTGTA+TGG + chr5.1:34911927-34911946 MS.gene071096:CDS 30.0%
TTCATTTGGTACCATTGTTT+AGG + chr5.1:34911440-34911459 MS.gene071096:intron 30.0%
TTTAACACCCTGAAAAATAG+AGG + chr5.1:34911392-34911411 MS.gene071096:intron 30.0%
! AAACCTTGTTTAGAATTCGA+AGG - chr5.1:34911105-34911124 None:intergenic 30.0%
! CTAAGCGTCATAAAGATTTT+TGG + chr5.1:34912001-34912020 MS.gene071096:CDS 30.0%
! GTTTTTGCTTGAATCGAATT+AGG + chr5.1:34910818-34910837 MS.gene071096:CDS 30.0%
!! ATCATCACTTTTATCATGCT+TGG - chr5.1:34910878-34910897 None:intergenic 30.0%
!!! TCATAAAGATTTTTGGCTCT+TGG + chr5.1:34912008-34912027 MS.gene071096:CDS 30.0%
AAGCCTTCGAATTCTAAACA+AGG + chr5.1:34911099-34911118 MS.gene071096:CDS 35.0%
AGAAAAGGGACCAAAAATAG+TGG + chr5.1:34911783-34911802 MS.gene071096:CDS 35.0%
AGTAACAGAAGGGAAAGAAA+AGG + chr5.1:34911768-34911787 MS.gene071096:CDS 35.0%
ATTCGATTCAAGCAAAAACC+TGG - chr5.1:34910817-34910836 None:intergenic 35.0%
ATTGAGATTGCAGTAACAGA+AGG + chr5.1:34911757-34911776 MS.gene071096:CDS 35.0%
CTAGTGAGTTACACTTCATT+TGG + chr5.1:34911426-34911445 MS.gene071096:intron 35.0%
GTAACAGAAGGGAAAGAAAA+GGG + chr5.1:34911769-34911788 MS.gene071096:CDS 35.0%
TTGAGATTGCAGTAACAGAA+GGG + chr5.1:34911758-34911777 MS.gene071096:CDS 35.0%
TTGTAATCTGAAAATGCCTG+AGG + chr5.1:34911293-34911312 MS.gene071096:CDS 35.0%
! TCAGATGGTAGCATAGTTTT+AGG - chr5.1:34911330-34911349 None:intergenic 35.0%
! TGATGATGAAGCTACTAGTA+AGG + chr5.1:34911224-34911243 MS.gene071096:CDS 35.0%
! TTGCCATACAATGTGCATTT+TGG - chr5.1:34911933-34911952 None:intergenic 35.0%
! TTGTCACTTACTTACATGGA+TGG - chr5.1:34911668-34911687 None:intergenic 35.0%
! TTTGCTTCCTCCACTATTTT+TGG - chr5.1:34911796-34911815 None:intergenic 35.0%
!! TCACACTCCTCTATTTTTCA+GGG - chr5.1:34911402-34911421 None:intergenic 35.0%
!!! GATTCTAGTTTTGAAGCCAA+AGG + chr5.1:34911009-34911028 MS.gene071096:CDS 35.0%
AAAGGGACCAAAAATAGTGG+AGG + chr5.1:34911786-34911805 MS.gene071096:CDS 40.0%
AACAAGGGTCAGTAGTTAGT+AGG + chr5.1:34910968-34910987 MS.gene071096:CDS 40.0%
AGAAAAAGAGGTCCACAACA+TGG + chr5.1:34911848-34911867 MS.gene071096:CDS 40.0%
ATGGCGTCTTCTAATGATGT+GGG + chr5.1:34911867-34911886 MS.gene071096:CDS 40.0%
TACTCACACTGTTCAGAATC+AGG + chr5.1:34911050-34911069 MS.gene071096:CDS 40.0%
TAGTAAGGAGACAGATCCAA+GGG + chr5.1:34911239-34911258 MS.gene071096:CDS 40.0%
TCGCGATACAACCTAAACAA+TGG - chr5.1:34911454-34911473 None:intergenic 40.0%
TGCGAAGAGAAATTTGACGA+TGG + chr5.1:34910940-34910959 MS.gene071096:CDS 40.0%
TTGACGATGGTGTGAAACAA+GGG + chr5.1:34910953-34910972 MS.gene071096:CDS 40.0%
TTTGACGATGGTGTGAAACA+AGG + chr5.1:34910952-34910971 MS.gene071096:CDS 40.0%
!! CTCACACTCCTCTATTTTTC+AGG - chr5.1:34911403-34911422 None:intergenic 40.0%
!! TCATGCTTGGCTTGTATAGT+TGG - chr5.1:34910865-34910884 None:intergenic 40.0%
CATGGCGTCTTCTAATGATG+TGG + chr5.1:34911866-34911885 MS.gene071096:CDS 45.0%
CATTAGAAGACGCCATGTTG+TGG - chr5.1:34911863-34911882 None:intergenic 45.0%
CTAGTAAGGAGACAGATCCA+AGG + chr5.1:34911238-34911257 MS.gene071096:CDS 45.0%
GAAGCAAGTTCATAAGCCCT+TGG - chr5.1:34911258-34911277 None:intergenic 45.0%
GTGGAGGAAGCAAAAAGACA+AGG + chr5.1:34911802-34911821 MS.gene071096:CDS 45.0%
TTAGGAGCTAAACTCACCTC+AGG - chr5.1:34911312-34911331 None:intergenic 45.0%
!! AAGCCAAAGGTGCTTTGCAA+TGG + chr5.1:34911022-34911041 MS.gene071096:CDS 45.0%
!! AGCCAAAGGTGCTTTGCAAT+GGG + chr5.1:34911023-34911042 MS.gene071096:CDS 45.0%
!!! TGGTTTTGGGGCAGAAAAAG+AGG + chr5.1:34911836-34911855 MS.gene071096:CDS 45.0%
AAGAGAGGAGCAAGGTTACC+AGG + chr5.1:34910796-34910815 MS.gene071096:CDS 50.0%
ATCGAATTAGGCCACATGCG+AGG + chr5.1:34910830-34910849 MS.gene071096:CDS 50.0%
CGTCTTCTAATGATGTGGGC+TGG + chr5.1:34911871-34911890 MS.gene071096:CDS 50.0%
CTGGCAATAGAGTCACTGGT+GGG + chr5.1:34911890-34911909 MS.gene071096:CDS 50.0%
GGAAGCAAAAAGACAAGGCG+TGG + chr5.1:34911807-34911826 MS.gene071096:CDS 50.0%
TCGAATTAGGCCACATGCGA+GGG + chr5.1:34910831-34910850 MS.gene071096:CDS 50.0%
TGGCAATAGAGTCACTGGTG+GGG + chr5.1:34911891-34911910 MS.gene071096:CDS 50.0%
! AAGACAAGGCGTGGCACTTT+TGG + chr5.1:34911816-34911835 MS.gene071096:CDS 50.0%
! TGCCCATTGCAAAGCACCTT+TGG - chr5.1:34911028-34911047 None:intergenic 50.0%
!!! AGGCGTGGCACTTTTGGTTT+TGG + chr5.1:34911822-34911841 MS.gene071096:CDS 50.0%
!!! GCGTGGCACTTTTGGTTTTG+GGG + chr5.1:34911824-34911843 MS.gene071096:CDS 50.0%
!!! GGCGTGGCACTTTTGGTTTT+GGG + chr5.1:34911823-34911842 MS.gene071096:CDS 50.0%
CAATAGAGTCACTGGTGGGG+TGG + chr5.1:34911894-34911913 MS.gene071096:CDS 55.0%
GCTGGCAATAGAGTCACTGG+TGG + chr5.1:34911889-34911908 MS.gene071096:CDS 55.0%
!! TGGGCTGGCAATAGAGTCAC+TGG + chr5.1:34911886-34911905 MS.gene071096:CDS 55.0%
GGCGAACGCACCCTCGCATG+TGG - chr5.1:34910844-34910863 None:intergenic 70.0%


Chromosome Type Strat End Strand Name
chr5.1 gene 34910790 34912035 34910790 ID=MS.gene071096
chr5.1 mRNA 34910790 34912035 34910790 ID=MS.gene071096.t1;Parent=MS.gene071096
chr5.1 exon 34910790 34911120 34910790 ID=MS.gene071096.t1.exon1;Parent=MS.gene071096.t1
chr5.1 CDS 34910790 34911120 34910790 ID=cds.MS.gene071096.t1;Parent=MS.gene071096.t1
chr5.1 exon 34911220 34911314 34911220 ID=MS.gene071096.t1.exon2;Parent=MS.gene071096.t1
chr5.1 CDS 34911220 34911314 34911220 ID=cds.MS.gene071096.t1;Parent=MS.gene071096.t1
chr5.1 exon 34911751 34912035 34911751 ID=MS.gene071096.t1.exon3;Parent=MS.gene071096.t1
chr5.1 CDS 34911751 34912035 34911751 ID=cds.MS.gene071096.t1;Parent=MS.gene071096.t1
Gene Sequence

>MS.gene071096

ATGGGCAAGAGAGGAGCAAGGTTACCAGGTTTTTGCTTGAATCGAATTAGGCCACATGCGAGGGTGCGTTCGCCAACTATACAAGCCAAGCATGATAAAAGTGATGATGCTAAAATTGATCAGAAAATTACTGAGAATTCATGCAGTGTTTGCGAAGAGAAATTTGACGATGGTGTGAAACAAGGGTCAGTAGTTAGTAGGAAGATTATGATTGTGATTGATTCTAGTTTTGAAGCCAAAGGTGCTTTGCAATGGGCACTTACTCACACTGTTCAGAATCAGGATACTATAGTTCTTCTTCATGTCATGAAGCCTTCGAATTCTAAACAAGGTTTGTGAAACCACTGATATCATTGTATGTTTTCTCTTCAAATTTGGCTTATTTTTTTGTGATTGAAACATATCAAGTATGATTCATTCAATATGGCAGAAACTGATGATGAAGCTACTAGTAAGGAGACAGATCCAAGGGCTTATGAACTTGCTTCATCTTTCAAGAATATTTGTAATCTGAAAATGCCTGAGGTGAGTTTAGCTCCTAAAACTATGCTACCATCTGAAAATTTAGATTTATATCTAAGAGTAATGCTAGCAACATACATTTTAACACCCTGAAAAATAGAGGAGTGTGAGTGACTAGTGAGTTACACTTCATTTGGTACCATTGTTTAGGTTGTATCGCGATGTATTTTATCTGATATTCTACATTTTTCCGAGATTTTAACATTTAACCTTTGAAATAATTTTAAGTAAATTTGTTAAAATTCTAGTTCTAGATTGTGAATATCAATCAACATTAAATCCTTAAATTCTTTGTATGATGATGTTGAGACAATATAATGTAAATAAACAAGGCATGCCAAATGTAATAAATTCCATCCATGTAAGTAAGTGACAATATATTTTACTTTATATGAAATGTAATAATTAAATGTTGAGACTGTATATATGATCCTGATAGGTACAAATTGAGATTGCAGTAACAGAAGGGAAAGAAAAGGGACCAAAAATAGTGGAGGAAGCAAAAAGACAAGGCGTGGCACTTTTGGTTTTGGGGCAGAAAAAGAGGTCCACAACATGGCGTCTTCTAATGATGTGGGCTGGCAATAGAGTCACTGGTGGGGTGGTAGAGTATTGTATCCAAAATGCACATTGTATGGCAATTGCTGTGAGAAGAAAGAGTAAGAAAATTGGAGGGTATATGATTACTACTAAGCGTCATAAAGATTTTTGGCTCTTGGCTTGA

Protein sequence

>MS.gene071096.t1

MGKRGARLPGFCLNRIRPHARVRSPTIQAKHDKSDDAKIDQKITENSCSVCEEKFDDGVKQGSVVSRKIMIVIDSSFEAKGALQWALTHTVQNQDTIVLLHVMKPSNSKQETDDEATSKETDPRAYELASSFKNICNLKMPEVQIEIAVTEGKEKGPKIVEEAKRQGVALLVLGQKKRSTTWRLLMMWAGNRVTGGVVEYCIQNAHCMAIAVRRKSKKIGGYMITTKRHKDFWLLA