AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene63882


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene63882.t1 MTR_5g094600 94.203 138 8 0 1 138 1 138 1.18e-77 226
MS.gene63882.t1 MTR_5g094600 89.899 99 10 0 1 99 1 99 4.18e-43 138
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene63882.t1 AT5G55570 53.957 139 62 1 1 137 4 142 6.78e-45 144
MS.gene63882.t1 AT5G55570 51.562 128 60 1 1 126 4 131 1.22e-34 117

Find 18 sgRNAs with CRISPR-Local

Find 47 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ATGTTGTACAATACATTAAC+TGG 0.326787 5.1:+75837768 None:intergenic
TGTTACTATGTTCCTAGCTT+TGG 0.346506 5.1:+75838621 None:intergenic
CAAATTGTGGTTGGAACTAT+AGG 0.347370 5.1:-75838448 MS.gene63882:intron
TCAATAAACATACCACATTC+TGG 0.351241 5.1:+75838014 None:intergenic
TTTCAGGTGGATTTCTTCCT+TGG 0.372047 5.1:-75837813 MS.gene63882:intron
GATTTCTTCCTTGGCAATCC+TGG 0.380191 5.1:-75837804 MS.gene63882:CDS
TCAATCCCTGCCACCACAAA+AGG 0.427439 5.1:+75838220 None:intergenic
TGTGAGATGTGTGGAGGATC+AGG 0.462362 5.1:-75838071 MS.gene63882:CDS
CATGTGATTTCCACAGGAGC+CGG 0.482809 5.1:+75838472 None:intergenic
ATTTGCCATGTGATTTCCAC+AGG 0.496879 5.1:+75838466 None:intergenic
CTTTAACTATTGCCAAAGCT+AGG 0.525649 5.1:-75838633 MS.gene63882:CDS
ATCACATGGCAAATTGTGGT+TGG 0.532719 5.1:-75838457 MS.gene63882:CDS
GCTTTGGCAATAGTTAAAGA+AGG 0.548231 5.1:+75838637 None:intergenic
AGTACTTGATCCGGCTCCTG+TGG 0.548369 5.1:-75838482 MS.gene63882:CDS
TGTAACCACAGTACTTGATC+CGG 0.578314 5.1:-75838491 MS.gene63882:CDS
CGGCTCCTGTGGAAATCACA+TGG 0.593483 5.1:-75838471 MS.gene63882:CDS
GGAAATCACATGGCAAATTG+TGG 0.664563 5.1:-75838461 MS.gene63882:CDS
AGGAGCCGGATCAAGTACTG+TGG 0.738031 5.1:+75838486 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TTTTGGTTCTCAAATATTTA+AGG - chr5.1:75838551-75838570 MS.gene63882:CDS 20.0%
! AACAACAAAAAGAAGAACAA+GGG - chr5.1:75837911-75837930 MS.gene63882:intron 25.0%
! CTTCATATGCTATATATTTC+AGG - chr5.1:75838618-75838637 MS.gene63882:CDS 25.0%
!! ATATGAAGAAATGATTTGTG+AGG + chr5.1:75838606-75838625 None:intergenic 25.0%
!! TTAGGGATAAGAACTATTTT+CGG - chr5.1:75838407-75838426 MS.gene63882:intron 25.0%
!!! ATTGTTTTGAAATTTGTAGC+TGG - chr5.1:75838197-75838216 MS.gene63882:intron 25.0%
!!! CTACTTCTCATTGATTTTTT+TGG - chr5.1:75838534-75838553 MS.gene63882:CDS 25.0%
!!! TTGTTTTGAAATTTGTAGCT+GGG - chr5.1:75838198-75838217 MS.gene63882:intron 25.0%
CAAAAAAAATGTGAGATGTG+TGG - chr5.1:75838367-75838386 MS.gene63882:intron 30.0%
CAACAACAAAAAGAAGAACA+AGG - chr5.1:75837910-75837929 MS.gene63882:intron 30.0%
CATATGCTATATATTTCAGG+TGG - chr5.1:75838621-75838640 MS.gene63882:CDS 30.0%
TCAATAAACATACCACATTC+TGG + chr5.1:75838436-75838455 None:intergenic 30.0%
! TCTAGTTAATTTAGCTCACA+TGG - chr5.1:75838072-75838091 MS.gene63882:CDS 30.0%
! TGAGAAAAAGCTGTGATTTT+GGG - chr5.1:75837871-75837890 MS.gene63882:intron 30.0%
AAAAAATGTGAGATGTGTGG+AGG - chr5.1:75838370-75838389 MS.gene63882:intron 35.0%
ACAAAAAGAAGAACAAGGGT+AGG - chr5.1:75837915-75837934 MS.gene63882:intron 35.0%
CAAATTGTGGTTGGAACTAT+AGG - chr5.1:75837999-75838018 MS.gene63882:intron 35.0%
CTTTAACTATTGCCAAAGCT+AGG - chr5.1:75837814-75837833 MS.gene63882:intron 35.0%
GCTTTGGCAATAGTTAAAGA+AGG + chr5.1:75837813-75837832 None:intergenic 35.0%
TGTTACTATGTTCCTAGCTT+TGG + chr5.1:75837829-75837848 None:intergenic 35.0%
! GAGAAAAAGCTGTGATTTTG+GGG - chr5.1:75837872-75837891 MS.gene63882:intron 35.0%
! GTGAGAAAAAGCTGTGATTT+TGG - chr5.1:75837870-75837889 MS.gene63882:intron 35.0%
!! AAATCACAGCTTTTTCTCAC+TGG + chr5.1:75837870-75837889 None:intergenic 35.0%
!!! AGGATCAGGACTTGTTTTTA+GGG - chr5.1:75838390-75838409 MS.gene63882:intron 35.0%
ATATTCGATATGTCGAGACG+CGG - chr5.1:75838111-75838130 MS.gene63882:intron 40.0%
ATCACATGGCAAATTGTGGT+TGG - chr5.1:75837990-75838009 MS.gene63882:intron 40.0%
ATTTGCCATGTGATTTCCAC+AGG + chr5.1:75837984-75838003 None:intergenic 40.0%
GGAAATCACATGGCAAATTG+TGG - chr5.1:75837986-75838005 MS.gene63882:intron 40.0%
TGTAACCACAGTACTTGATC+CGG - chr5.1:75837956-75837975 MS.gene63882:intron 40.0%
! AATCTTTTCCAGGATTGCCA+AGG + chr5.1:75838654-75838673 None:intergenic 40.0%
! ACTGGAGAAGAATCTTTTCC+AGG + chr5.1:75838664-75838683 None:intergenic 40.0%
! TTTCAGGTGGATTTCTTCCT+TGG - chr5.1:75838634-75838653 MS.gene63882:CDS 40.0%
!! ACAGCTTTTTCTCACTGGTA+AGG + chr5.1:75837865-75837884 None:intergenic 40.0%
!! GAGGATCAGGACTTGTTTTT+AGG - chr5.1:75838389-75838408 MS.gene63882:intron 40.0%
!!! TATTTTCGGTGTCCAGAATG+TGG - chr5.1:75838421-75838440 MS.gene63882:intron 40.0%
GATTTCTTCCTTGGCAATCC+TGG - chr5.1:75838643-75838662 MS.gene63882:CDS 45.0%
TATTCGATATGTCGAGACGC+GGG - chr5.1:75838112-75838131 MS.gene63882:intron 45.0%
! AGCTGGGATTACACCTTTTG+TGG - chr5.1:75838214-75838233 MS.gene63882:CDS 45.0%
! ATTACACCTTTTGTGGTGGC+AGG - chr5.1:75838221-75838240 MS.gene63882:CDS 45.0%
! TGGGATTACACCTTTTGTGG+TGG - chr5.1:75838217-75838236 MS.gene63882:CDS 45.0%
! TTACACCTTTTGTGGTGGCA+GGG - chr5.1:75838222-75838241 MS.gene63882:CDS 45.0%
CATGTGATTTCCACAGGAGC+CGG + chr5.1:75837978-75837997 None:intergenic 50.0%
TCAATCCCTGCCACCACAAA+AGG + chr5.1:75838230-75838249 None:intergenic 50.0%
TGTGAGATGTGTGGAGGATC+AGG - chr5.1:75838376-75838395 MS.gene63882:intron 50.0%
AGTACTTGATCCGGCTCCTG+TGG - chr5.1:75837965-75837984 MS.gene63882:intron 55.0%
CGGCTCCTGTGGAAATCACA+TGG - chr5.1:75837976-75837995 MS.gene63882:intron 55.0%
! AGGAGCCGGATCAAGTACTG+TGG + chr5.1:75837964-75837983 None:intergenic 55.0%


Chromosome Type Strat End Strand Name
chr5.1 gene 75837783 75838686 75837783 ID=MS.gene63882
chr5.1 mRNA 75837783 75838686 75837783 ID=MS.gene63882.t1;Parent=MS.gene63882
chr5.1 exon 75838449 75838686 75838449 ID=MS.gene63882.t1.exon1;Parent=MS.gene63882.t1
chr5.1 CDS 75838449 75838686 75838449 ID=cds.MS.gene63882.t1;Parent=MS.gene63882.t1
chr5.1 exon 75838204 75838253 75838204 ID=MS.gene63882.t1.exon2;Parent=MS.gene63882.t1
chr5.1 CDS 75838204 75838253 75838204 ID=cds.MS.gene63882.t1;Parent=MS.gene63882.t1
chr5.1 exon 75838027 75838108 75838027 ID=MS.gene63882.t1.exon3;Parent=MS.gene63882.t1
chr5.1 CDS 75838027 75838108 75838027 ID=cds.MS.gene63882.t1;Parent=MS.gene63882.t1
chr5.1 exon 75837783 75837829 75837783 ID=MS.gene63882.t1.exon4;Parent=MS.gene63882.t1
chr5.1 CDS 75837783 75837829 75837783 ID=cds.MS.gene63882.t1;Parent=MS.gene63882.t1
Gene Sequence

>MS.gene63882

ATGGAAGCTTTAGTTTGTTGTTCTCTGCCTTCTTTAACTATTGCCAAAGCTAGGAACATAGTAACACATAATTGTTGTTCCTTACCAGTGAGAAAAAGCTGTGATTTTGGGGTTAAGAATGCAAGAACAACAACAAAAAGAAGAACAAGGGTAGGTGTTGTGTCTGTGAGTGATGTAACCACAGTACTTGATCCGGCTCCTGTGGAAATCACATGGCAAATTGTGGTTGGAACTATAGGTAATATCTTGTTTACTTTAATGTTAATCTATTTAGAAAGAGAATGACTAGTCTAGTTAATTTAGCTCACATGGTAAAAAAATTGTATAGATATTCGATATGTCGAGACGCGGGTTCTAACTCGTAAGTACTTAGTATTGTATTGTGTTATTTGAGTTTTTGATTTTGAGTGTTTTATTGTTTTGAAATTTGTAGCTGGGATTACACCTTTTGTGGTGGCAGGGATTGAATTTAGCAAGAGAATTGTAAGTCACTTTATTTGCTTGATTATTGCTTTCTCATAAATTATGAATCTCATTCTTGTGTGTTTTTTGTCATCAATTTTGAATATTTGTTACAGATTGCTCAAAAAAAATGTGAGATGTGTGGAGGATCAGGACTTGTTTTTAGGGATAAGAACTATTTTCGGTGTCCAGAATGTGGTATGTTTATTGAATTCTCTTAATCTTGATTATAAGCATTATTATCATCATTTTGATCATGCTTTAGTTTAAAATGACAATTAGAAACTTGCTACTTCTCATTGATTTTTTTGGTTCTCAAATATTTAAGGTAAGTTAATTACTTGTGTGAAATCGATTGCCTCACAAATCATTTCTTCATATGCTATATATTTCAGGTGGATTTCTTCCTTGGCAATCCTGGAAAAGATTCTTCTCCAGTTAA

Protein sequence

>MS.gene63882.t1

MEALVCCSLPSLTIAKARNIVTHNCCSLPVRKSCDFGVKNARTTTKRRTRVGVVSVSDVTTVLDPAPVEITWQIVVGTIAGITPFVVAGIEFSKRIIAQKKCEMCGGSGLVFRDKNYFRCPECGGFLPWQSWKRFFSS