AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene53795

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene53795.t1 MTR_0268s0080 98.788 330 4 0 1 330 1 330 0.0 678
MS.gene53795.t1 MTR_1g050472 98.182 330 6 0 1 330 1 330 0.0 672
MS.gene53795.t1 MTR_7g029110 97.879 330 7 0 1 330 1 330 0.0 670
MS.gene53795.t1 MTR_8g469010 92.727 330 19 1 1 330 1 325 0.0 637
MS.gene53795.t1 MTR_4g117370 76.615 325 75 1 6 330 18 341 0.0 531
MS.gene53795.t1 MTR_6g005270 67.442 43 14 0 265 307 25 67 1.54e-13 65.5
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene53795.t1 AT3G27060 83.735 332 52 2 1 330 1 332 0.0 558
MS.gene53795.t1 AT3G23580 76.615 325 75 1 6 330 18 341 0.0 518

Find 60 sgRNAs with CRISPR-Local

Find 79 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTTGTACATTTCCCAGATTT+TGG 0.151339 7.2:-70179433 None:intergenic
CATTCCATGTATCGCGAAAA+AGG 0.263160 7.2:+70179767 MS.gene53795:CDS
ATTTGTTGCTGATAGATTAT+TGG 0.266016 7.2:+70180142 MS.gene53795:CDS
CAATCCAATACCCCAAAATC+TGG 0.320986 7.2:+70179421 MS.gene53795:CDS
TGCAATCTGGAAACCGTAAA+AGG 0.337118 7.2:-70179649 None:intergenic
AGGCTGATTGGGCGATGAAA+TGG 0.358474 7.2:+70179787 MS.gene53795:CDS
TTTGTTGCTGATAGATTATT+GGG 0.363819 7.2:+70180143 MS.gene53795:CDS
GGTGCGAGAAGTGGTTCTTC+TGG 0.368731 7.2:-70179372 None:intergenic
GTTGCATTTGCTTGTGTAGA+AGG 0.373024 7.2:+70179843 MS.gene53795:CDS
ATTTCTTTGAGAAGCGAGTT+GGG 0.385241 7.2:+70180246 MS.gene53795:CDS
ACCGTAAAAGGCTCGTGCTT+CGG 0.385674 7.2:-70179637 None:intergenic
ATGTTCAGAATCCGTTTGAT+TGG 0.390491 7.2:+70180192 MS.gene53795:CDS
GAAAATCGCGCAGAAGCTTC+CGG 0.409737 7.2:-70179877 None:intergenic
AGGCTCGTGCTTCGGAGACT+TGG 0.439806 7.2:-70179629 None:intergenic
ATACAGAATCGGTCTGGGTT+TGG 0.441730 7.2:-70179393 None:intergenic
GCCTTCTTCGCCGCCTCAGA+CGG 0.442189 7.2:+70179564 MS.gene53795:CDS
TCAGAATCCGTTTGATTGGA+TGG 0.443597 7.2:+70180196 MS.gene53795:CDS
CTGTTATGAATAGCTTGAAT+GGG 0.453833 7.2:+70180285 MS.gene53795:CDS
TCCGTCTGAGGCGGCGAAGA+AGG 0.458076 7.2:-70179565 None:intergenic
TCTGTTATGAATAGCTTGAA+TGG 0.458759 7.2:+70180284 MS.gene53795:CDS
CGACGCGCTTCCTTGCGCGT+TGG 0.462960 7.2:+70180082 MS.gene53795:CDS
GCGCTTCCTTGCGCGTTGGT+TGG 0.468741 7.2:+70180086 MS.gene53795:CDS
CGAAATAAGCTCGTTTGAGA+AGG 0.470666 7.2:-70179934 None:intergenic
GGCGGTCCAGAATGAGGCTT+CGG 0.476778 7.2:-70179460 None:intergenic
ATGGAATTGATTTCGCTTCA+AGG 0.479094 7.2:+70180215 MS.gene53795:CDS
ATCAATTCCATCCAATCAAA+CGG 0.480364 7.2:-70180203 None:intergenic
GGAGGAAAGATCGACTTCTT+CGG 0.499480 7.2:-70179481 None:intergenic
AATTTCTTTGAGAAGCGAGT+TGG 0.501037 7.2:+70180245 MS.gene53795:CDS
GGGAACATACAGAATCGGTC+TGG 0.504168 7.2:-70179399 None:intergenic
AGTGGTTCTTCTGGAAAAGC+AGG 0.510370 7.2:-70179363 None:intergenic
GATAGATTATTGGGTGAACT+TGG 0.513434 7.2:+70180152 MS.gene53795:CDS
GTTGTTCCAGTGCTTGAGAT+CGG 0.515525 7.2:-70179502 None:intergenic
GGAACATACAGAATCGGTCT+GGG 0.519029 7.2:-70179398 None:intergenic
TTCTTCGGCGGTCCAGAATG+AGG 0.524296 7.2:-70179466 None:intergenic
GCAATGCTGTTGAAATTGAA+AGG 0.535339 7.2:+70180048 MS.gene53795:CDS
TTCGAGGACAATTCCGTCTG+AGG 0.536756 7.2:-70179577 None:intergenic
TTTCCTCCGATCTCAAGCAC+TGG 0.537267 7.2:+70179496 MS.gene53795:CDS
TCTGGGTTTGGTGCGAGAAG+TGG 0.546005 7.2:-70179381 None:intergenic
TGCGCGTTGGTTGGTATGAA+CGG 0.549799 7.2:+70180095 MS.gene53795:CDS
TGGAATTGATTTCGCTTCAA+GGG 0.551257 7.2:+70180216 MS.gene53795:CDS
CAAGGACGTGTGAGATGAAG+TGG 0.552828 7.2:-70179542 None:intergenic
GGATTGGGAACATACAGAAT+CGG 0.556653 7.2:-70179404 None:intergenic
AATCCAATACCCCAAAATCT+GGG 0.556684 7.2:+70179422 MS.gene53795:CDS
GAGCTTATTTCGCGTGACGA+AGG 0.562239 7.2:+70179945 MS.gene53795:CDS
CAATGCTGTTGAAATTGAAA+GGG 0.563996 7.2:+70180049 MS.gene53795:CDS
ATTGTCCTCGAAAATCTCGC+TGG 0.568595 7.2:+70179588 MS.gene53795:CDS
CACTGGAACAACCTCACAGA+CGG 0.586656 7.2:+70179513 MS.gene53795:CDS
TCGTTTGAGAAGGTTAATCC+CGG 0.587906 7.2:-70179924 None:intergenic
CTGAGGCGGCGAAGAAGGCA+AGG 0.588500 7.2:-70179560 None:intergenic
AATCGCTTATATATGTCTCA+AGG 0.594122 7.2:-70179707 None:intergenic
TTCATACCAACCAACGCGCA+AGG 0.601918 7.2:-70180092 None:intergenic
GAGGACAATTCCGTCTGAGG+CGG 0.603534 7.2:-70179574 None:intergenic
ATGAATAGCTTGAATGGGAA+TGG 0.603815 7.2:+70180290 MS.gene53795:CDS
TTTCTTTGAGAAGCGAGTTG+GGG 0.604666 7.2:+70180247 MS.gene53795:CDS
ACTAACTTCAGAGCGTGTGA+AGG 0.618034 7.2:+70180016 MS.gene53795:CDS
GTTCCAGTGCTTGAGATCGG+AGG 0.623496 7.2:-70179499 None:intergenic
GGAAAGATCGACTTCTTCGG+CGG 0.687608 7.2:-70179478 None:intergenic
AGTGGCGTTCGCCGTCTGTG+AGG 0.694180 7.2:-70179524 None:intergenic
GAAGAGAATACATCTCAGAG+TGG 0.694344 7.2:-70179683 None:intergenic
GCGTTGGTTGGTATGAACGG+TGG 0.700772 7.2:+70180098 MS.gene53795:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! TTTGTTGCTGATAGATTATT+GGG + chr7.2:70180143-70180162 MS.gene53795:CDS 25.0%
!! ATTTGTTGCTGATAGATTAT+TGG + chr7.2:70180142-70180161 MS.gene53795:CDS 25.0%
AATCGCTTATATATGTCTCA+AGG - chr7.2:70179710-70179729 None:intergenic 30.0%
ATCAATTCCATCCAATCAAA+CGG - chr7.2:70180206-70180225 None:intergenic 30.0%
CAATGCTGTTGAAATTGAAA+GGG + chr7.2:70180049-70180068 MS.gene53795:CDS 30.0%
CTGTTATGAATAGCTTGAAT+GGG + chr7.2:70180285-70180304 MS.gene53795:CDS 30.0%
TCTGTTATGAATAGCTTGAA+TGG + chr7.2:70180284-70180303 MS.gene53795:CDS 30.0%
! GGATATTTTCAATTGCAATC+TGG - chr7.2:70179665-70179684 None:intergenic 30.0%
! TTGTACATTTCCCAGATTTT+GGG - chr7.2:70179435-70179454 None:intergenic 30.0%
! TTTGTACATTTCCCAGATTT+TGG - chr7.2:70179436-70179455 None:intergenic 30.0%
!!! ATTTTCTGGTTGAAAAAACG+TGG + chr7.2:70179894-70179913 MS.gene53795:CDS 30.0%
!!! TGCTGATTTTTGCTTTAGTT+TGG + chr7.2:70180316-70180335 MS.gene53795:CDS 30.0%
AAAAAACGTGGTTTAATGCC+GGG + chr7.2:70179906-70179925 MS.gene53795:CDS 35.0%
AATCCAATACCCCAAAATCT+GGG + chr7.2:70179422-70179441 MS.gene53795:CDS 35.0%
ATGAATAGCTTGAATGGGAA+TGG + chr7.2:70180290-70180309 MS.gene53795:CDS 35.0%
ATGTTCAGAATCCGTTTGAT+TGG + chr7.2:70180192-70180211 MS.gene53795:CDS 35.0%
GAAAAAACGTGGTTTAATGC+CGG + chr7.2:70179905-70179924 MS.gene53795:CDS 35.0%
GATAGATTATTGGGTGAACT+TGG + chr7.2:70180152-70180171 MS.gene53795:CDS 35.0%
GCAATGCTGTTGAAATTGAA+AGG + chr7.2:70180048-70180067 MS.gene53795:CDS 35.0%
! AATTTCTTTGAGAAGCGAGT+TGG + chr7.2:70180245-70180264 MS.gene53795:CDS 35.0%
! ATGGAATTGATTTCGCTTCA+AGG + chr7.2:70180215-70180234 MS.gene53795:CDS 35.0%
! ATTTCTTTGAGAAGCGAGTT+GGG + chr7.2:70180246-70180265 MS.gene53795:CDS 35.0%
! GTAGAAGGAATTTTCTTCTC+CGG + chr7.2:70179858-70179877 MS.gene53795:CDS 35.0%
! TGGAATTGATTTCGCTTCAA+GGG + chr7.2:70180216-70180235 MS.gene53795:CDS 35.0%
! TGTACATTTCCCAGATTTTG+GGG - chr7.2:70179434-70179453 None:intergenic 35.0%
!!! AGATTTTGGGGTATTGGATT+GGG - chr7.2:70179422-70179441 None:intergenic 35.0%
CAATCCAATACCCCAAAATC+TGG + chr7.2:70179421-70179440 MS.gene53795:CDS 40.0%
CATTCCATGTATCGCGAAAA+AGG + chr7.2:70179767-70179786 MS.gene53795:CDS 40.0%
CGAAATAAGCTCGTTTGAGA+AGG - chr7.2:70179937-70179956 None:intergenic 40.0%
GAAGAGAATACATCTCAGAG+TGG - chr7.2:70179686-70179705 None:intergenic 40.0%
GGATTGGGAACATACAGAAT+CGG - chr7.2:70179407-70179426 None:intergenic 40.0%
GTTGCATTTGCTTGTGTAGA+AGG + chr7.2:70179843-70179862 MS.gene53795:CDS 40.0%
TATCGCGAAAAAGGCTGATT+GGG + chr7.2:70179776-70179795 MS.gene53795:CDS 40.0%
TCAGAATCCGTTTGATTGGA+TGG + chr7.2:70180196-70180215 MS.gene53795:CDS 40.0%
TCGTTTGAGAAGGTTAATCC+CGG - chr7.2:70179927-70179946 None:intergenic 40.0%
TGCAATCTGGAAACCGTAAA+AGG - chr7.2:70179652-70179671 None:intergenic 40.0%
! TTTCTTTGAGAAGCGAGTTG+GGG + chr7.2:70180247-70180266 MS.gene53795:CDS 40.0%
!! CTTTTTCGCGATACATGGAA+TGG - chr7.2:70179769-70179788 None:intergenic 40.0%
!!! CAGATTTTGGGGTATTGGAT+TGG - chr7.2:70179423-70179442 None:intergenic 40.0%
!!! TTTCCCAGATTTTGGGGTAT+TGG - chr7.2:70179428-70179447 None:intergenic 40.0%
AAAAAGCCGAAGCCTCATTC+TGG + chr7.2:70179454-70179473 MS.gene53795:CDS 45.0%
ACTAACTTCAGAGCGTGTGA+AGG + chr7.2:70180016-70180035 MS.gene53795:CDS 45.0%
ATACAGAATCGGTCTGGGTT+TGG - chr7.2:70179396-70179415 None:intergenic 45.0%
ATTGTCCTCGAAAATCTCGC+TGG + chr7.2:70179588-70179607 MS.gene53795:CDS 45.0%
GGAACATACAGAATCGGTCT+GGG - chr7.2:70179401-70179420 None:intergenic 45.0%
GTATCGCGAAAAAGGCTGAT+TGG + chr7.2:70179775-70179794 MS.gene53795:CDS 45.0%
GTTGTTCCAGTGCTTGAGAT+CGG - chr7.2:70179505-70179524 None:intergenic 45.0%
! AGTGGTTCTTCTGGAAAAGC+AGG - chr7.2:70179366-70179385 None:intergenic 45.0%
! ATCTTCCAGCGAGATTTTCG+AGG - chr7.2:70179596-70179615 None:intergenic 45.0%
! GGAGGAAAGATCGACTTCTT+CGG - chr7.2:70179484-70179503 None:intergenic 45.0%
!! TCAGCCTTTTTCGCGATACA+TGG - chr7.2:70179774-70179793 None:intergenic 45.0%
ACCGTAAAAGGCTCGTGCTT+CGG - chr7.2:70179640-70179659 None:intergenic 50.0%
AGGCTGATTGGGCGATGAAA+TGG + chr7.2:70179787-70179806 MS.gene53795:CDS 50.0%
CAAGGACGTGTGAGATGAAG+TGG - chr7.2:70179545-70179564 None:intergenic 50.0%
CACTGGAACAACCTCACAGA+CGG + chr7.2:70179513-70179532 MS.gene53795:CDS 50.0%
GAAAATCGCGCAGAAGCTTC+CGG - chr7.2:70179880-70179899 None:intergenic 50.0%
GAGCTTATTTCGCGTGACGA+AGG + chr7.2:70179945-70179964 MS.gene53795:CDS 50.0%
GGGAACATACAGAATCGGTC+TGG - chr7.2:70179402-70179421 None:intergenic 50.0%
TTCATACCAACCAACGCGCA+AGG - chr7.2:70180095-70180114 None:intergenic 50.0%
TTCGAGGACAATTCCGTCTG+AGG - chr7.2:70179580-70179599 None:intergenic 50.0%
TTTCCTCCGATCTCAAGCAC+TGG + chr7.2:70179496-70179515 MS.gene53795:CDS 50.0%
! GAAGCTTCTGCGCGATTTTC+TGG + chr7.2:70179880-70179899 MS.gene53795:CDS 50.0%
! GGAAAGATCGACTTCTTCGG+CGG - chr7.2:70179481-70179500 None:intergenic 50.0%
! TCCGAAGCACGAGCCTTTTA+CGG + chr7.2:70179636-70179655 MS.gene53795:CDS 50.0%
!! TGCGCGTTGGTTGGTATGAA+CGG + chr7.2:70180095-70180114 MS.gene53795:CDS 50.0%
GAGGACAATTCCGTCTGAGG+CGG - chr7.2:70179577-70179596 None:intergenic 55.0%
GGTGCGAGAAGTGGTTCTTC+TGG - chr7.2:70179375-70179394 None:intergenic 55.0%
GTTCCAGTGCTTGAGATCGG+AGG - chr7.2:70179502-70179521 None:intergenic 55.0%
TTCTTCGGCGGTCCAGAATG+AGG - chr7.2:70179469-70179488 None:intergenic 55.0%
!! GCGTTGGTTGGTATGAACGG+TGG + chr7.2:70180098-70180117 MS.gene53795:CDS 55.0%
!! TCTGGGTTTGGTGCGAGAAG+TGG - chr7.2:70179384-70179403 None:intergenic 55.0%
AGGCTCGTGCTTCGGAGACT+TGG - chr7.2:70179632-70179651 None:intergenic 60.0%
GGCGGTCCAGAATGAGGCTT+CGG - chr7.2:70179463-70179482 None:intergenic 60.0%
AGTGGCGTTCGCCGTCTGTG+AGG - chr7.2:70179527-70179546 None:intergenic 65.0%
CTGAGGCGGCGAAGAAGGCA+AGG - chr7.2:70179563-70179582 None:intergenic 65.0%
GCCTTCTTCGCCGCCTCAGA+CGG + chr7.2:70179564-70179583 MS.gene53795:CDS 65.0%
! GCGCTTCCTTGCGCGTTGGT+TGG + chr7.2:70180086-70180105 MS.gene53795:CDS 65.0%
! TCCGTCTGAGGCGGCGAAGA+AGG - chr7.2:70179568-70179587 None:intergenic 65.0%
CGACGCGCTTCCTTGCGCGT+TGG + chr7.2:70180082-70180101 MS.gene53795:CDS 70.0%


Chromosome Type Strat End Strand Name
chr7.2 gene 70179360 70180352 70179360 ID=MS.gene53795
chr7.2 mRNA 70179360 70180352 70179360 ID=MS.gene53795.t1;Parent=MS.gene53795
chr7.2 exon 70179360 70180352 70179360 ID=MS.gene53795.t1.exon1;Parent=MS.gene53795.t1
chr7.2 CDS 70179360 70180352 70179360 ID=cds.MS.gene53795.t1;Parent=MS.gene53795.t1
Gene Sequence

>MS.gene53795

ATGCCTGCTTTTCCAGAAGAACCACTTCTCGCACCAAACCCAGACCGATTCTGTATGTTCCCAATCCAATACCCCAAAATCTGGGAAATGTACAAAAAAGCCGAAGCCTCATTCTGGACCGCCGAAGAAGTCGATCTTTCCTCCGATCTCAAGCACTGGAACAACCTCACAGACGGCGAACGCCACTTCATCTCACACGTCCTTGCCTTCTTCGCCGCCTCAGACGGAATTGTCCTCGAAAATCTCGCTGGAAGATTCATGAAAGAAGTCCAAGTCTCCGAAGCACGAGCCTTTTACGGTTTCCAGATTGCAATTGAAAATATCCACTCTGAGATGTATTCTCTTCTCCTTGAGACATATATAAGCGATTCTGCTGAAAAGAATCGCTTATTTCACGCAATTGAAACCATTCCATGTATCGCGAAAAAGGCTGATTGGGCGATGAAATGGATCGATTCAAGCGATTCTTTTGCAGAAAGAATTGTTGCATTTGCTTGTGTAGAAGGAATTTTCTTCTCCGGAAGCTTCTGCGCGATTTTCTGGTTGAAAAAACGTGGTTTAATGCCGGGATTAACCTTCTCAAACGAGCTTATTTCGCGTGACGAAGGTCTACATTGTGATTTTGCTTGTTTGTTATACTCACTTCTACGCAAGAAACTAACTTCAGAGCGTGTGAAGGAAATTGTATGCAATGCTGTTGAAATTGAAAGGGAATTTGTCTGCGACGCGCTTCCTTGCGCGTTGGTTGGTATGAACGGTGGATTGATGAGTACTTATATTGAATTTGTTGCTGATAGATTATTGGGTGAACTTGGTTGTGAAAAAGTTTATAATGTTCAGAATCCGTTTGATTGGATGGAATTGATTTCGCTTCAAGGGAAGACGAATTTCTTTGAGAAGCGAGTTGGGGAGTATCAGAAAGCTTCTGTTATGAATAGCTTGAATGGGAATGGTGCTGCTGATTTTTGCTTTAGTTTGGATGAAGATTTTTAG
Protein sequence

>MS.gene53795.t1

MPAFPEEPLLAPNPDRFCMFPIQYPKIWEMYKKAEASFWTAEEVDLSSDLKHWNNLTDGERHFISHVLAFFAASDGIVLENLAGRFMKEVQVSEARAFYGFQIAIENIHSEMYSLLLETYISDSAEKNRLFHAIETIPCIAKKADWAMKWIDSSDSFAERIVAFACVEGIFFSGSFCAIFWLKKRGLMPGLTFSNELISRDEGLHCDFACLLYSLLRKKLTSERVKEIVCNAVEIEREFVCDALPCALVGMNGGLMSTYIEFVADRLLGELGCEKVYNVQNPFDWMELISLQGKTNFFEKRVGEYQKASVMNSLNGNGAADFCFSLDEDF