AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene049263

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene049263.t1 MTR_8g461300 81.026 195 23 5 53 236 9 200 1.68e-108 311
MS.gene049263.t1 MTR_4g055800 49.388 245 90 10 1 234 71 292 2.08e-57 184
MS.gene049263.t1 MTR_3g080680 40.367 218 98 8 26 234 4 198 4.59e-33 119
MS.gene049263.t1 MTR_3g082420 39.744 234 115 8 8 234 7 221 2.68e-30 112
MS.gene049263.t1 MTR_3g082340 39.506 162 92 4 75 234 65 222 8.22e-24 95.5
MS.gene049263.t1 MTR_3g083030 36.910 233 108 14 14 235 26 230 2.64e-21 89.0
MS.gene049263.t1 MTR_3g083050 35.912 181 92 9 63 235 43 207 3.48e-17 77.4
MS.gene049263.t1 MTR_3g083080 34.500 200 108 10 43 234 21 205 4.29e-17 77.4
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 55 sgRNAs with CRISPR-Local

Find 66 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GCTTAAATCGGAACCGTATT+TGG 0.084140 3.3:-80049820 MS.gene049263:CDS
CACACTTTCTTCGCAGAATT+TGG 0.126426 3.3:+80049878 None:intergenic
TTCGATTTCGGTTCCTGTTC+CGG 0.247494 3.3:+80049846 None:intergenic
GATTTAAGCCGTTTCGATTT+CGG 0.271164 3.3:+80049834 None:intergenic
CTTAAATCGGAACCGTATTT+GGG 0.330165 3.3:-80049819 MS.gene049263:CDS
TCACGACGCTTATACCAAAA+TGG 0.333746 3.3:+80049651 None:intergenic
TCACTATACTCAGAATCTTC+TGG 0.339930 3.3:+80049717 None:intergenic
TGGTTCTATGTATACGAATA+AGG 0.367166 3.3:-80049628 MS.gene049263:CDS
CTACTTCTTTATATGCTCCT+AGG 0.380060 3.3:-80049279 MS.gene049263:CDS
CCGTATTTGGGATCGGGATC+GGG 0.382770 3.3:-80049807 MS.gene049263:CDS
TGTGAAATCGGAACCGGAAC+AGG 0.406008 3.3:-80049859 MS.gene049263:CDS
ATGACACACTCTTTGACAAC+AGG 0.418178 3.3:+80049148 None:intergenic
GAAATCGAAACGGCTTAAAT+CGG 0.418268 3.3:-80049832 MS.gene049263:CDS
CCCGATCCCGATCCCAAATA+CGG 0.434354 3.3:+80049807 None:intergenic
CACTGTCCACCAGGTTGTGC+TGG 0.442305 3.3:-80049454 MS.gene049263:CDS
CTGCGAAGAAAGTGTGAAAT+CGG 0.443953 3.3:-80049871 MS.gene049263:CDS
GGAGGACAAACGGCTGAAAT+CGG 0.447703 3.3:-80049742 MS.gene049263:CDS
ACCGTATTTGGGATCGGGAT+CGG 0.451395 3.3:-80049808 MS.gene049263:CDS
ACTTTATGAAACACAAAGGT+TGG 0.454208 3.3:+80049325 None:intergenic
TACGCTGAAGTACATGAGTC+TGG 0.463215 3.3:+80049182 None:intergenic
CAATCAAAATAATATTAAGC+AGG 0.465295 3.3:-80049350 MS.gene049263:CDS
TTCATCTGAGGAGGAGGAGG+AGG 0.472966 3.3:-80049766 MS.gene049263:CDS
TCGGAACCGTATTTGGGATC+GGG 0.479730 3.3:-80049813 MS.gene049263:CDS
ATCGGAACCGTATTTGGGAT+CGG 0.506992 3.3:-80049814 MS.gene049263:CDS
AGATTCATCTGAGGAGGAGG+AGG 0.525846 3.3:-80049769 MS.gene049263:CDS
AGAAAGTGTGAAATCGGAAC+CGG 0.531108 3.3:-80049865 MS.gene049263:CDS
GTTGTCAAGTGTACCCATCC+TGG 0.532074 3.3:-80049304 MS.gene049263:CDS
GTAGTGTTTCAAAATGTCGA+TGG 0.539331 3.3:-80049913 None:intergenic
ATCTTCATCGGTTAAGTCGA+GGG 0.545269 3.3:+80049420 None:intergenic
TACTTCTTTATATGCTCCTA+GGG 0.547879 3.3:-80049278 MS.gene049263:CDS
AACAGGAACCGAAATCGAAA+CGG 0.558710 3.3:-80049842 MS.gene049263:CDS
GATGCTATCCACTGTCCACC+AGG 0.563532 3.3:-80049463 MS.gene049263:CDS
GCATATAAAGAAGTAGCACC+AGG 0.567371 3.3:+80049286 None:intergenic
GTATACGAATAAGGCTTGGA+AGG 0.568027 3.3:-80049619 MS.gene049263:CDS
TGAAGATTCATCTGAGGAGG+AGG 0.568516 3.3:-80049772 MS.gene049263:CDS
CTTCAAAGCAGCATTGCAGA+GGG 0.572155 3.3:+80049378 None:intergenic
AAAGTAATGTAATACGCCCT+AGG 0.574461 3.3:+80049262 None:intergenic
TGTCCACCAGGTTGTGCTGG+CGG 0.578846 3.3:-80049451 MS.gene049263:CDS
CTATGTATACGAATAAGGCT+TGG 0.579383 3.3:-80049623 MS.gene049263:CDS
TAAAGAAGTAGCACCAGGAT+GGG 0.590468 3.3:+80049291 None:intergenic
AGTAGGGAGCACATCTTCAT+CGG 0.590789 3.3:+80049408 None:intergenic
AATCAAAATAATATTAAGCA+GGG 0.591058 3.3:-80049349 MS.gene049263:CDS
CGATGAAGATTCATCTGAGG+AGG 0.599534 3.3:-80049775 MS.gene049263:CDS
ACAATACCGCCAGCACAACC+TGG 0.600366 3.3:+80049445 None:intergenic
CATCTTCATCGGTTAAGTCG+AGG 0.606603 3.3:+80049419 None:intergenic
TCTTCAAAGCAGCATTGCAG+AGG 0.609112 3.3:+80049377 None:intergenic
ATAAAGAAGTAGCACCAGGA+TGG 0.610411 3.3:+80049290 None:intergenic
GACAACTTTATGAAACACAA+AGG 0.610440 3.3:+80049321 None:intergenic
AAAGTTGTTAGAGCACGAGC+AGG 0.617312 3.3:+80049205 None:intergenic
ACACGATGAAGATTCATCTG+AGG 0.634373 3.3:-80049778 MS.gene049263:CDS
CAGCACAACCTGGTGGACAG+TGG 0.663371 3.3:+80049455 None:intergenic
TAAGGCTTGGAAGGATCGTG+AGG 0.666952 3.3:-80049610 MS.gene049263:CDS
TCTTCATCGGTTAAGTCGAG+GGG 0.670562 3.3:+80049421 None:intergenic
TGAGTATAGTGATGAAGACG+AGG 0.686862 3.3:-80049706 MS.gene049263:CDS
ATACCGCCAGCACAACCTGG+TGG 0.701849 3.3:+80049448 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AATCAAAATAATATTAAGCA+GGG - chr3.3:80049686-80049705 MS.gene049263:CDS 15.0%
!! CAATCAAAATAATATTAAGC+AGG - chr3.3:80049685-80049704 MS.gene049263:CDS 20.0%
! AGCAAAAGCTAAAAAGAAAA+AGG - chr3.3:80049799-80049818 MS.gene049263:CDS 25.0%
! GCAAAAGCTAAAAAGAAAAA+GGG - chr3.3:80049800-80049819 MS.gene049263:CDS 25.0%
!!! CTTAATTTTGATTGATTTGC+AGG - chr3.3:80049544-80049563 MS.gene049263:intron 25.0%
AAAGCTAAAAAGAAAAAGGG+AGG - chr3.3:80049803-80049822 MS.gene049263:CDS 30.0%
ACTTTATGAAACACAAAGGT+TGG + chr3.3:80049713-80049732 None:intergenic 30.0%
GACAACTTTATGAAACACAA+AGG + chr3.3:80049717-80049736 None:intergenic 30.0%
TACTTCTTTATATGCTCCTA+GGG - chr3.3:80049757-80049776 MS.gene049263:CDS 30.0%
! ACAATGACAGTTTTCCATTT+TGG - chr3.3:80049370-80049389 MS.gene049263:CDS 30.0%
! TGGTTCTATGTATACGAATA+AGG - chr3.3:80049407-80049426 MS.gene049263:CDS 30.0%
AAAGTAATGTAATACGCCCT+AGG + chr3.3:80049776-80049795 None:intergenic 35.0%
CTACTTCTTTATATGCTCCT+AGG - chr3.3:80049756-80049775 MS.gene049263:CDS 35.0%
CTATGTATACGAATAAGGCT+TGG - chr3.3:80049412-80049431 MS.gene049263:CDS 35.0%
CTTAAATCGGAACCGTATTT+GGG - chr3.3:80049216-80049235 MS.gene049263:CDS 35.0%
GAAATCGAAACGGCTTAAAT+CGG - chr3.3:80049203-80049222 MS.gene049263:CDS 35.0%
GATTTAAGCCGTTTCGATTT+CGG + chr3.3:80049204-80049223 None:intergenic 35.0%
TCACTATACTCAGAATCTTC+TGG + chr3.3:80049321-80049340 None:intergenic 35.0%
AACAGGAACCGAAATCGAAA+CGG - chr3.3:80049193-80049212 MS.gene049263:CDS 40.0%
ACACGATGAAGATTCATCTG+AGG - chr3.3:80049257-80049276 MS.gene049263:CDS 40.0%
ATAAAGAAGTAGCACCAGGA+TGG + chr3.3:80049748-80049767 None:intergenic 40.0%
ATGACACACTCTTTGACAAC+AGG + chr3.3:80049890-80049909 None:intergenic 40.0%
CACACTTTCTTCGCAGAATT+TGG + chr3.3:80049160-80049179 None:intergenic 40.0%
GCATATAAAGAAGTAGCACC+AGG + chr3.3:80049752-80049771 None:intergenic 40.0%
GCTTAAATCGGAACCGTATT+TGG - chr3.3:80049215-80049234 MS.gene049263:CDS 40.0%
GTATACGAATAAGGCTTGGA+AGG - chr3.3:80049416-80049435 MS.gene049263:CDS 40.0%
TAAAGAAGTAGCACCAGGAT+GGG + chr3.3:80049747-80049766 None:intergenic 40.0%
TCACGACGCTTATACCAAAA+TGG + chr3.3:80049387-80049406 None:intergenic 40.0%
TGAGTATAGTGATGAAGACG+AGG - chr3.3:80049329-80049348 MS.gene049263:CDS 40.0%
! AGAAAGTGTGAAATCGGAAC+CGG - chr3.3:80049170-80049189 MS.gene049263:CDS 40.0%
! ATCTTCATCGGTTAAGTCGA+GGG + chr3.3:80049618-80049637 None:intergenic 40.0%
! CTGCGAAGAAAGTGTGAAAT+CGG - chr3.3:80049164-80049183 MS.gene049263:CDS 40.0%
!! TTTTGGTATAAGCGTCGTGA+TGG - chr3.3:80049387-80049406 MS.gene049263:CDS 40.0%
AAAGTTGTTAGAGCACGAGC+AGG + chr3.3:80049833-80049852 None:intergenic 45.0%
CGATGAAGATTCATCTGAGG+AGG - chr3.3:80049260-80049279 MS.gene049263:CDS 45.0%
CTTCAAAGCAGCATTGCAGA+GGG + chr3.3:80049660-80049679 None:intergenic 45.0%
TACGCTGAAGTACATGAGTC+TGG + chr3.3:80049856-80049875 None:intergenic 45.0%
TCTTCAAAGCAGCATTGCAG+AGG + chr3.3:80049661-80049680 None:intergenic 45.0%
TGAAGATTCATCTGAGGAGG+AGG - chr3.3:80049263-80049282 MS.gene049263:CDS 45.0%
TTCGATTTCGGTTCCTGTTC+CGG + chr3.3:80049192-80049211 None:intergenic 45.0%
! AGTAGGGAGCACATCTTCAT+CGG + chr3.3:80049630-80049649 None:intergenic 45.0%
! ATCGGAACCGTATTTGGGAT+CGG - chr3.3:80049221-80049240 MS.gene049263:CDS 45.0%
! CATCTTCATCGGTTAAGTCG+AGG + chr3.3:80049619-80049638 None:intergenic 45.0%
! TCTTCATCGGTTAAGTCGAG+GGG + chr3.3:80049617-80049636 None:intergenic 45.0%
!!! TGCAGAGGGTTTTGAGAGTA+GGG + chr3.3:80049646-80049665 None:intergenic 45.0%
!!! TTGCAGAGGGTTTTGAGAGT+AGG + chr3.3:80049647-80049666 None:intergenic 45.0%
AGATTCATCTGAGGAGGAGG+AGG - chr3.3:80049266-80049285 MS.gene049263:CDS 50.0%
CGCTCTAGCGAACTAAGTGT+AGG - chr3.3:80049471-80049490 MS.gene049263:CDS 50.0%
GGAGGACAAACGGCTGAAAT+CGG - chr3.3:80049293-80049312 MS.gene049263:CDS 50.0%
GTTGTCAAGTGTACCCATCC+TGG - chr3.3:80049731-80049750 MS.gene049263:CDS 50.0%
TAAGGCTTGGAAGGATCGTG+AGG - chr3.3:80049425-80049444 MS.gene049263:CDS 50.0%
TGTGAAATCGGAACCGGAAC+AGG - chr3.3:80049176-80049195 MS.gene049263:CDS 50.0%
! ACCGTATTTGGGATCGGGAT+CGG - chr3.3:80049227-80049246 MS.gene049263:CDS 50.0%
! TCGGAACCGTATTTGGGATC+GGG - chr3.3:80049222-80049241 MS.gene049263:CDS 50.0%
ACAATACCGCCAGCACAACC+TGG + chr3.3:80049593-80049612 None:intergenic 55.0%
AGGAGGAGGAGGAGGACAAA+CGG - chr3.3:80049283-80049302 MS.gene049263:CDS 55.0%
CCCGATCCCGATCCCAAATA+CGG + chr3.3:80049231-80049250 None:intergenic 55.0%
GATGCTATCCACTGTCCACC+AGG - chr3.3:80049572-80049591 MS.gene049263:CDS 55.0%
TTCATCTGAGGAGGAGGAGG+AGG - chr3.3:80049269-80049288 MS.gene049263:CDS 55.0%
! CCGTATTTGGGATCGGGATC+GGG - chr3.3:80049228-80049247 MS.gene049263:CDS 55.0%
ATACCGCCAGCACAACCTGG+TGG + chr3.3:80049590-80049609 None:intergenic 60.0%
ATCTGAGGAGGAGGAGGAGG+AGG - chr3.3:80049272-80049291 MS.gene049263:CDS 60.0%
CACTGTCCACCAGGTTGTGC+TGG - chr3.3:80049581-80049600 MS.gene049263:CDS 60.0%
TGTCCACCAGGTTGTGCTGG+CGG - chr3.3:80049584-80049603 MS.gene049263:CDS 60.0%
! CAGCACAACCTGGTGGACAG+TGG + chr3.3:80049583-80049602 None:intergenic 60.0%
TGAGGAGGAGGAGGAGGAGG+AGG - chr3.3:80049275-80049294 MS.gene049263:CDS 65.0%


Chromosome Type Strat End Strand Name
chr3.3 gene 80049135 80049922 80049135 ID=MS.gene049263
chr3.3 mRNA 80049135 80049922 80049135 ID=MS.gene049263.t1;Parent=MS.gene049263
chr3.3 exon 80049569 80049922 80049569 ID=MS.gene049263.t1.exon1;Parent=MS.gene049263.t1
chr3.3 CDS 80049569 80049922 80049569 ID=cds.MS.gene049263.t1;Parent=MS.gene049263.t1
chr3.3 exon 80049135 80049491 80049135 ID=MS.gene049263.t1.exon2;Parent=MS.gene049263.t1
chr3.3 CDS 80049135 80049491 80049135 ID=cds.MS.gene049263.t1;Parent=MS.gene049263.t1
Gene Sequence

>MS.gene049263

ATGTCGATGGAATTGCGCGCAACCAAATTCTGCGAAGAAAGTGTGAAATCGGAACCGGAACAGGAACCGAAATCGAAACGGCTTAAATCGGAACCGTATTTGGGATCGGGATCGGGACAGAAACACGATGAAGATTCATCTGAGGAGGAGGAGGAGGAGGAGGACAAACGGCTGAAATCGGATCCAGAAGATTCTGAGTATAGTGATGAAGACGAGGAGAACTTGTGTGTGCATGACAATGACAGTTTTCCATTTTGGTATAAGCGTCGTGATGGTTCTATGTATACGAATAAGGCTTGGAAGGATCGTGAGGCTCAAATTCTTGACTATAAAAAGCGCTCTAGCGAACTAAGTGTAGGCATCTATCAATTTCAATTTCAATTTCATTTGTTTCACTTATAAACAATCTCTTAATTTTGATTGATTTGCAGGTCTACGATGCTATCCACTGTCCACCAGGTTGTGCTGGCGGTATTGTACCCCTCGACTTAACCGATGAAGATGTGCTCCCTACTCTCAAAACCCTCTGCAATGCTGCTTTGAAGATTTACAATCAAAATAATATTAAGCAGGGTCCAACCTTTGTGTTTCATAAAGTTGTCAAGTGTACCCATCCTGGTGCTACTTCTTTATATGCTCCTAGGGCGTATTACATTACTTTTAAAGCAAAAGCTAAAAAGAAAAAGGGAGGAAGACCTGCTCGTGCTCTAACAACTTTCCAGACTCATGTACTTCAGCGTAAAGATAAAGATCCTGTTGTCAAAGAGTGTGTCATTAAAAATATCTAA
Protein sequence

>MS.gene049263.t1

MSMELRATKFCEESVKSEPEQEPKSKRLKSEPYLGSGSGQKHDEDSSEEEEEEEDKRLKSDPEDSEYSDEDEENLCVHDNDSFPFWYKRRDGSMYTNKAWKDREAQILDYKKRSSELSVYDAIHCPPGCAGGIVPLDLTDEDVLPTLKTLCNAALKIYNQNNIKQGPTFVFHKVVKCTHPGATSLYAPRAYYITFKAKAKKKKGGRPARALTTFQTHVLQRKDKDPVVKECVIKNI