AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene24054


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene24054.t1 MTR_1g068965 99.265 136 1 0 1 136 28 163 1.65e-95 276
MS.gene24054.t1 MTR_4g021290 98.529 136 2 0 1 136 1 136 1.69e-94 273
MS.gene24054.t1 MTR_3g005450 98.529 136 2 0 1 136 1 136 1.69e-94 273
MS.gene24054.t1 MTR_3g005430 98.529 136 2 0 1 136 1 136 1.69e-94 273
MS.gene24054.t1 MTR_7g067490 97.059 136 4 0 1 136 1 136 8.60e-93 268
MS.gene24054.t1 MTR_4g108310 97.368 114 3 0 1 114 1 114 8.02e-76 223
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene24054.t1 AT5G39850 93.382 136 9 0 1 136 1 136 1.88e-88 258
MS.gene24054.t1 AT5G15200 82.667 150 23 1 1 150 1 147 1.96e-85 248
MS.gene24054.t1 AT5G15200 88.235 136 16 0 1 136 1 136 1.08e-83 246

Find 56 sgRNAs with CRISPR-Local

Find 86 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CAGACACTTGTATTCAAATC+TGG 0.328033 1.4:+55071645 MS.gene24054:CDS
GTTTCATAGGGTTGGAAGGC+AGG 0.358634 1.4:+55072342 MS.gene24054:intron
ATCATGCTAGGGTTCTTATC+AGG 0.370005 1.4:+55071685 MS.gene24054:CDS
TTCGGTGCAAGAGGGAGCTT+TGG 0.394293 1.4:+55071424 MS.gene24054:CDS
AACAGACAAGACCATATTAC+AGG 0.419240 1.4:-55072071 None:intergenic
ACAGATTCCTTGCATTGTTA+CGG 0.425233 1.4:-55071473 None:intergenic
TCCCTATGAGAAGGAACGTT+TGG 0.433604 1.4:+55071368 MS.gene24054:CDS
AATGGAGGGCTCCTGTAATA+TGG 0.435184 1.4:+55072060 MS.gene24054:CDS
GGTGAACATCCCATCCTTCA+TGG 0.437604 1.4:+55072366 MS.gene24054:CDS
TCCTTGCATTGTTACGGATA+CGG 0.449433 1.4:-55071467 None:intergenic
ATCCAAACGTTCCTTCTCAT+AGG 0.454177 1.4:-55071370 None:intergenic
GGTGCAAGAGGGAGCTTTGG+AGG 0.455063 1.4:+55071427 MS.gene24054:CDS
AAGATAGATACTCACAGTTC+CGG 0.468521 1.4:-55071220 None:intergenic
TTGAAGCTGGTCGGAGAGTA+CGG 0.474460 1.4:+55071399 MS.gene24054:CDS
TGGTTAAAGTTGCTTTCTAC+CGG 0.476762 1.4:+55071201 MS.gene24054:CDS
GAACCCTCGTCGTATCTTTG+AGG 0.479838 1.4:+55071512 MS.gene24054:CDS
GAACAAACTTGATTATGTCT+TGG 0.487846 1.4:+55071587 MS.gene24054:CDS
CCTAGCATGATGAATGGACT+TGG 0.491509 1.4:-55071673 None:intergenic
TGGTCGGAGAGTACGGTCTT+CGG 0.495090 1.4:+55071406 MS.gene24054:CDS
AACCCTCGTCGTATCTTTGA+GGG 0.518161 1.4:+55071513 MS.gene24054:CDS
CCTCTCCATTGTTCAAGTAA+TGG 0.520401 1.4:+55072042 MS.gene24054:CDS
AAGAACCCTAGCATGATGAA+TGG 0.528751 1.4:-55071679 None:intergenic
TTCTATGTATCGAAGGTAGT+AGG 0.530410 1.4:+55072017 MS.gene24054:CDS
TCAACCCTCACCATGAAGGA+TGG 0.531047 1.4:-55072376 None:intergenic
CCAAGTCCATTCATCATGCT+AGG 0.540233 1.4:+55071673 MS.gene24054:CDS
ACTTGTATTCAAATCTGGTA+TGG 0.540887 1.4:+55071650 MS.gene24054:CDS
CTCCATTGTTCAAGTAATGG+AGG 0.542473 1.4:+55072045 MS.gene24054:CDS
TCCAAACGTTCCTTCTCATA+GGG 0.547779 1.4:-55071369 None:intergenic
GCCCTCCATTACTTGAACAA+TGG 0.548100 1.4:-55072047 None:intergenic
TTTGGTTTCATAGGGTTGGA+AGG 0.553079 1.4:+55072338 MS.gene24054:intron
GTGCAAGAGGGAGCTTTGGA+GGG 0.553805 1.4:+55071428 MS.gene24054:CDS
CAACCCTCACCATGAAGGAT+GGG 0.569875 1.4:-55072375 None:intergenic
TGAATCAACCCTCACCATGA+AGG 0.571223 1.4:-55072380 None:intergenic
TGCAAGGAATCTGTTGACCT+TGG 0.574046 1.4:+55071482 MS.gene24054:CDS
TTATCAGGCAGAGACACATC+AGG 0.576233 1.4:+55071700 MS.gene24054:CDS
AGGGTGAAGCGCTATTGAGA+AGG 0.577811 1.4:+55071532 MS.gene24054:CDS
TTTGGATGCTGAGTTGAAGC+TGG 0.580359 1.4:+55071386 MS.gene24054:CDS
AGTACGGTCTTCGGTGCAAG+AGG 0.589539 1.4:+55071415 MS.gene24054:CDS
CAAGTCCATTCATCATGCTA+GGG 0.590386 1.4:+55071674 MS.gene24054:CDS
CATCCCATCCTTCATGGTGA+GGG 0.593258 1.4:+55072372 MS.gene24054:CDS
TCCATTGTTCAAGTAATGGA+GGG 0.593301 1.4:+55072046 MS.gene24054:CDS
GCCGTATCCGTAACAATGCA+AGG 0.595109 1.4:+55071466 MS.gene24054:CDS
TCATAGGGTTGGAAGGCAGG+TGG 0.599698 1.4:+55072345 MS.gene24054:intron
GCCGCGTCGTCCCTATGAGA+AGG 0.609369 1.4:+55071359 MS.gene24054:CDS
CAATATGTTCTATGTATCGA+AGG 0.609617 1.4:+55072010 MS.gene24054:CDS
ACATCCCATCCTTCATGGTG+AGG 0.616704 1.4:+55072371 MS.gene24054:CDS
ACGAGGGTTCTTCTCATCCA+AGG 0.618972 1.4:-55071499 None:intergenic
TTGAGAAGGATGTTTAAGCA+TGG 0.626035 1.4:+55071546 MS.gene24054:CDS
GATGCTGAGTTGAAGCTGGT+CGG 0.640820 1.4:+55071390 MS.gene24054:CDS
ATTTGAATACAAGTGTCTGA+AGG 0.654254 1.4:-55071641 None:intergenic
TGAATACAAGTGTCTGAAGG+CGG 0.659618 1.4:-55071638 None:intergenic
CCATTACTTGAACAATGGAG+AGG 0.673901 1.4:-55072042 None:intergenic
GTACGGTCTTCGGTGCAAGA+GGG 0.685910 1.4:+55071416 MS.gene24054:CDS
TCACCCTCAAAGATACGACG+AGG 0.726164 1.4:-55071516 None:intergenic
CACCCTCAAAGATACGACGA+GGG 0.739733 1.4:-55071515 None:intergenic
TCCTTCTCATAGGGACGACG+CGG 0.747203 1.4:-55071360 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAATAAATAAATAAACATCA+GGG - chr1.4:55072272-55072291 None:intergenic 10.0%
!! AAATATGAAAAATATAAACA+AGG - chr1.4:55072233-55072252 None:intergenic 10.0%
!! AATTAATGATAATAATGAAA+TGG - chr1.4:55071246-55071265 None:intergenic 10.0%
!! TAAATAAATAAATAAACATC+AGG - chr1.4:55072273-55072292 None:intergenic 10.0%
!!! ATGTATGATAATATTATTTT+TGG + chr1.4:55072320-55072339 MS.gene24054:intron 10.0%
!! AATAAATAAATAAACATCAG+GGG - chr1.4:55072271-55072290 None:intergenic 15.0%
!!! AATATTATTTTTGGTTTCAT+AGG + chr1.4:55072329-55072348 MS.gene24054:intron 15.0%
!!! ATATTATTTTTGGTTTCATA+GGG + chr1.4:55072330-55072349 MS.gene24054:intron 15.0%
!! CAAAACATGTATTGAATTAA+AGG - chr1.4:55071863-55071882 None:intergenic 20.0%
!!! ACAATTGTTTGTTGAATTTA+TGG + chr1.4:55071284-55071303 MS.gene24054:intron 20.0%
!!! GAGAGAATATCTTTTTTTTT+TGG + chr1.4:55072192-55072211 MS.gene24054:intron 20.0%
!!! TGAATTTTTCTGATTTTTCA+TGG + chr1.4:55071766-55071785 MS.gene24054:intron 20.0%
!!! TTCATATTTTGTATGCTTAT+TGG + chr1.4:55072244-55072263 MS.gene24054:intron 20.0%
! AGTCTTAACGAAATATGTTT+GGG + chr1.4:55072296-55072315 MS.gene24054:intron 25.0%
!! TAGTCTTAACGAAATATGTT+TGG + chr1.4:55072295-55072314 MS.gene24054:intron 25.0%
!!! GTTTGCTTTTAATCATGAAA+TGG + chr1.4:55071805-55071824 MS.gene24054:intron 25.0%
!!! TTTTTTTTGGTTACTCTGAA+TGG + chr1.4:55072205-55072224 MS.gene24054:intron 25.0%
AATCATGAAATGGAGTATAC+AGG + chr1.4:55071815-55071834 MS.gene24054:intron 30.0%
ACTTGTATTCAAATCTGGTA+TGG + chr1.4:55071650-55071669 MS.gene24054:CDS 30.0%
ATTGAATACACATACACAGA+TGG + chr1.4:55071321-55071340 MS.gene24054:intron 30.0%
ATTTGAATACAAGTGTCTGA+AGG - chr1.4:55071644-55071663 None:intergenic 30.0%
CAATATGTTCTATGTATCGA+AGG + chr1.4:55072010-55072029 MS.gene24054:CDS 30.0%
GAACAAACTTGATTATGTCT+TGG + chr1.4:55071587-55071606 MS.gene24054:CDS 30.0%
TTGAATACACATACACAGAT+GGG + chr1.4:55071322-55071341 MS.gene24054:intron 30.0%
!! TTCAAGTTGCCAACAAAAAT+GGG - chr1.4:55071899-55071918 None:intergenic 30.0%
!!! GTAACTTGCATTTTTTCTAG+CGG + chr1.4:55071968-55071987 MS.gene24054:intron 30.0%
!!! TACTCAAATGTCACTGATTT+TGG + chr1.4:55072103-55072122 MS.gene24054:intron 30.0%
!!! TATTTTTGGTTTCATAGGGT+TGG + chr1.4:55072334-55072353 MS.gene24054:intron 30.0%
AACAGACAAGACCATATTAC+AGG - chr1.4:55072074-55072093 None:intergenic 35.0%
AAGATAGATACTCACAGTTC+CGG - chr1.4:55071223-55071242 None:intergenic 35.0%
ACAGATTCCTTGCATTGTTA+CGG - chr1.4:55071476-55071495 None:intergenic 35.0%
CAGACACTTGTATTCAAATC+TGG + chr1.4:55071645-55071664 MS.gene24054:CDS 35.0%
TTCTATGTATCGAAGGTAGT+AGG + chr1.4:55072017-55072036 MS.gene24054:CDS 35.0%
TTGAGAAGGATGTTTAAGCA+TGG + chr1.4:55071546-55071565 MS.gene24054:CDS 35.0%
! TCAAGTTGCCAACAAAAATG+GGG - chr1.4:55071898-55071917 None:intergenic 35.0%
! TCCATTGTTCAAGTAATGGA+GGG + chr1.4:55072046-55072065 MS.gene24054:CDS 35.0%
! TGGTTAAAGTTGCTTTCTAC+CGG + chr1.4:55071201-55071220 MS.gene24054:CDS 35.0%
!! GTTCAAGTTGCCAACAAAAA+TGG - chr1.4:55071900-55071919 None:intergenic 35.0%
!!! ATTTTTTCTAGCGGCTGTTA+TGG + chr1.4:55071977-55071996 MS.gene24054:intron 35.0%
AAGAACCCTAGCATGATGAA+TGG - chr1.4:55071682-55071701 None:intergenic 40.0%
ATCATGCTAGGGTTCTTATC+AGG + chr1.4:55071685-55071704 MS.gene24054:CDS 40.0%
ATCCAAACGTTCCTTCTCAT+AGG - chr1.4:55071373-55071392 None:intergenic 40.0%
CAAGTCCATTCATCATGCTA+GGG + chr1.4:55071674-55071693 MS.gene24054:CDS 40.0%
CCATTACTTGAACAATGGAG+AGG - chr1.4:55072045-55072064 None:intergenic 40.0%
CCTCTCCATTGTTCAAGTAA+TGG + chr1.4:55072042-55072061 MS.gene24054:CDS 40.0%
CTCCATTGTTCAAGTAATGG+AGG + chr1.4:55072045-55072064 MS.gene24054:CDS 40.0%
GTGAATGAAGTGAAGAGAGA+TGG + chr1.4:55072170-55072189 MS.gene24054:intron 40.0%
TCCAAACGTTCCTTCTCATA+GGG - chr1.4:55071372-55071391 None:intergenic 40.0%
TCCTTGCATTGTTACGGATA+CGG - chr1.4:55071470-55071489 None:intergenic 40.0%
TGAATACAAGTGTCTGAAGG+CGG - chr1.4:55071641-55071660 None:intergenic 40.0%
! TTTGGTTTCATAGGGTTGGA+AGG + chr1.4:55072338-55072357 MS.gene24054:intron 40.0%
!! GACTAAAGCTACTGCTTTTC+TGG + chr1.4:55071924-55071943 MS.gene24054:intron 40.0%
AACCCTCGTCGTATCTTTGA+GGG + chr1.4:55071513-55071532 MS.gene24054:CDS 45.0%
AATGGAGGGCTCCTGTAATA+TGG + chr1.4:55072060-55072079 MS.gene24054:CDS 45.0%
CCAAGTCCATTCATCATGCT+AGG + chr1.4:55071673-55071692 MS.gene24054:CDS 45.0%
GCCCTCCATTACTTGAACAA+TGG - chr1.4:55072050-55072069 None:intergenic 45.0%
TCCCTATGAGAAGGAACGTT+TGG + chr1.4:55071368-55071387 MS.gene24054:CDS 45.0%
TGCAAGGAATCTGTTGACCT+TGG + chr1.4:55071482-55071501 MS.gene24054:CDS 45.0%
TTATCAGGCAGAGACACATC+AGG + chr1.4:55071700-55071719 MS.gene24054:CDS 45.0%
! CCTAGCATGATGAATGGACT+TGG - chr1.4:55071676-55071695 None:intergenic 45.0%
! TTTGGATGCTGAGTTGAAGC+TGG + chr1.4:55071386-55071405 MS.gene24054:CDS 45.0%
!! TGCTACTGCCCCATTTTTGT+TGG + chr1.4:55071887-55071906 MS.gene24054:intron 45.0%
!!! CTGCTTTTCTGGCTTTTCTC+TGG + chr1.4:55071935-55071954 MS.gene24054:intron 45.0%
ACATCCCATCCTTCATGGTG+AGG + chr1.4:55072371-55072390 MS.gene24054:CDS 50.0%
ACGAGGGTTCTTCTCATCCA+AGG - chr1.4:55071502-55071521 None:intergenic 50.0%
CAACCCTCACCATGAAGGAT+GGG - chr1.4:55072378-55072397 None:intergenic 50.0%
CACCCTCAAAGATACGACGA+GGG - chr1.4:55071518-55071537 None:intergenic 50.0%
CATCCCATCCTTCATGGTGA+GGG + chr1.4:55072372-55072391 MS.gene24054:CDS 50.0%
GAACCCTCGTCGTATCTTTG+AGG + chr1.4:55071512-55071531 MS.gene24054:CDS 50.0%
GCCGTATCCGTAACAATGCA+AGG + chr1.4:55071466-55071485 MS.gene24054:CDS 50.0%
GGTGAACATCCCATCCTTCA+TGG + chr1.4:55072366-55072385 MS.gene24054:CDS 50.0%
GTTTCATAGGGTTGGAAGGC+AGG + chr1.4:55072342-55072361 MS.gene24054:intron 50.0%
TCAACCCTCACCATGAAGGA+TGG - chr1.4:55072379-55072398 None:intergenic 50.0%
TCACCCTCAAAGATACGACG+AGG - chr1.4:55071519-55071538 None:intergenic 50.0%
TTGAAGCTGGTCGGAGAGTA+CGG + chr1.4:55071399-55071418 MS.gene24054:CDS 50.0%
! AGGGTGAAGCGCTATTGAGA+AGG + chr1.4:55071532-55071551 MS.gene24054:CDS 50.0%
! GATGCTGAGTTGAAGCTGGT+CGG + chr1.4:55071390-55071409 MS.gene24054:CDS 50.0%
TCATAGGGTTGGAAGGCAGG+TGG + chr1.4:55072345-55072364 MS.gene24054:intron 55.0%
TCCTTCTCATAGGGACGACG+CGG - chr1.4:55071363-55071382 None:intergenic 55.0%
! AGTACGGTCTTCGGTGCAAG+AGG + chr1.4:55071415-55071434 MS.gene24054:CDS 55.0%
! GTACGGTCTTCGGTGCAAGA+GGG + chr1.4:55071416-55071435 MS.gene24054:CDS 55.0%
! TGGTCGGAGAGTACGGTCTT+CGG + chr1.4:55071406-55071425 MS.gene24054:CDS 55.0%
! TTCGGTGCAAGAGGGAGCTT+TGG + chr1.4:55071424-55071443 MS.gene24054:CDS 55.0%
!! GTGCAAGAGGGAGCTTTGGA+GGG + chr1.4:55071428-55071447 MS.gene24054:CDS 55.0%
! GGTGCAAGAGGGAGCTTTGG+AGG + chr1.4:55071427-55071446 MS.gene24054:CDS 60.0%
GCCGCGTCGTCCCTATGAGA+AGG + chr1.4:55071359-55071378 MS.gene24054:CDS 65.0%


Chromosome Type Strat End Strand Name
chr1.4 gene 55071200 55072398 55071200 ID=MS.gene24054
chr1.4 mRNA 55071200 55072398 55071200 ID=MS.gene24054.t1;Parent=MS.gene24054
chr1.4 exon 55071200 55071227 55071200 ID=MS.gene24054.t1.exon1;Parent=MS.gene24054.t1
chr1.4 CDS 55071200 55071227 55071200 ID=cds.MS.gene24054.t1;Parent=MS.gene24054.t1
chr1.4 exon 55071340 55071721 55071340 ID=MS.gene24054.t1.exon2;Parent=MS.gene24054.t1
chr1.4 CDS 55071340 55071721 55071340 ID=cds.MS.gene24054.t1;Parent=MS.gene24054.t1
chr1.4 exon 55071988 55072081 55071988 ID=MS.gene24054.t1.exon3;Parent=MS.gene24054.t1
chr1.4 CDS 55071988 55072081 55071988 ID=cds.MS.gene24054.t1;Parent=MS.gene24054.t1
chr1.4 exon 55072351 55072398 55072351 ID=MS.gene24054.t1.exon4;Parent=MS.gene24054.t1
chr1.4 CDS 55072351 55072398 55072351 ID=cds.MS.gene24054.t1;Parent=MS.gene24054.t1
Gene Sequence

>MS.gene24054

ATGGTTAAAGTTGCTTTCTACCGGAACTGTGAGTATCTATCTTCCATTTCATTATTATCATTAATTGATTCTGTTGTTATATGTACAATTGTTTGTTGAATTTATGGTTGATTTTGTTTGAATTGAATACACATACACAGATGGGAAAACATTCAAGAAGCCGCGTCGTCCCTATGAGAAGGAACGTTTGGATGCTGAGTTGAAGCTGGTCGGAGAGTACGGTCTTCGGTGCAAGAGGGAGCTTTGGAGGGTTCAGTATGCTCTGAGCCGTATCCGTAACAATGCAAGGAATCTGTTGACCTTGGATGAGAAGAACCCTCGTCGTATCTTTGAGGGTGAAGCGCTATTGAGAAGGATGTTTAAGCATGGTCTTCTTGATGAAACTCAGAACAAACTTGATTATGTCTTGGCTCTCACTGTTGAGAATTTTCTTGAACGCCGCCTTCAGACACTTGTATTCAAATCTGGTATGGCCAAGTCCATTCATCATGCTAGGGTTCTTATCAGGCAGAGACACATCAGGTATATATTGATTATTTGAATTCTCATTTTATTGCTTTTAATCATGAATTTTTCTGATTTTTCATGGAACAGCTTATGTATAAGTTTGCTTTTAATCATGAAATGGAGTATACAGGCTTAACGTGTCTTTGCTTGTTTCCTTTAATTCAATACATGTTTTGTTGTTGCTACTGCCCCATTTTTGTTGGCAACTTGAACTTTAGACTAAAGCTACTGCTTTTCTGGCTTTTCTCTGGACTCTCTTTCGTAACTTGCATTTTTTCTAGCGGCTGTTATGGTAGTTTTCATCAATATGTTCTATGTATCGAAGGTAGTAGGATCCTCTCCATTGTTCAAGTAATGGAGGGCTCCTGTAATATGGTCTTGTCTGTTTAATTAAAATACTCAAATGTCACTGATTTTGGAAATGTGTAATATCATTTTTACACTTAAAACTATAATTGTTAATGTGAATGAAGTGAAGAGAGATGGAGAGAATATCTTTTTTTTTTGGTTACTCTGAATGGATCCTTGTTTATATTTTTCATATTTTGTATGCTTATTGGTCCCCTGATGTTTATTTATTTATTTATTTAGTCTTAACGAAATATGTTTGGGAATGTATGATAATATTATTTTTGGTTTCATAGGGTTGGAAGGCAGGTGGTGAACATCCCATCCTTCATGGTGAGGGTTGA

Protein sequence

>MS.gene24054.t1

MVKVAFYRNYGKTFKKPRRPYEKERLDAELKLVGEYGLRCKRELWRVQYALSRIRNNARNLLTLDEKNPRRIFEGEALLRRMFKHGLLDETQNKLDYVLALTVENFLERRLQTLVFKSGMAKSIHHARVLIRQRHISGCYGSFHQYVLCIEGSRILSIVQVMEGSCNMGWKAGGEHPILHGEG