AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene34409


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene34409.t1 MTR_1g102780 97.000 200 5 1 1 199 1 200 2.25e-138 385
MS.gene34409.t1 MTR_1g102800 91.960 199 14 1 1 199 1 197 5.32e-110 313
MS.gene34409.t1 MTR_1g102570 88.333 180 19 1 20 199 21 198 4.52e-109 310
MS.gene34409.t1 MTR_1g102830 81.667 180 19 2 20 199 21 186 2.51e-101 290
MS.gene34409.t1 MTR_1g102810 78.142 183 26 2 17 199 14 182 1.69e-98 283
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene34409.t1 AT3G22840 53.731 201 85 4 1 199 1 195 2.72e-62 192
MS.gene34409.t1 AT4G14690 50.990 202 87 4 1 199 1 193 8.78e-57 178

Find 56 sgRNAs with CRISPR-Local

Find 79 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CAGAAGGGATGTTGTTAAAT+TGG 0.214729 1.2:+76355379 None:intergenic
GGTGCTGATGGTGGTGTAAT+TGG 0.245963 1.2:+76355091 None:intergenic
TGGTGGAATTCCATGGTTCT+TGG 0.288858 1.2:-76354746 MS.gene34409:CDS
GGTGGAATTCCATGGTTCTT+GGG 0.299911 1.2:-76354745 MS.gene34409:CDS
GTTGGTTGTGGTTGTGGTGG+TGG 0.344690 1.2:+76355064 None:intergenic
TGTGGTTGTGGTGGTGGAGT+TGG 0.352890 1.2:+76355070 None:intergenic
ATTGGGTCTACAGGCACCTT+TGG 0.360861 1.2:+76355109 None:intergenic
TATGTTGGGTTTGATTGCTT+TGG 0.370659 1.2:-76354605 MS.gene34409:CDS
AATGGAAGGTTGGCTATGAT+TGG 0.393839 1.2:-76354832 MS.gene34409:CDS
GGTCTGTTTGATCAAATATC+TGG 0.404965 1.2:-76354769 MS.gene34409:CDS
CCATTGATTCTCTCAGGTGC+TGG 0.411549 1.2:+76354850 None:intergenic
GGTGGTGGAGTTGGTGCTGA+TGG 0.417357 1.2:+76355079 None:intergenic
AACCTTCCATTGATTCTCTC+AGG 0.436061 1.2:+76354844 None:intergenic
GTGCTGATGGTGGTGTAATT+GGG 0.440700 1.2:+76355092 None:intergenic
GTATAGGTTGGTTGTGGTTG+TGG 0.448474 1.2:+76355058 None:intergenic
GAATGGTAGAATTGCTATGT+TGG 0.450278 1.2:-76354620 MS.gene34409:CDS
CTAGCATTTCTTCTCAAGCT+TGG 0.450671 1.2:+76355348 None:intergenic
CACCTTTGGTGAACGTGTAT+AGG 0.459386 1.2:+76355042 None:intergenic
TTGTTAAATTGGTTAACTCT+AGG 0.463045 1.2:+76355390 None:intergenic
GTGGAATTCCATGGTTCTTG+GGG 0.468120 1.2:-76354744 MS.gene34409:CDS
GGTGGAGTTGGTGCTGATGG+TGG 0.468618 1.2:+76355082 None:intergenic
CGGATTTGATGGCATTTGGT+GGG 0.485102 1.2:-76354873 MS.gene34409:CDS
TCGGATTTGATGGCATTTGG+TGG 0.487791 1.2:-76354874 MS.gene34409:CDS
GAAATGCTAGCCTCAAAGTT+CGG 0.488413 1.2:-76355335 MS.gene34409:CDS
AATGGTAGAATTGCTATGTT+GGG 0.492247 1.2:-76354619 MS.gene34409:CDS
TCTAGGCCTGCTAGAAATGC+TGG 0.515845 1.2:+76355407 None:intergenic
GGTGGTGTAATTGGGTCTAC+AGG 0.516474 1.2:+76355100 None:intergenic
CCAGCACCTGAGAGAATCAA+TGG 0.516939 1.2:-76354850 MS.gene34409:CDS
TAGGTTGGTTGTGGTTGTGG+TGG 0.520190 1.2:+76355061 None:intergenic
CAGCCATGGACCGAACTTTG+AGG 0.527132 1.2:+76355325 None:intergenic
CGAAAACATTACCTCAGCCA+TGG 0.528935 1.2:+76355311 None:intergenic
CAAAGTTCGGTCCATGGCTG+AGG 0.533870 1.2:-76355322 MS.gene34409:intron
GGTGGAGATAGCAAATGGAC+AGG 0.537366 1.2:-76354791 MS.gene34409:CDS
AGTGTGGAGTCTAAGTCAAA+AGG 0.538159 1.2:-76354670 MS.gene34409:CDS
CCATGACCAGCATTTCTAGC+AGG 0.549312 1.2:-76355413 MS.gene34409:CDS
CCTGCTAGAAATGCTGGTCA+TGG 0.550870 1.2:+76355413 None:intergenic
GAACGTGTATAGGTTGGTTG+TGG 0.557227 1.2:+76355052 None:intergenic
TGAGAGAATCAATGGAAGGT+TGG 0.560259 1.2:-76354842 MS.gene34409:CDS
TAGACTCCACACTAACCCCT+TGG 0.562091 1.2:+76354680 None:intergenic
TAGCCTCAAAGTTCGGTCCA+TGG 0.581082 1.2:-76355328 MS.gene34409:CDS
AAGCTTGGCATATACACAGA+AGG 0.589450 1.2:+76355363 None:intergenic
CTATAGAAATCTATTACACA+AGG 0.595515 1.2:+76354554 None:intergenic
AACCTATACACGTTCACCAA+AGG 0.599727 1.2:-76355044 MS.gene34409:intron
TGTCCTCAGATGCTGAGTTG+TGG 0.599794 1.2:-76354642 MS.gene34409:CDS
ATTCCACAACTCAGCATCTG+AGG 0.606044 1.2:+76354639 None:intergenic
TTTGATCAAATATCTGGTGG+TGG 0.612951 1.2:-76354763 MS.gene34409:CDS
TTTGGTGAACGTGTATAGGT+TGG 0.617927 1.2:+76355046 None:intergenic
AGCTTGGCATATACACAGAA+GGG 0.622653 1.2:+76355364 None:intergenic
TATCTGGTGGTGGAATTCCA+TGG 0.624337 1.2:-76354753 MS.gene34409:CDS
CTGTTTGATCAAATATCTGG+TGG 0.626873 1.2:-76354766 MS.gene34409:CDS
AGGGCAGAAAGAGCAACCAA+AGG 0.630670 1.2:-76355125 MS.gene34409:CDS
ACACTTGTCCCCAAGAACCA+TGG 0.633615 1.2:+76354736 None:intergenic
GTGGAGATAGCAAATGGACA+GGG 0.635471 1.2:-76354790 MS.gene34409:CDS
TCAGATGCTGAGTTGTGGAA+TGG 0.641735 1.2:-76354637 MS.gene34409:CDS
CACCTGAGAGAATCAATGGA+AGG 0.646646 1.2:-76354846 MS.gene34409:CDS
TATAGAAATCTATTACACAA+GGG 0.717921 1.2:+76354555 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAATAATAATGATGAAAATA+TGG - chr1.2:76355102-76355121 MS.gene34409:CDS 10.0%
!! CATCATTATTATTTATTAAA+AGG + chr1.2:76355096-76355115 None:intergenic 10.0%
!!! AGTTTTTCATTACATTTATC+AGG - chr1.2:76354868-76354887 MS.gene34409:CDS 20.0%
! TTCATTACATTTATCAGGAA+GGG - chr1.2:76354873-76354892 MS.gene34409:CDS 25.0%
! TTGTTAAATTGGTTAACTCT+AGG + chr1.2:76354630-76354649 None:intergenic 25.0%
! TTTCATTACATTTATCAGGA+AGG - chr1.2:76354872-76354891 MS.gene34409:CDS 25.0%
!! CGAAAACAGATTTAACTTTA+AGG - chr1.2:76354727-76354746 MS.gene34409:CDS 25.0%
!! GCTTTTACAGAATATGTTAA+GGG - chr1.2:76355434-76355453 MS.gene34409:CDS 25.0%
AATGGTAGAATTGCTATGTT+GGG - chr1.2:76355398-76355417 MS.gene34409:CDS 30.0%
TGCATAATGCAACAAGTTAA+TGG - chr1.2:76354783-76354802 MS.gene34409:CDS 30.0%
! GGCTTTTACAGAATATGTTA+AGG - chr1.2:76355433-76355452 MS.gene34409:CDS 30.0%
!! CTTTGATTCCATTTTTCCAA+GGG - chr1.2:76355321-76355340 MS.gene34409:intron 30.0%
!! TCTTTGATTCCATTTTTCCA+AGG - chr1.2:76355320-76355339 MS.gene34409:intron 30.0%
!! TTTGATTCCATTTTTCCAAG+GGG - chr1.2:76355322-76355341 MS.gene34409:intron 30.0%
CAGAAGGGATGTTGTTAAAT+TGG + chr1.2:76354641-76354660 None:intergenic 35.0%
CTGTTTGATCAAATATCTGG+TGG - chr1.2:76355251-76355270 MS.gene34409:intron 35.0%
GAATGGTAGAATTGCTATGT+TGG - chr1.2:76355397-76355416 MS.gene34409:CDS 35.0%
GGTCTGTTTGATCAAATATC+TGG - chr1.2:76355248-76355267 MS.gene34409:intron 35.0%
TATGTTGGGTTTGATTGCTT+TGG - chr1.2:76355412-76355431 MS.gene34409:CDS 35.0%
TTTACTACTATGCTCACCTT+TGG + chr1.2:76354992-76355011 None:intergenic 35.0%
TTTGATCAAATATCTGGTGG+TGG - chr1.2:76355254-76355273 MS.gene34409:intron 35.0%
! CACAAAGTTTTCGGATTTGA+TGG - chr1.2:76355133-76355152 MS.gene34409:intron 35.0%
!! TTTTCGGATTTGATGGCATT+TGG - chr1.2:76355140-76355159 MS.gene34409:intron 35.0%
!!! ATTGGTTTTGTAGCTGCTAT+GGG - chr1.2:76355203-76355222 MS.gene34409:intron 35.0%
AACCTATACACGTTCACCAA+AGG - chr1.2:76354973-76354992 MS.gene34409:intron 40.0%
AAGCTTGGCATATACACAGA+AGG + chr1.2:76354657-76354676 None:intergenic 40.0%
ACACTAACCCCTTGGAAAAA+TGG + chr1.2:76355332-76355351 None:intergenic 40.0%
AGCTTGGCATATACACAGAA+GGG + chr1.2:76354656-76354675 None:intergenic 40.0%
AGTGTGGAGTCTAAGTCAAA+AGG - chr1.2:76355347-76355366 MS.gene34409:CDS 40.0%
CTAGCATTTCTTCTCAAGCT+TGG + chr1.2:76354672-76354691 None:intergenic 40.0%
TGAGAGAATCAATGGAAGGT+TGG - chr1.2:76355175-76355194 MS.gene34409:intron 40.0%
TTTGGTGAACGTGTATAGGT+TGG + chr1.2:76354974-76354993 None:intergenic 40.0%
! AATGGAAGGTTGGCTATGAT+TGG - chr1.2:76355185-76355204 MS.gene34409:intron 40.0%
! GAAATGCTAGCCTCAAAGTT+CGG - chr1.2:76354682-76354701 MS.gene34409:CDS 40.0%
! GCAGATGAGCACAAAGTTTT+CGG - chr1.2:76355124-76355143 MS.gene34409:CDS 40.0%
!! AACCTTCCATTGATTCTCTC+AGG + chr1.2:76355176-76355195 None:intergenic 40.0%
!! ATTTTTCCAAGGGGTTAGTG+TGG - chr1.2:76355331-76355350 MS.gene34409:CDS 40.0%
!!! GATTGGTTTTGTAGCTGCTA+TGG - chr1.2:76355202-76355221 MS.gene34409:intron 40.0%
!!! TTGGTTTTGTAGCTGCTATG+GGG - chr1.2:76355204-76355223 MS.gene34409:intron 40.0%
ATTCCACAACTCAGCATCTG+AGG + chr1.2:76355381-76355400 None:intergenic 45.0%
CACCTGAGAGAATCAATGGA+AGG - chr1.2:76355171-76355190 MS.gene34409:intron 45.0%
CACCTTTGGTGAACGTGTAT+AGG + chr1.2:76354978-76354997 None:intergenic 45.0%
CGAAAACATTACCTCAGCCA+TGG + chr1.2:76354709-76354728 None:intergenic 45.0%
GGTGGAATTCCATGGTTCTT+GGG - chr1.2:76355272-76355291 MS.gene34409:intron 45.0%
GTGGAATTCCATGGTTCTTG+GGG - chr1.2:76355273-76355292 MS.gene34409:intron 45.0%
GTGGAGATAGCAAATGGACA+GGG - chr1.2:76355227-76355246 MS.gene34409:intron 45.0%
TCAGATGCTGAGTTGTGGAA+TGG - chr1.2:76355380-76355399 MS.gene34409:CDS 45.0%
TGGTGGAATTCCATGGTTCT+TGG - chr1.2:76355271-76355290 MS.gene34409:intron 45.0%
! CGGATTTGATGGCATTTGGT+GGG - chr1.2:76355144-76355163 MS.gene34409:intron 45.0%
! TCGGATTTGATGGCATTTGG+TGG - chr1.2:76355143-76355162 MS.gene34409:intron 45.0%
!! GAACGTGTATAGGTTGGTTG+TGG + chr1.2:76354968-76354987 None:intergenic 45.0%
!! GTATAGGTTGGTTGTGGTTG+TGG + chr1.2:76354962-76354981 None:intergenic 45.0%
!! GTGCTGATGGTGGTGTAATT+GGG + chr1.2:76354928-76354947 None:intergenic 45.0%
!! TATCTGGTGGTGGAATTCCA+TGG - chr1.2:76355264-76355283 MS.gene34409:intron 45.0%
!!! TGGTTTTGTAGCTGCTATGG+GGG - chr1.2:76355205-76355224 MS.gene34409:intron 45.0%
!! ATCATTATTATTTATTAAAA+GGG + chr1.2:76355095-76355114 None:intergenic 5.0%
ACACTTGTCCCCAAGAACCA+TGG + chr1.2:76355284-76355303 None:intergenic 50.0%
AGGGCAGAAAGAGCAACCAA+AGG - chr1.2:76354892-76354911 MS.gene34409:CDS 50.0%
ATGGGGGTGGAGATAGCAAA+TGG - chr1.2:76355221-76355240 MS.gene34409:intron 50.0%
ATTGGGTCTACAGGCACCTT+TGG + chr1.2:76354911-76354930 None:intergenic 50.0%
CCAGCACCTGAGAGAATCAA+TGG - chr1.2:76355167-76355186 MS.gene34409:intron 50.0%
CCTGCTAGAAATGCTGGTCA+TGG + chr1.2:76354607-76354626 None:intergenic 50.0%
GGTGGAGATAGCAAATGGAC+AGG - chr1.2:76355226-76355245 MS.gene34409:intron 50.0%
GGTGGTGTAATTGGGTCTAC+AGG + chr1.2:76354920-76354939 None:intergenic 50.0%
TAGACTCCACACTAACCCCT+TGG + chr1.2:76355340-76355359 None:intergenic 50.0%
TAGCCTCAAAGTTCGGTCCA+TGG - chr1.2:76354689-76354708 MS.gene34409:CDS 50.0%
TCTAGGCCTGCTAGAAATGC+TGG + chr1.2:76354613-76354632 None:intergenic 50.0%
TGTCCTCAGATGCTGAGTTG+TGG - chr1.2:76355375-76355394 MS.gene34409:CDS 50.0%
! TTTTGTAGCTGCTATGGGGG+TGG - chr1.2:76355208-76355227 MS.gene34409:intron 50.0%
!! CCATGACCAGCATTTCTAGC+AGG - chr1.2:76354604-76354623 MS.gene34409:CDS 50.0%
!! CCATTGATTCTCTCAGGTGC+TGG + chr1.2:76355170-76355189 None:intergenic 50.0%
!! GGTGCTGATGGTGGTGTAAT+TGG + chr1.2:76354929-76354948 None:intergenic 50.0%
!! TAGGTTGGTTGTGGTTGTGG+TGG + chr1.2:76354959-76354978 None:intergenic 50.0%
CAAAGTTCGGTCCATGGCTG+AGG - chr1.2:76354695-76354714 MS.gene34409:CDS 55.0%
CAGCCATGGACCGAACTTTG+AGG + chr1.2:76354695-76354714 None:intergenic 55.0%
GTTGGTTGTGGTTGTGGTGG+TGG + chr1.2:76354956-76354975 None:intergenic 55.0%
!! TGTGGTTGTGGTGGTGGAGT+TGG + chr1.2:76354950-76354969 None:intergenic 55.0%
!! GGTGGAGTTGGTGCTGATGG+TGG + chr1.2:76354938-76354957 None:intergenic 60.0%
!! GGTGGTGGAGTTGGTGCTGA+TGG + chr1.2:76354941-76354960 None:intergenic 60.0%


Chromosome Type Strat End Strand Name
chr1.2 gene 76354567 76355472 76354567 ID=MS.gene34409
chr1.2 mRNA 76354567 76355472 76354567 ID=MS.gene34409.t1;Parent=MS.gene34409
chr1.2 exon 76355323 76355472 76355323 ID=MS.gene34409.t1.exon1;Parent=MS.gene34409.t1
chr1.2 CDS 76355323 76355472 76355323 ID=cds.MS.gene34409.t1;Parent=MS.gene34409.t1
chr1.2 exon 76355045 76355149 76355045 ID=MS.gene34409.t1.exon2;Parent=MS.gene34409.t1
chr1.2 CDS 76355045 76355149 76355045 ID=cds.MS.gene34409.t1;Parent=MS.gene34409.t1
chr1.2 exon 76354567 76354911 76354567 ID=MS.gene34409.t1.exon3;Parent=MS.gene34409.t1
chr1.2 CDS 76354567 76354911 76354567 ID=cds.MS.gene34409.t1;Parent=MS.gene34409.t1
Gene Sequence

>MS.gene34409

ATGGCTGTTTCATCTTATCAATCTATCATGTCAAGCTCCATGACCAGCATTTCTAGCAGGCCTAGAGTTAACCAATTTAACAACATCCCTTCTGTGTATATGCCAAGCTTGAGAAGAAATGCTAGCCTCAAAGTTCGGTCCATGGCTGAGGTAATGTTTTCGAAAACAGATTTAACTTTAAGGCTGCATATTTATACATATTGTATTTTTTGTACATGCATAATGCAACAAGTTAATGGTATATGCTTTAAGAATCATGTTAATGATATAAAATAGTCATTGCTATTATTTAATAAATTATAGTTTTTCATTACATTTATCAGGAAGGGCAGAAAGAGCAACCAAAGGTGCCTGTAGACCCAATTACACCACCATCAGCACCAACTCCACCACCACAACCACAACCAACCTATACACGTTCACCAAAGGTGAGCATAGTAGTAAATAAAATTATCTCTGTTTATTCTTAATTATGTGAAAGAAATTAATTTTGCAAAGTACTAAATTAAGTCAAAATTTATGAGACCCTTTTAATAAATAATAATGATGAAAATATGGCAGATGAGCACAAAGTTTTCGGATTTGATGGCATTTGGTGGGCCAGCACCTGAGAGAATCAATGGAAGGTTGGCTATGATTGGTTTTGTAGCTGCTATGGGGGTGGAGATAGCAAATGGACAGGGTCTGTTTGATCAAATATCTGGTGGTGGAATTCCATGGTTCTTGGGGACAAGTGTGTTGTTGTCACTTGCTTCTTTGATTCCATTTTTCCAAGGGGTTAGTGTGGAGTCTAAGTCAAAAGGTGTCATGTCCTCAGATGCTGAGTTGTGGAATGGTAGAATTGCTATGTTGGGTTTGATTGCTTTGGCTTTTACAGAATATGTTAAGGGTACTGCCCTTGTGTAA

Protein sequence

>MS.gene34409.t1

MAVSSYQSIMSSSMTSISSRPRVNQFNNIPSVYMPSLRRNASLKVRSMAEEGQKEQPKVPVDPITPPSAPTPPPQPQPTYTRSPKMSTKFSDLMAFGGPAPERINGRLAMIGFVAAMGVEIANGQGLFDQISGGGIPWFLGTSVLLSLASLIPFFQGVSVESKSKGVMSSDAELWNGRIAMLGLIALAFTEYVKGTALV