AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene52301


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene52301.t1 MTR_2g094040 70.464 237 34 8 1 230 1 208 6.16e-103 299
MS.gene52301.t1 MTR_3g005800 60.204 196 72 3 75 270 1 190 2.26e-80 241
MS.gene52301.t1 MTR_3g005790 49.640 139 63 3 83 221 10 141 1.52e-44 148
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene52301.t1 AT1G72175 53.333 180 78 3 91 270 10 183 5.96e-51 166
MS.gene52301.t1 AT1G22510 53.889 180 77 3 91 270 10 183 9.60e-45 150
MS.gene52301.t1 AT1G72175 53.947 152 64 3 119 270 4 149 2.27e-38 132
MS.gene52301.t1 AT1G22510 54.088 159 67 3 112 270 49 201 3.98e-33 120
MS.gene52301.t1 AT4G33940 28.022 182 123 4 81 262 64 237 3.03e-21 90.5
MS.gene52301.t1 AT4G33940 27.941 136 91 3 81 216 64 192 7.96e-14 68.9

Find 64 sgRNAs with CRISPR-Local

Find 79 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GGTTGAAAAGAAAGGGAAAT+TGG 0.207524 7.3:-23961963 MS.gene52301:CDS
GGCTAAGATAGAAGAAGAAT+TGG 0.288794 7.3:-23962047 MS.gene52301:CDS
GGCAAAGTATTGATCTATAA+AGG 0.294780 7.3:+23961296 None:intergenic
TCATCGACCCGTTACCCTTT+TGG 0.297940 7.3:-23961750 MS.gene52301:CDS
GGTTGAAGAGAAAGTGAAAT+TGG 0.301053 7.3:-23962086 MS.gene52301:CDS
TGAATTCCAATCAGAACTTC+AGG 0.330596 7.3:+23961671 None:intergenic
GGAAGAAGATTAATGTAATT+AGG 0.352640 7.3:+23961332 None:intergenic
TCTATCTTAGCCTCTAACCC+TGG 0.356011 7.3:+23962058 None:intergenic
GAAGAAAAGGTTGAAAAGAA+AGG 0.390677 7.3:-23961971 MS.gene52301:CDS
GTTGAAAAGAAAGGGAAATT+GGG 0.390750 7.3:-23961962 MS.gene52301:CDS
CACGACCCTGAAGTTCTGAT+TGG 0.390853 7.3:-23961677 MS.gene52301:CDS
TCAAAGAGTCTCTGAGTAAT+GGG 0.393871 7.3:+23961611 None:intergenic
ATTCGGAAAAGTTGGTCTCT+TGG 0.403931 7.3:-23961362 MS.gene52301:CDS
AGAGAAAAGGAAAGGGAAAT+CGG 0.414418 7.3:-23962020 MS.gene52301:CDS
ATTGGAAAACCCAGGGTTAG+AGG 0.416917 7.3:-23962068 MS.gene52301:CDS
GGGTGAAGAGAAAGGGAAAT+CGG 0.418833 7.3:-23962149 MS.gene52301:CDS
GTGAAGCTACATGCTCTCAT+TGG 0.435563 7.3:-23961847 MS.gene52301:CDS
CTATCTTAGCCTCTAACCCT+GGG 0.438058 7.3:+23962059 None:intergenic
AAAAGCCTCCGCACGAGAAA+AGG 0.440424 7.3:+23961584 None:intergenic
AACTTGTACAATCGCTGATT+GGG 0.444017 7.3:-23961816 MS.gene52301:CDS
AAGAAAAGGTTGAAAAGAAA+GGG 0.445187 7.3:-23961970 MS.gene52301:CDS
CTACCTCAGCTTCTAACCCT+AGG 0.452493 7.3:+23961936 None:intergenic
GCTAAGATAGAAGAAGAATT+GGG 0.456108 7.3:-23962046 MS.gene52301:CDS
ATGTAGCTTCACATATAATC+TGG 0.464921 7.3:+23961858 None:intergenic
CAACTTGTACAATCGCTGAT+TGG 0.465387 7.3:-23961817 MS.gene52301:CDS
AAGAATTGGGTGAAGAGAAA+AGG 0.466239 7.3:-23962033 MS.gene52301:CDS
CCTTCTGGGATGATGTCAAT+GGG 0.470014 7.3:+23961467 None:intergenic
CAATACTTTGCCTCCGTCAC+GGG 0.478130 7.3:-23961285 MS.gene52301:CDS
GCAAAGTATTGATCTATAAA+GGG 0.479128 7.3:+23961297 None:intergenic
GTAGGAACCAAAAGGGTAAC+GGG 0.484752 7.3:+23961743 None:intergenic
ACACGAGCTCTGAAAAGAAA+AGG 0.485582 7.3:+23961530 None:intergenic
GGAGACTGAGAGAGAAGAAA+TGG 0.487507 7.3:-23962107 MS.gene52301:CDS
ATCAAAGAGTCTCTGAGTAA+TGG 0.493238 7.3:+23961610 None:intergenic
AAAGGGAAATTGGGAAACCT+AGG 0.493922 7.3:-23961953 MS.gene52301:CDS
GCTGAGGTAGAAGAAGAGAA+AGG 0.494774 7.3:-23961923 MS.gene52301:CDS
AAGAAAAGGAAGAGATGTAT+CGG 0.495031 7.3:+23961544 None:intergenic
CTGAGGTAGAAGAAGAGAAA+GGG 0.500548 7.3:-23961922 MS.gene52301:CDS
ACCTTCTGGGATGATGTCAA+TGG 0.502368 7.3:+23961466 None:intergenic
GCAGGAATATTCGGAAAAGT+TGG 0.504703 7.3:-23961370 MS.gene52301:intron
GAGAAAGGGAAATTGAAAGA+AGG 0.506259 7.3:-23961908 MS.gene52301:CDS
AGAGGGTGAGATAGAAGAAA+AGG 0.508654 7.3:-23961984 MS.gene52301:CDS
AACTACAACTGCGACGATGA+TGG 0.510417 7.3:-23961713 MS.gene52301:CDS
CTCTCTCAGTCTCCAACGCT+AGG 0.520593 7.3:+23962116 None:intergenic
TGGGTGAAGAGAAAAGGAAA+GGG 0.526426 7.3:-23962027 MS.gene52301:CDS
TCAATACTTTGCCTCCGTCA+CGG 0.533287 7.3:-23961286 MS.gene52301:CDS
TTGGGTGAAGAGAAAAGGAA+AGG 0.536616 7.3:-23962028 MS.gene52301:CDS
GAATTCCAATCAGAACTTCA+GGG 0.553145 7.3:+23961672 None:intergenic
AACGAAAATTACGCCCGTGA+CGG 0.561983 7.3:+23961272 None:intergenic
AGTAGGAACCAAAAGGGTAA+CGG 0.564577 7.3:+23961742 None:intergenic
TGACAGTGTGGACATTTACA+AGG 0.564971 7.3:+23961770 None:intergenic
AGAAAAGGAAGAGATGTATC+GGG 0.571993 7.3:+23961545 None:intergenic
GGAAAACGAAAACCTAGCGT+TGG 0.582482 7.3:-23962128 MS.gene52301:CDS
GAAAATTACGCCCGTGACGG+AGG 0.584757 7.3:+23961275 None:intergenic
TATAAAGGGCAGCAACATGT+AGG 0.587058 7.3:+23961311 None:intergenic
AAACCTAGGGTTAGAAGCTG+AGG 0.601923 7.3:-23961939 MS.gene52301:CDS
AAGGGAAATTGGGAAACCTA+GGG 0.602237 7.3:-23961952 MS.gene52301:CDS
CCCATTGACATCATCCCAGA+AGG 0.615355 7.3:-23961467 MS.gene52301:intron
ATCGGAAGAAATATCGTCAG+AGG 0.626223 7.3:-23962002 MS.gene52301:CDS
AAGTGAAATTGGAAAACCCA+GGG 0.639009 7.3:-23962075 MS.gene52301:CDS
TCGGAAGAAATATCGTCAGA+GGG 0.641570 7.3:-23962001 MS.gene52301:CDS
ACATTTACAAGGTTCAATGT+CGG 0.657703 7.3:+23961781 None:intergenic
AAAGTGAAATTGGAAAACCC+AGG 0.679877 7.3:-23962076 MS.gene52301:CDS
CTTCTGGGATGATGTCAATG+GGG 0.725072 7.3:+23961468 None:intergenic
GTAACGGGTCGATGACAGTG+TGG 0.759412 7.3:+23961758 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! AAGAAAAGGTTGAAAAGAAA+GGG - chr7.3:23961448-23961467 MS.gene52301:intron 25.0%
! AATGGAAAAATATAACCTTC+TGG + chr7.3:23961969-23961988 None:intergenic 25.0%
! ATGGAAAAATATAACCTTCT+GGG + chr7.3:23961968-23961987 None:intergenic 25.0%
! GGAAGAAGATTAATGTAATT+AGG + chr7.3:23962089-23962108 None:intergenic 25.0%
!! CAGACTTATAACACTATTTT+TGG - chr7.3:23961768-23961787 MS.gene52301:CDS 25.0%
!!! GCAAAGTATTGATCTATAAA+GGG + chr7.3:23962124-23962143 None:intergenic 25.0%
AAGAAAAGGAAGAGATGTAT+CGG + chr7.3:23961877-23961896 None:intergenic 30.0%
ACATTTACAAGGTTCAATGT+CGG + chr7.3:23961640-23961659 None:intergenic 30.0%
ACCAAAACAATTTCACAAGT+TGG + chr7.3:23961997-23962016 None:intergenic 30.0%
ATGTAGCTTCACATATAATC+TGG + chr7.3:23961563-23961582 None:intergenic 30.0%
GAAGAAAAGGTTGAAAAGAA+AGG - chr7.3:23961447-23961466 MS.gene52301:intron 30.0%
GCTAAGATAGAAGAAGAATT+GGG - chr7.3:23961372-23961391 MS.gene52301:intron 30.0%
GTTGAAAAGAAAGGGAAATT+GGG - chr7.3:23961456-23961475 MS.gene52301:intron 30.0%
! AATTTTGTTCCTTTTTCTGC+AGG - chr7.3:23962030-23962049 MS.gene52301:CDS 30.0%
! TCCAACTTGTGAAATTGTTT+TGG - chr7.3:23961993-23962012 MS.gene52301:CDS 30.0%
! TTTCACAAGTTGGACAAAAA+TGG + chr7.3:23961987-23962006 None:intergenic 30.0%
!! GGCAAAGTATTGATCTATAA+AGG + chr7.3:23962125-23962144 None:intergenic 30.0%
!! TTTTTCAGTAGGAACCAAAA+GGG + chr7.3:23961685-23961704 None:intergenic 30.0%
!!! CAGTTGTAGTTTTTTTCAGT+AGG + chr7.3:23961696-23961715 None:intergenic 30.0%
!!! TTTTTTCAGTAGGAACCAAA+AGG + chr7.3:23961686-23961705 None:intergenic 30.0%
AAAGTGAAATTGGAAAACCC+AGG - chr7.3:23961342-23961361 MS.gene52301:CDS 35.0%
AAGAATTGGGTGAAGAGAAA+AGG - chr7.3:23961385-23961404 MS.gene52301:intron 35.0%
AAGTGAAATTGGAAAACCCA+GGG - chr7.3:23961343-23961362 MS.gene52301:CDS 35.0%
AGAAAAGGAAGAGATGTATC+GGG + chr7.3:23961876-23961895 None:intergenic 35.0%
AGAGAAAAGGAAAGGGAAAT+CGG - chr7.3:23961398-23961417 MS.gene52301:intron 35.0%
ATCAAAGAGTCTCTGAGTAA+TGG + chr7.3:23961811-23961830 None:intergenic 35.0%
GAATTCCAATCAGAACTTCA+GGG + chr7.3:23961749-23961768 None:intergenic 35.0%
GAGAAAGGGAAATTGAAAGA+AGG - chr7.3:23961510-23961529 MS.gene52301:CDS 35.0%
GGCTAAGATAGAAGAAGAAT+TGG - chr7.3:23961371-23961390 MS.gene52301:intron 35.0%
GGTTGAAAAGAAAGGGAAAT+TGG - chr7.3:23961455-23961474 MS.gene52301:intron 35.0%
GGTTGAAGAGAAAGTGAAAT+TGG - chr7.3:23961332-23961351 MS.gene52301:CDS 35.0%
TCAAAGAGTCTCTGAGTAAT+GGG + chr7.3:23961810-23961829 None:intergenic 35.0%
TGAATTCCAATCAGAACTTC+AGG + chr7.3:23961750-23961769 None:intergenic 35.0%
! AACTTGTACAATCGCTGATT+GGG - chr7.3:23961602-23961621 MS.gene52301:CDS 35.0%
! CCTTTTTCTGCAGGAATATT+CGG - chr7.3:23962039-23962058 MS.gene52301:CDS 35.0%
AAAGGGAAATTGGGAAACCT+AGG - chr7.3:23961465-23961484 MS.gene52301:intron 40.0%
AAGGGAAATTGGGAAACCTA+GGG - chr7.3:23961466-23961485 MS.gene52301:intron 40.0%
AGAGGGTGAGATAGAAGAAA+AGG - chr7.3:23961434-23961453 MS.gene52301:intron 40.0%
AGTAGGAACCAAAAGGGTAA+CGG + chr7.3:23961679-23961698 None:intergenic 40.0%
ATCGGAAGAAATATCGTCAG+AGG - chr7.3:23961416-23961435 MS.gene52301:intron 40.0%
CAACTTGTACAATCGCTGAT+TGG - chr7.3:23961601-23961620 MS.gene52301:CDS 40.0%
CCGAATATTCCTGCAGAAAA+AGG + chr7.3:23962042-23962061 None:intergenic 40.0%
CTGAGGTAGAAGAAGAGAAA+GGG - chr7.3:23961496-23961515 MS.gene52301:CDS 40.0%
GCAGGAATATTCGGAAAAGT+TGG - chr7.3:23962048-23962067 MS.gene52301:CDS 40.0%
TATAAAGGGCAGCAACATGT+AGG + chr7.3:23962110-23962129 None:intergenic 40.0%
TCGGAAGAAATATCGTCAGA+GGG - chr7.3:23961417-23961436 MS.gene52301:intron 40.0%
TGACAGTGTGGACATTTACA+AGG + chr7.3:23961651-23961670 None:intergenic 40.0%
TGGGTGAAGAGAAAAGGAAA+GGG - chr7.3:23961391-23961410 MS.gene52301:intron 40.0%
TTGGGTGAAGAGAAAAGGAA+AGG - chr7.3:23961390-23961409 MS.gene52301:intron 40.0%
! ATTCGGAAAAGTTGGTCTCT+TGG - chr7.3:23962056-23962075 MS.gene52301:CDS 40.0%
! TTGATCTTCCTTTTCTCGTG+CGG - chr7.3:23961826-23961845 MS.gene52301:CDS 40.0%
!! ACACGAGCTCTGAAAAGAAA+AGG + chr7.3:23961891-23961910 None:intergenic 40.0%
AAACCTAGGGTTAGAAGCTG+AGG - chr7.3:23961479-23961498 MS.gene52301:CDS 45.0%
AACGAAAATTACGCCCGTGA+CGG + chr7.3:23962149-23962168 None:intergenic 45.0%
AACTACAACTGCGACGATGA+TGG - chr7.3:23961705-23961724 MS.gene52301:CDS 45.0%
ATTGGAAAACCCAGGGTTAG+AGG - chr7.3:23961350-23961369 MS.gene52301:CDS 45.0%
CTATCTTAGCCTCTAACCCT+GGG + chr7.3:23961362-23961381 None:intergenic 45.0%
GCTGAGGTAGAAGAAGAGAA+AGG - chr7.3:23961495-23961514 MS.gene52301:CDS 45.0%
GGAAAACGAAAACCTAGCGT+TGG - chr7.3:23961290-23961309 MS.gene52301:CDS 45.0%
GGAGACTGAGAGAGAAGAAA+TGG - chr7.3:23961311-23961330 MS.gene52301:CDS 45.0%
GGGTGAAGAGAAAGGGAAAT+CGG - chr7.3:23961269-23961288 MS.gene52301:CDS 45.0%
GTAGGAACCAAAAGGGTAAC+GGG + chr7.3:23961678-23961697 None:intergenic 45.0%
GTGAAGCTACATGCTCTCAT+TGG - chr7.3:23961571-23961590 MS.gene52301:CDS 45.0%
TCAATACTTTGCCTCCGTCA+CGG - chr7.3:23962132-23962151 MS.gene52301:CDS 45.0%
TCTATCTTAGCCTCTAACCC+TGG + chr7.3:23961363-23961382 None:intergenic 45.0%
!! ACCTTCTGGGATGATGTCAA+TGG + chr7.3:23961955-23961974 None:intergenic 45.0%
!! CCTTCTGGGATGATGTCAAT+GGG + chr7.3:23961954-23961973 None:intergenic 45.0%
!! CTTCTGGGATGATGTCAATG+GGG + chr7.3:23961953-23961972 None:intergenic 45.0%
AAAAGCCTCCGCACGAGAAA+AGG + chr7.3:23961837-23961856 None:intergenic 50.0%
CAATACTTTGCCTCCGTCAC+GGG - chr7.3:23962133-23962152 MS.gene52301:CDS 50.0%
CCCATTGACATCATCCCAGA+AGG - chr7.3:23961951-23961970 MS.gene52301:CDS 50.0%
CTACCTCAGCTTCTAACCCT+AGG + chr7.3:23961485-23961504 None:intergenic 50.0%
! ATCTTCCTTTTCTCGTGCGG+AGG - chr7.3:23961829-23961848 MS.gene52301:CDS 50.0%
! CACGACCCTGAAGTTCTGAT+TGG - chr7.3:23961741-23961760 MS.gene52301:CDS 50.0%
! TCATCGACCCGTTACCCTTT+TGG - chr7.3:23961668-23961687 MS.gene52301:CDS 50.0%
CTCTCTCAGTCTCCAACGCT+AGG + chr7.3:23961305-23961324 None:intergenic 55.0%
GAAAATTACGCCCGTGACGG+AGG + chr7.3:23962146-23962165 None:intergenic 55.0%
! TCTCGTGCGGAGGCTTTTCA+AGG - chr7.3:23961839-23961858 MS.gene52301:CDS 55.0%
!! GTAACGGGTCGATGACAGTG+TGG + chr7.3:23961663-23961682 None:intergenic 55.0%


Chromosome Type Strat End Strand Name
chr7.3 gene 23961267 23962173 23961267 ID=MS.gene52301
chr7.3 mRNA 23961267 23962173 23961267 ID=MS.gene52301.t1;Parent=MS.gene52301
chr7.3 exon 23961468 23962173 23961468 ID=MS.gene52301.t1.exon1;Parent=MS.gene52301.t1
chr7.3 CDS 23961468 23962173 23961468 ID=cds.MS.gene52301.t1;Parent=MS.gene52301.t1
chr7.3 exon 23961267 23961388 23961267 ID=MS.gene52301.t1.exon2;Parent=MS.gene52301.t1
chr7.3 CDS 23961267 23961388 23961267 ID=cds.MS.gene52301.t1;Parent=MS.gene52301.t1
Gene Sequence

>MS.gene52301

ATGGGTGAAGAGAAAGGGAAATCGGAAAACGAAAACCTAGCGTTGGAGACTGAGAGAGAAGAAATGGTTGAAGAGAAAGTGAAATTGGAAAACCCAGGGTTAGAGGCTAAGATAGAAGAAGAATTGGGTGAAGAGAAAAGGAAAGGGAAATCGGAAGAAATATCGTCAGAGGGTGAGATAGAAGAAAAGGTTGAAAAGAAAGGGAAATTGGGAAACCTAGGGTTAGAAGCTGAGGTAGAAGAAGAGAAAGGGAAATTGAAAGAAGGTACATGCTCAAAATGTCATGTAAAATTCCAGATTATATGTGAAGCTACATGCTCTCATTGGTTTTGTGCAACTTGTACAATCGCTGATTGGGAACAACAATCTACCGACATTGAACCTTGTAAATGTCCACACTGTCATCGACCCGTTACCCTTTTGGTTCCTACTGAAAAAAACTACAACTGCGACGATGATGGCAACAAGTATTTTCACGACCCTGAAGTTCTGATTGGAATTCAGACTTATAACACTATTTTTGGTGATCAATCTAAAGCTCCCATTACTCAGAGACTCTTTGATCTTCCTTTTCTCGTGCGGAGGCTTTTCAAGGATTTCATTCAGCCCGATACATCTCTTCCTTTTCTTTTCAGAGCTCGTGTCTTCATTACTATGATACTGATTGTTATATACATCTTCAGCCCCATTGACATCATCCCAGAAGGTTATATTTTTCCATTTTTGTCCAACTTGTGAAATTGTTTTGGTGAATTTATGTTTGAATTTTGTTCCTTTTTCTGCAGGAATATTCGGAAAAGTTGGTCTCTTGGATGATCTCCTAATTACATTAATCTTCTTCCTACATGTTGCTGCCCTTTATAGATCAATACTTTGCCTCCGTCACGGGCGTAATTTTCGTTTTTAG

Protein sequence

>MS.gene52301.t1

MGEEKGKSENENLALETEREEMVEEKVKLENPGLEAKIEEELGEEKRKGKSEEISSEGEIEEKVEKKGKLGNLGLEAEVEEEKGKLKEGTCSKCHVKFQIICEATCSHWFCATCTIADWEQQSTDIEPCKCPHCHRPVTLLVPTEKNYNCDDDGNKYFHDPEVLIGIQTYNTIFGDQSKAPITQRLFDLPFLVRRLFKDFIQPDTSLPFLFRARVFITMILIVIYIFSPIDIIPEGIFGKVGLLDDLLITLIFFLHVAALYRSILCLRHGRNFRF