AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene36293

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene36293.t1 MTR_2g102140 99.035 311 1 1 1 309 1 311 0.0 630
MS.gene36293.t1 MTR_4g012060 46.562 320 130 8 1 309 1 290 1.33e-76 236
MS.gene36293.t1 MTR_1g072110 38.406 138 61 4 140 271 115 234 2.37e-18 82.8
MS.gene36293.t1 MTR_7g095150 47.887 71 35 1 201 271 132 200 4.61e-15 73.2
MS.gene36293.t1 MTR_1g111640 28.340 247 96 9 29 268 26 198 5.88e-13 67.8
MS.gene36293.t1 MTR_1g103640 42.188 64 34 1 206 269 117 177 5.03e-12 65.1
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene36293.t1 AT1G79960 36.335 322 147 10 1 298 1 288 6.06e-47 160
MS.gene36293.t1 AT5G04820 35.338 133 62 4 137 269 102 210 2.77e-14 72.0
MS.gene36293.t1 AT4G14860 45.312 64 28 2 207 268 109 167 1.54e-11 62.8

Find 50 sgRNAs with CRISPR-Local

Find 63 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AAGCAGGTTACCATAGAATT+TGG 0.233067 2.2:-1714027 MS.gene36293:CDS
CGAGTCCTTACGATGATTTC+AGG 0.250240 2.2:-1714302 MS.gene36293:CDS
GAAAATTGATTGGGACTTCA+TGG 0.309098 2.2:-1714223 MS.gene36293:CDS
TTTGCAGCCAGAGAGCATTT+TGG 0.332403 2.2:+1714842 None:intergenic
CAGGAACCACCAATACGTTT+TGG 0.387081 2.2:+1714591 None:intergenic
ACAATCAAAGGAAAATTGAT+TGG 0.389239 2.2:-1714233 MS.gene36293:CDS
CTAAGAGGAACCAAATTCTA+TGG 0.390296 2.2:+1714017 None:intergenic
CAGGCGATCAATGCAAGAAT+TGG 0.391866 2.2:-1714283 MS.gene36293:CDS
TTTGTTGTTATTGTTGTTAA+CGG 0.409570 2.2:+1714761 None:intergenic
GTTAATCGAATTTGAGGTTG+TGG 0.421883 2.2:+1714864 None:intergenic
ATCAATGATCCTGAGTTGCC+TGG 0.427100 2.2:+1714495 None:intergenic
TATTGGTGGTTCCTGGTTGT+TGG 0.439269 2.2:-1714583 MS.gene36293:CDS
TTAGGATTGGTAGGGAAGTC+AGG 0.440786 2.2:-1714062 MS.gene36293:CDS
ATTGTTGTTAACGGCGTTAG+AGG 0.446207 2.2:+1714770 None:intergenic
CAAAACGTATTGGTGGTTCC+TGG 0.454127 2.2:-1714590 MS.gene36293:CDS
TTGATCTCATCACTGTTATG+AGG 0.467638 2.2:-1714131 MS.gene36293:CDS
GAATTGGTGGAATCAAAGTA+TGG 0.467801 2.2:-1714267 MS.gene36293:CDS
GAAGAATTCAGAGGCTGCTC+CGG 0.469764 2.2:-1714109 MS.gene36293:CDS
CGATTAACCAAAATGCTCTC+TGG 0.470779 2.2:-1714849 MS.gene36293:CDS
CGTGTAGCGTGAGAACTGTT+AGG 0.472831 2.2:-1714080 MS.gene36293:CDS
AACAGTGCAACACAATTCTC+AGG 0.479484 2.2:+1714336 None:intergenic
AGGCAACTCAGGATCATTGA+TGG 0.480266 2.2:-1714493 MS.gene36293:CDS
ACACCACCTCAAGATCTTTG+TGG 0.490451 2.2:-1714540 MS.gene36293:CDS
CAATCAAAGGAAAATTGATT+GGG 0.491479 2.2:-1714232 MS.gene36293:CDS
TGAAATTCTCAAAGAGAAAA+CGG 0.493044 2.2:+1714706 None:intergenic
AACAGCATCACCTTCAAAAG+AGG 0.511692 2.2:-1714400 MS.gene36293:CDS
TGAGAACTGTTAGGATTGGT+AGG 0.512241 2.2:-1714071 MS.gene36293:CDS
TTTGTGAAACCAGGCAACTC+AGG 0.516733 2.2:-1714504 MS.gene36293:CDS
TTTGTTGAGGTAATCTTGAA+GGG 0.525082 2.2:+1714902 None:intergenic
GCGATCAATGCAAGAATTGG+TGG 0.527393 2.2:-1714280 MS.gene36293:CDS
CTGAAATCATCGTAAGGACT+CGG 0.533629 2.2:+1714303 None:intergenic
AAATTCTATGGTAACCTGCT+TGG 0.538786 2.2:+1714029 None:intergenic
CTCACGCTACACGGCTTCGC+CGG 0.538841 2.2:+1714090 None:intergenic
GAGGAACCACCAAAACGTAT+TGG 0.549662 2.2:-1714600 MS.gene36293:CDS
TATGTTTCTGCCGTTATCCA+AGG 0.558329 2.2:+1714797 None:intergenic
CTAACAGTTCTCACGCTACA+CGG 0.576486 2.2:+1714081 None:intergenic
GCACGATTCTTTGTGAAACC+AGG 0.577857 2.2:-1714513 MS.gene36293:CDS
AGCGTGAGAACTGTTAGGAT+TGG 0.588361 2.2:-1714075 MS.gene36293:CDS
CAGGAAGAAGAAGACCAAGC+AGG 0.606262 2.2:-1714043 MS.gene36293:CDS
TCTCGGTGACTCCAACAACC+AGG 0.608261 2.2:+1714572 None:intergenic
GTAAGATTGAAAACAATCAA+AGG 0.608557 2.2:-1714245 MS.gene36293:CDS
GAACCACCAAAACGTATTGG+TGG 0.614019 2.2:-1714597 MS.gene36293:CDS
GCTGAGCCACAAAGATCTTG+AGG 0.618030 2.2:+1714534 None:intergenic
GATCGCCTGAAATCATCGTA+AGG 0.625029 2.2:+1714297 None:intergenic
TGTGATGATTGTGATCATCA+TGG 0.625055 2.2:+1714364 None:intergenic
GAGAACTGTTAGGATTGGTA+GGG 0.631326 2.2:-1714070 MS.gene36293:CDS
GGTGGTGTTGTAATGAATCT+CGG 0.636568 2.2:+1714555 None:intergenic
AATTGATTGGGACTTCATGG+AGG 0.677814 2.2:-1714220 MS.gene36293:CDS
TGTTATGAGGAAGAATTCAG+AGG 0.682074 2.2:-1714118 MS.gene36293:CDS
GAGCCACAAAGATCTTGAGG+TGG 0.753269 2.2:+1714537 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TTTGTTGTTATTGTTGTTAA+CGG + chr2.2:1714183-1714202 None:intergenic 20.0%
!!! TTTTGTTTTTGATTTTGTTG+AGG + chr2.2:1714055-1714074 None:intergenic 20.0%
! ACAATCAAAGGAAAATTGAT+TGG - chr2.2:1714708-1714727 MS.gene36293:CDS 25.0%
! CAACAAAAACAAAAGAATCT+CGG - chr2.2:1714304-1714323 MS.gene36293:CDS 25.0%
! CAATCAAAGGAAAATTGATT+GGG - chr2.2:1714709-1714728 MS.gene36293:CDS 25.0%
! GTAAGATTGAAAACAATCAA+AGG - chr2.2:1714696-1714715 MS.gene36293:CDS 25.0%
! TGAAATTCTCAAAGAGAAAA+CGG + chr2.2:1714238-1714257 None:intergenic 25.0%
!!! ATTTTGGTTAATCGAATTTG+AGG + chr2.2:1714086-1714105 None:intergenic 25.0%
TTTGTTGAGGTAATCTTGAA+GGG + chr2.2:1714042-1714061 None:intergenic 30.0%
! AAGGAAAAAGATGGTGTTTT+GGG + chr2.2:1714128-1714147 None:intergenic 30.0%
! ACTACAATAACCTCTTTTGA+AGG + chr2.2:1714554-1714573 None:intergenic 30.0%
! TTTTGTTGAGGTAATCTTGA+AGG + chr2.2:1714043-1714062 None:intergenic 30.0%
AAATTCTATGGTAACCTGCT+TGG + chr2.2:1714915-1714934 None:intergenic 35.0%
AAGCAGGTTACCATAGAATT+TGG - chr2.2:1714914-1714933 MS.gene36293:CDS 35.0%
CTAAGAGGAACCAAATTCTA+TGG + chr2.2:1714927-1714946 None:intergenic 35.0%
GAAAATTGATTGGGACTTCA+TGG - chr2.2:1714718-1714737 MS.gene36293:CDS 35.0%
GAATTGGTGGAATCAAAGTA+TGG - chr2.2:1714674-1714693 MS.gene36293:CDS 35.0%
TGTGATGATTGTGATCATCA+TGG + chr2.2:1714580-1714599 None:intergenic 35.0%
TGTTATGAGGAAGAATTCAG+AGG - chr2.2:1714823-1714842 MS.gene36293:CDS 35.0%
TTGATCTCATCACTGTTATG+AGG - chr2.2:1714810-1714829 MS.gene36293:CDS 35.0%
! CAAAACACCATCTTTTTCCT+TGG - chr2.2:1714127-1714146 MS.gene36293:CDS 35.0%
! CAAGGAAAAAGATGGTGTTT+TGG + chr2.2:1714129-1714148 None:intergenic 35.0%
! CCATCTTTTTCCTTGGATAA+CGG - chr2.2:1714134-1714153 MS.gene36293:CDS 35.0%
! GTTAATCGAATTTGAGGTTG+TGG + chr2.2:1714080-1714099 None:intergenic 35.0%
!!! AGGGTTTTTTGAAGCTTCTT+AGG + chr2.2:1714023-1714042 None:intergenic 35.0%
AACAGCATCACCTTCAAAAG+AGG - chr2.2:1714541-1714560 MS.gene36293:CDS 40.0%
AACAGTGCAACACAATTCTC+AGG + chr2.2:1714608-1714627 None:intergenic 40.0%
AATTGATTGGGACTTCATGG+AGG - chr2.2:1714721-1714740 MS.gene36293:CDS 40.0%
CCGTTATCCAAGGAAAAAGA+TGG + chr2.2:1714137-1714156 None:intergenic 40.0%
CGATTAACCAAAATGCTCTC+TGG - chr2.2:1714092-1714111 MS.gene36293:CDS 40.0%
CTCGGATGAAAAAAACAACG+AGG - chr2.2:1714322-1714341 MS.gene36293:CDS 40.0%
CTGAAATCATCGTAAGGACT+CGG + chr2.2:1714641-1714660 None:intergenic 40.0%
! ATTGTTGTTAACGGCGTTAG+AGG + chr2.2:1714174-1714193 None:intergenic 40.0%
! GAGAACTGTTAGGATTGGTA+GGG - chr2.2:1714871-1714890 MS.gene36293:CDS 40.0%
! TATGTTTCTGCCGTTATCCA+AGG + chr2.2:1714147-1714166 None:intergenic 40.0%
! TGAGAACTGTTAGGATTGGT+AGG - chr2.2:1714870-1714889 MS.gene36293:CDS 40.0%
!! GGTGGTGTTGTAATGAATCT+CGG + chr2.2:1714389-1714408 None:intergenic 40.0%
ACACCACCTCAAGATCTTTG+TGG - chr2.2:1714401-1714420 MS.gene36293:CDS 45.0%
AGCGTGAGAACTGTTAGGAT+TGG - chr2.2:1714866-1714885 MS.gene36293:CDS 45.0%
AGGCAACTCAGGATCATTGA+TGG - chr2.2:1714448-1714467 MS.gene36293:CDS 45.0%
ATCAATGATCCTGAGTTGCC+TGG + chr2.2:1714449-1714468 None:intergenic 45.0%
CAGGCGATCAATGCAAGAAT+TGG - chr2.2:1714658-1714677 MS.gene36293:CDS 45.0%
CGAGTCCTTACGATGATTTC+AGG - chr2.2:1714639-1714658 MS.gene36293:CDS 45.0%
CTAACAGTTCTCACGCTACA+CGG + chr2.2:1714863-1714882 None:intergenic 45.0%
GAACCACCAAAACGTATTGG+TGG - chr2.2:1714344-1714363 MS.gene36293:CDS 45.0%
GAGGAACCACCAAAACGTAT+TGG - chr2.2:1714341-1714360 MS.gene36293:CDS 45.0%
GATCGCCTGAAATCATCGTA+AGG + chr2.2:1714647-1714666 None:intergenic 45.0%
GCACGATTCTTTGTGAAACC+AGG - chr2.2:1714428-1714447 MS.gene36293:CDS 45.0%
GCGATCAATGCAAGAATTGG+TGG - chr2.2:1714661-1714680 MS.gene36293:CDS 45.0%
TTTGTGAAACCAGGCAACTC+AGG - chr2.2:1714437-1714456 MS.gene36293:CDS 45.0%
! CAAAACGTATTGGTGGTTCC+TGG - chr2.2:1714351-1714370 MS.gene36293:CDS 45.0%
! CAGGAACCACCAATACGTTT+TGG + chr2.2:1714353-1714372 None:intergenic 45.0%
! GAACCACCAATACGTTTTGG+TGG + chr2.2:1714350-1714369 None:intergenic 45.0%
! TATTGGTGGTTCCTGGTTGT+TGG - chr2.2:1714358-1714377 MS.gene36293:CDS 45.0%
! TTAGGATTGGTAGGGAAGTC+AGG - chr2.2:1714879-1714898 MS.gene36293:CDS 45.0%
!!! TTTGCAGCCAGAGAGCATTT+TGG + chr2.2:1714102-1714121 None:intergenic 45.0%
CAGGAAGAAGAAGACCAAGC+AGG - chr2.2:1714898-1714917 MS.gene36293:CDS 50.0%
CGTGTAGCGTGAGAACTGTT+AGG - chr2.2:1714861-1714880 MS.gene36293:CDS 50.0%
GAAGAATTCAGAGGCTGCTC+CGG - chr2.2:1714832-1714851 MS.gene36293:CDS 50.0%
GAGCCACAAAGATCTTGAGG+TGG + chr2.2:1714407-1714426 None:intergenic 50.0%
GCTGAGCCACAAAGATCTTG+AGG + chr2.2:1714410-1714429 None:intergenic 50.0%
TCTCGGTGACTCCAACAACC+AGG + chr2.2:1714372-1714391 None:intergenic 55.0%
CTCACGCTACACGGCTTCGC+CGG + chr2.2:1714854-1714873 None:intergenic 65.0%


Chromosome Type Strat End Strand Name
chr2.2 gene 1714017 1714946 1714017 ID=MS.gene36293
chr2.2 mRNA 1714017 1714946 1714017 ID=MS.gene36293.t1;Parent=MS.gene36293
chr2.2 exon 1714017 1714946 1714017 ID=MS.gene36293.t1.exon1;Parent=MS.gene36293.t1
chr2.2 CDS 1714017 1714946 1714017 ID=cds.MS.gene36293.t1;Parent=MS.gene36293.t1
Gene Sequence

>MS.gene36293

ATGCCTAAGAAGCTTCAAAAAACCCTTCAAGATTACCTCAACAAAATCAAAAACAAAAATCCACAACCTCAAATTCGATTAACCAAAATGCTCTCTGGCTGCAAACATCCCAAAACACCATCTTTTTCCTTGGATAACGGCAGAAACATATCATCCTCTAACGCCGTTAACAACAATAACAACAAAATCAATGATGCTGCAACACTAGCTGACGTTGACCGTTTTCTCTTTGAGAATTTCAAGTCTCTATATTTCAAAGATGATGAAGAAACAGAACAAAACAACAACAACAAAAACAAAAGAATCTCGGATGAAAAAAACAACGAGGAACCACCAAAACGTATTGGTGGTTCCTGGTTGTTGGAGTCACCGAGATTCATTACAACACCACCTCAAGATCTTTGTGGCTCAGCACGATTCTTTGTGAAACCAGGCAACTCAGGATCATTGATGGAAGATGCACTGTCTCTAACAAACAGTGATGAAGCTGATTCGAGTAATTCGAATAATTCAAATTCATCATCAACAGCATCACCTTCAAAAGAGGTTATTGTAGTAAACCATGATGATCACAATCATCACACTCTTCCTGAGAATTGTGTTGCACTGTTATCATATTCTCCGAGTCCTTACGATGATTTCAGGCGATCAATGCAAGAATTGGTGGAATCAAAGTATGGTAAGATTGAAAACAATCAAAGGAAAATTGATTGGGACTTCATGGAGGAGATTTTGTTTTGTTATCTTAATGTTAATGAGAAAAAATCTCATAAGTTTATATTAAGTGCTTTTGTTGATCTCATCACTGTTATGAGGAAGAATTCAGAGGCTGCTCCGGCGAAGCCGTGTAGCGTGAGAACTGTTAGGATTGGTAGGGAAGTCAGGAAGAAGAAGACCAAGCAGGTTACCATAGAATTTGGTTCCTCTTAG
Protein sequence

>MS.gene36293.t1

MPKKLQKTLQDYLNKIKNKNPQPQIRLTKMLSGCKHPKTPSFSLDNGRNISSSNAVNNNNNKINDAATLADVDRFLFENFKSLYFKDDEETEQNNNNKNKRISDEKNNEEPPKRIGGSWLLESPRFITTPPQDLCGSARFFVKPGNSGSLMEDALSLTNSDEADSSNSNNSNSSSTASPSKEVIVVNHDDHNHHTLPENCVALLSYSPSPYDDFRRSMQELVESKYGKIENNQRKIDWDFMEEILFCYLNVNEKKSHKFILSAFVDLITVMRKNSEAAPAKPCSVRTVRIGREVRKKKTKQVTIEFGSS