AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene56507


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene56507.t1 MTR_4g082360 65.862 290 84 7 1 285 1 280 5.22e-106 310
MS.gene56507.t1 MTR_4g082355 62.718 287 102 4 1 285 1 284 7.43e-98 289
MS.gene56507.t1 MTR_4g082365 52.857 280 105 4 1 278 1 255 6.02e-83 250
MS.gene56507.t1 MTR_4g082550 32.308 325 136 12 4 269 11 310 5.72e-23 97.1
MS.gene56507.t1 MTR_4g096890 28.571 294 169 13 4 269 12 292 4.84e-11 62.8
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene56507.t1 AT3G11810 33.439 314 166 7 4 275 14 326 4.87e-38 137

Find 77 sgRNAs with CRISPR-Local

Find 90 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTTGGACGTTTACATGATTT+TGG 0.176385 4.2:-27348602 MS.gene56507:CDS
AGTCCCACTTGTGGTTTATT+TGG 0.226722 4.2:-27348620 MS.gene56507:CDS
TCTAGTCTATTATGGAATTA+AGG 0.232332 4.2:+27348279 None:intergenic
GAAGTTGAAGAAGTGGAATT+TGG 0.233912 4.2:-27348328 MS.gene56507:CDS
AGTTTCCAGCTTCTCCTTAA+TGG 0.257266 4.2:+27348538 None:intergenic
AAATATAACAAAACAAAGTT+AGG 0.287977 4.2:+27348664 None:intergenic
TGGTGGGTGGGTTGTGTTGA+AGG 0.317375 4.2:+27348983 None:intergenic
GTTGGGGTTTGGAACCATTA+AGG 0.318251 4.2:-27348552 MS.gene56507:CDS
GTGGGGTTGGTAATGGTGGG+TGG 0.324989 4.2:+27348970 None:intergenic
CGGCGGAGGTGGCGAGGAGG+GGG 0.336505 4.2:+27348794 None:intergenic
TTTCTCTTTATGTTTCTCAT+TGG 0.336811 4.2:-27348742 MS.gene56507:CDS
TGTGGTGGGGTTGGTAATGG+TGG 0.370934 4.2:+27348966 None:intergenic
CATCGATTAGTGGTTATAGT+TGG 0.378825 4.2:-27348450 MS.gene56507:CDS
AAGTTGAAGAAGTGGAATTT+GGG 0.381890 4.2:-27348327 MS.gene56507:CDS
GGTGGAATCACGTTGGGGTT+TGG 0.387654 4.2:-27348563 MS.gene56507:CDS
AGAGGAAAGAGAGGGGAAGG+AGG 0.392894 4.2:+27349034 None:intergenic
GATTGTGGTGGGGTTGGTAA+TGG 0.418184 4.2:+27348963 None:intergenic
ATTAAGGAGAAGCTGGAAAC+TGG 0.427521 4.2:-27348536 MS.gene56507:CDS
TGTAGTGGTGGAATCACGTT+GGG 0.429158 4.2:-27348569 MS.gene56507:CDS
ATCGATTAGTGGTTATAGTT+GGG 0.432064 4.2:-27348449 MS.gene56507:CDS
TGACGGCGGAGGTGGCGAGG+AGG 0.433770 4.2:+27348791 None:intergenic
ACGGCGGAGGTGGCGAGGAG+GGG 0.433896 4.2:+27348793 None:intergenic
GAGGGGAAGGAGGAAGATGA+GGG 0.434317 4.2:+27349044 None:intergenic
AGAGGGGAAGGAGGAAGATG+AGG 0.440647 4.2:+27349043 None:intergenic
GGTTAGTCATGAAGTCGATA+TGG 0.441486 4.2:+27348686 None:intergenic
TGAGTTGGTAGATGAGGGAG+AGG 0.444374 4.2:+27349016 None:intergenic
TTTGACAGGTTGATTAAAGA+AGG 0.447665 4.2:+27348855 None:intergenic
AGTGAAAGTGACGGCGGAGG+TGG 0.448228 4.2:+27348783 None:intergenic
ATGGCTTCTTTGAGTTTGAC+AGG 0.455773 4.2:+27348841 None:intergenic
TGGGGTTGGTAATGGTGGGT+GGG 0.463533 4.2:+27348971 None:intergenic
GGAAGTGGTGATGGATTTGA+TGG 0.464194 4.2:+27348822 None:intergenic
AGATGAGGGAGAGGAAAGAG+AGG 0.467128 4.2:+27349025 None:intergenic
GGGGAAGAAGGAAGTGGTGA+TGG 0.469954 4.2:+27348813 None:intergenic
GGGAGAGGAAAGAGAGGGGA+AGG 0.471420 4.2:+27349031 None:intergenic
ACATGATGAAGTTGAAGAAG+TGG 0.477972 4.2:-27348335 MS.gene56507:CDS
AGATGGAAGAGGTAAGGAAG+AGG 0.486051 4.2:+27348923 None:intergenic
AAGAGAAGATGGAAGAGGTA+AGG 0.488350 4.2:+27348917 None:intergenic
GACGGCGGAGGTGGCGAGGA+GGG 0.489494 4.2:+27348792 None:intergenic
GGGATGTTGACATCGATTAG+TGG 0.493411 4.2:-27348460 MS.gene56507:CDS
TGGAACCATTAAGGAGAAGC+TGG 0.500836 4.2:-27348543 MS.gene56507:CDS
GATGGCACTATAAGAGAAGA+TGG 0.501228 4.2:+27348906 None:intergenic
TGGAAGAGGTAAGGAAGAGG+AGG 0.510217 4.2:+27348926 None:intergenic
AGTGAAAGCACCGCAAGTAT+AGG 0.515408 4.2:+27348406 None:intergenic
CGTGGTTTCTCCTATACTTG+CGG 0.518316 4.2:-27348416 MS.gene56507:CDS
GGAAGATGAGGGAAAGAGTG+AGG 0.538897 4.2:+27349055 None:intergenic
GTGGTGGGGTTGGTAATGGT+GGG 0.540006 4.2:+27348967 None:intergenic
AGTGGAATTTGGGAAGGAAA+AGG 0.544513 4.2:-27348317 MS.gene56507:CDS
AATATAACAAAACAAAGTTA+GGG 0.546540 4.2:+27348665 None:intergenic
AAAGATGATTGTGGTGGGGT+TGG 0.549565 4.2:+27348957 None:intergenic
GAGCATGAGTTGGTAGATGA+GGG 0.556437 4.2:+27349011 None:intergenic
GAGAGTGAAAGTGACGGCGG+AGG 0.556656 4.2:+27348780 None:intergenic
GATGAGGGAGAGGAAAGAGA+GGG 0.561976 4.2:+27349026 None:intergenic
TGAGCATGAGTTGGTAGATG+AGG 0.563215 4.2:+27349010 None:intergenic
GCTTTCACTTTACAGTATTG+CGG 0.575903 4.2:-27348392 MS.gene56507:CDS
TGAAGAAGTGGAATTTGGGA+AGG 0.577294 4.2:-27348323 MS.gene56507:CDS
ATGAGGGAGAGGAAAGAGAG+GGG 0.577407 4.2:+27349027 None:intergenic
AAGTGACGGCGGAGGTGGCG+AGG 0.578409 4.2:+27348788 None:intergenic
GATTCTTATAGTCCCACTTG+TGG 0.579316 4.2:-27348629 MS.gene56507:CDS
GGTGAAAGTGATTGTAGTGG+TGG 0.584735 4.2:-27348581 MS.gene56507:CDS
ACTATAAGAGAAGATGGAAG+AGG 0.587360 4.2:+27348912 None:intergenic
ACGTCCAAATAAACCACAAG+TGG 0.588152 4.2:+27348616 None:intergenic
AACTGGTGAAAGGAATGAAA+AGG 0.591857 4.2:-27348519 MS.gene56507:CDS
GCTGTAGGTGATGGTGATGA+TGG 0.593392 4.2:+27348888 None:intergenic
GGTGAAAGGAATGAAAAGGT+TGG 0.594891 4.2:-27348515 MS.gene56507:CDS
GAAGGCGTTGTAAACGCTGT+AGG 0.602360 4.2:+27348873 None:intergenic
GAAGGTCTTTGAGCATGAGT+TGG 0.610047 4.2:+27349001 None:intergenic
TTTGGTGAAAGTGATTGTAG+TGG 0.612338 4.2:-27348584 MS.gene56507:CDS
AGAAGCTGGAAACTGGTGAA+AGG 0.623879 4.2:-27348529 MS.gene56507:CDS
GAAAGAGTGAGGTAGTGACC+AGG 0.630176 4.2:+27349066 None:intergenic
GAAGTAGAGAGTGAAAGTGA+CGG 0.630975 4.2:+27348774 None:intergenic
GTCATAATAAATTCTCAACC+TGG 0.635020 4.2:-27349084 MS.gene56507:CDS
GTTGTAAACGCTGTAGGTGA+TGG 0.651201 4.2:+27348879 None:intergenic
TTGTAGTGGTGGAATCACGT+TGG 0.659689 4.2:-27348570 MS.gene56507:CDS
GTAGAGAGTGAAAGTGACGG+CGG 0.661736 4.2:+27348777 None:intergenic
ATTTGGGAAGGAAAAGGACG+AGG 0.663443 4.2:-27348311 MS.gene56507:CDS
CGTCCAAATAAACCACAAGT+GGG 0.677797 4.2:+27348617 None:intergenic
GTAGTGGTGGAATCACGTTG+GGG 0.688303 4.2:-27348568 MS.gene56507:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAATATAACAAAACAAAGTT+AGG + chr4.2:27348750-27348769 None:intergenic 15.0%
!! AATATAACAAAACAAAGTTA+GGG + chr4.2:27348749-27348768 None:intergenic 15.0%
!!! CTTTTCATCATTTTTATATT+AGG - chr4.2:27348702-27348721 MS.gene56507:CDS 15.0%
!!! CTTTGTTTTGTTATATTTCA+TGG - chr4.2:27348752-27348771 MS.gene56507:CDS 20.0%
! GATAAACAAAAAGATGATTG+TGG + chr4.2:27348466-27348485 None:intergenic 25.0%
! TTTCTCTTTATGTTTCTCAT+TGG - chr4.2:27348669-27348688 MS.gene56507:CDS 25.0%
AAACAAAAAGATGATTGTGG+TGG + chr4.2:27348463-27348482 None:intergenic 30.0%
AACAAAAAGATGATTGTGGT+GGG + chr4.2:27348462-27348481 None:intergenic 30.0%
AAGTTGAAGAAGTGGAATTT+GGG - chr4.2:27349084-27349103 MS.gene56507:CDS 30.0%
ATCGATTAGTGGTTATAGTT+GGG - chr4.2:27348962-27348981 MS.gene56507:CDS 30.0%
GTCATAATAAATTCTCAACC+TGG - chr4.2:27348327-27348346 MS.gene56507:CDS 30.0%
! TTTGGACGTTTACATGATTT+TGG - chr4.2:27348809-27348828 MS.gene56507:CDS 30.0%
!! TTTGACAGGTTGATTAAAGA+AGG + chr4.2:27348559-27348578 None:intergenic 30.0%
AACTGGTGAAAGGAATGAAA+AGG - chr4.2:27348892-27348911 MS.gene56507:CDS 35.0%
ACAAAAAGATGATTGTGGTG+GGG + chr4.2:27348461-27348480 None:intergenic 35.0%
ACATGATGAAGTTGAAGAAG+TGG - chr4.2:27349076-27349095 MS.gene56507:CDS 35.0%
ACTATAAGAGAAGATGGAAG+AGG + chr4.2:27348502-27348521 None:intergenic 35.0%
GAAGTTGAAGAAGTGGAATT+TGG - chr4.2:27349083-27349102 MS.gene56507:CDS 35.0%
GCTTTCACTTTACAGTATTG+CGG - chr4.2:27349019-27349038 MS.gene56507:CDS 35.0%
TTTGGTGAAAGTGATTGTAG+TGG - chr4.2:27348827-27348846 MS.gene56507:CDS 35.0%
! CATCGATTAGTGGTTATAGT+TGG - chr4.2:27348961-27348980 MS.gene56507:CDS 35.0%
! TAGAGAAGATCCCAGATTTT+TGG + chr4.2:27348297-27348316 None:intergenic 35.0%
! TAGTTGGGTTATGATTTTCG+TGG - chr4.2:27348977-27348996 MS.gene56507:CDS 35.0%
!!! GGCTTTTTCAACCTTGTTTT+TGG - chr4.2:27348917-27348936 MS.gene56507:CDS 35.0%
AAGAGAAGATGGAAGAGGTA+AGG + chr4.2:27348497-27348516 None:intergenic 40.0%
ACGTCCAAATAAACCACAAG+TGG + chr4.2:27348798-27348817 None:intergenic 40.0%
AGTCCCACTTGTGGTTTATT+TGG - chr4.2:27348791-27348810 MS.gene56507:CDS 40.0%
AGTGGAATTTGGGAAGGAAA+AGG - chr4.2:27349094-27349113 MS.gene56507:CDS 40.0%
AGTTTCCAGCTTCTCCTTAA+TGG + chr4.2:27348876-27348895 None:intergenic 40.0%
ATTAAGGAGAAGCTGGAAAC+TGG - chr4.2:27348875-27348894 MS.gene56507:CDS 40.0%
CGTCCAAATAAACCACAAGT+GGG + chr4.2:27348797-27348816 None:intergenic 40.0%
GAAGTAGAGAGTGAAAGTGA+CGG + chr4.2:27348640-27348659 None:intergenic 40.0%
GATGGCACTATAAGAGAAGA+TGG + chr4.2:27348508-27348527 None:intergenic 40.0%
GATTCTTATAGTCCCACTTG+TGG - chr4.2:27348782-27348801 MS.gene56507:CDS 40.0%
GGTGAAAGGAATGAAAAGGT+TGG - chr4.2:27348896-27348915 MS.gene56507:CDS 40.0%
TGAAGAAGTGGAATTTGGGA+AGG - chr4.2:27349088-27349107 MS.gene56507:CDS 40.0%
! ATGGCTTCTTTGAGTTTGAC+AGG + chr4.2:27348573-27348592 None:intergenic 40.0%
! GGTTAGTCATGAAGTCGATA+TGG + chr4.2:27348728-27348747 None:intergenic 40.0%
AGAAGCTGGAAACTGGTGAA+AGG - chr4.2:27348882-27348901 MS.gene56507:CDS 45.0%
AGATGGAAGAGGTAAGGAAG+AGG + chr4.2:27348491-27348510 None:intergenic 45.0%
ATTTGGGAAGGAAAAGGACG+AGG - chr4.2:27349100-27349119 MS.gene56507:CDS 45.0%
CGTGGTTTCTCCTATACTTG+CGG - chr4.2:27348995-27349014 MS.gene56507:CDS 45.0%
GAAGGTCTTTGAGCATGAGT+TGG + chr4.2:27348413-27348432 None:intergenic 45.0%
GGTGAAAGTGATTGTAGTGG+TGG - chr4.2:27348830-27348849 MS.gene56507:CDS 45.0%
GTTGTAAACGCTGTAGGTGA+TGG + chr4.2:27348535-27348554 None:intergenic 45.0%
TGGAACCATTAAGGAGAAGC+TGG - chr4.2:27348868-27348887 MS.gene56507:CDS 45.0%
TTGCAACGCAGCCAAAAACA+AGG + chr4.2:27348931-27348950 None:intergenic 45.0%
! AAAGATGATTGTGGTGGGGT+TGG + chr4.2:27348457-27348476 None:intergenic 45.0%
! GGGATGTTGACATCGATTAG+TGG - chr4.2:27348951-27348970 MS.gene56507:CDS 45.0%
! GTTGGGGTTTGGAACCATTA+AGG - chr4.2:27348859-27348878 MS.gene56507:CDS 45.0%
! TGTAGTGGTGGAATCACGTT+GGG - chr4.2:27348842-27348861 MS.gene56507:CDS 45.0%
! TTGTAGTGGTGGAATCACGT+TGG - chr4.2:27348841-27348860 MS.gene56507:CDS 45.0%
!! AGTGAAAGCACCGCAAGTAT+AGG + chr4.2:27349008-27349027 None:intergenic 45.0%
!! GAGCATGAGTTGGTAGATGA+GGG + chr4.2:27348403-27348422 None:intergenic 45.0%
!! GGAAGTGGTGATGGATTTGA+TGG + chr4.2:27348592-27348611 None:intergenic 45.0%
!! TGAGCATGAGTTGGTAGATG+AGG + chr4.2:27348404-27348423 None:intergenic 45.0%
!!! TGTTTTTGGCTGCGTTGCAA+GGG - chr4.2:27348931-27348950 MS.gene56507:CDS 45.0%
!!! TTGTTTTTGGCTGCGTTGCA+AGG - chr4.2:27348930-27348949 MS.gene56507:CDS 45.0%
AGATGAGGGAGAGGAAAGAG+AGG + chr4.2:27348389-27348408 None:intergenic 50.0%
ATGAGGGAGAGGAAAGAGAG+GGG + chr4.2:27348387-27348406 None:intergenic 50.0%
GAAAGAGTGAGGTAGTGACC+AGG + chr4.2:27348348-27348367 None:intergenic 50.0%
GATGAGGGAGAGGAAAGAGA+GGG + chr4.2:27348388-27348407 None:intergenic 50.0%
GGAAGATGAGGGAAAGAGTG+AGG + chr4.2:27348359-27348378 None:intergenic 50.0%
GTAGAGAGTGAAAGTGACGG+CGG + chr4.2:27348637-27348656 None:intergenic 50.0%
TGGAAGAGGTAAGGAAGAGG+AGG + chr4.2:27348488-27348507 None:intergenic 50.0%
! GCTGTAGGTGATGGTGATGA+TGG + chr4.2:27348526-27348545 None:intergenic 50.0%
! GTAGTGGTGGAATCACGTTG+GGG - chr4.2:27348843-27348862 MS.gene56507:CDS 50.0%
!! GAAGGCGTTGTAAACGCTGT+AGG + chr4.2:27348541-27348560 None:intergenic 50.0%
!! GATTGTGGTGGGGTTGGTAA+TGG + chr4.2:27348451-27348470 None:intergenic 50.0%
!! TGAGTTGGTAGATGAGGGAG+AGG + chr4.2:27348398-27348417 None:intergenic 50.0%
AGAGGAAAGAGAGGGGAAGG+AGG + chr4.2:27348380-27348399 None:intergenic 55.0%
AGAGGGGAAGGAGGAAGATG+AGG + chr4.2:27348371-27348390 None:intergenic 55.0%
GAGGGGAAGGAGGAAGATGA+GGG + chr4.2:27348370-27348389 None:intergenic 55.0%
GGGGAAGAAGGAAGTGGTGA+TGG + chr4.2:27348601-27348620 None:intergenic 55.0%
GGTGGAATCACGTTGGGGTT+TGG - chr4.2:27348848-27348867 MS.gene56507:CDS 55.0%
!! GTGGTGGGGTTGGTAATGGT+GGG + chr4.2:27348447-27348466 None:intergenic 55.0%
!! TGGGGTTGGTAATGGTGGGT+GGG + chr4.2:27348443-27348462 None:intergenic 55.0%
!! TGGTGGGTGGGTTGTGTTGA+AGG + chr4.2:27348431-27348450 None:intergenic 55.0%
!! TGTGGTGGGGTTGGTAATGG+TGG + chr4.2:27348448-27348467 None:intergenic 55.0%
AGTGAAAGTGACGGCGGAGG+TGG + chr4.2:27348631-27348650 None:intergenic 60.0%
GAGAGTGAAAGTGACGGCGG+AGG + chr4.2:27348634-27348653 None:intergenic 60.0%
GAGGAGGGGGAAGAAGGAAG+TGG + chr4.2:27348607-27348626 None:intergenic 60.0%
GGGAGAGGAAAGAGAGGGGA+AGG + chr4.2:27348383-27348402 None:intergenic 60.0%
!! GTGGGGTTGGTAATGGTGGG+TGG + chr4.2:27348444-27348463 None:intergenic 60.0%
AAGTGACGGCGGAGGTGGCG+AGG + chr4.2:27348626-27348645 None:intergenic 70.0%
GGTGGCGAGGAGGGGGAAGA+AGG + chr4.2:27348613-27348632 None:intergenic 70.0%
ACGGCGGAGGTGGCGAGGAG+GGG + chr4.2:27348621-27348640 None:intergenic 75.0%
GACGGCGGAGGTGGCGAGGA+GGG + chr4.2:27348622-27348641 None:intergenic 75.0%
TGACGGCGGAGGTGGCGAGG+AGG + chr4.2:27348623-27348642 None:intergenic 75.0%
! CGGCGGAGGTGGCGAGGAGG+GGG + chr4.2:27348620-27348639 None:intergenic 80.0%


Chromosome Type Strat End Strand Name
chr4.2 gene 27348288 27349145 27348288 ID=MS.gene56507
chr4.2 mRNA 27348288 27349145 27348288 ID=MS.gene56507.t1;Parent=MS.gene56507
chr4.2 exon 27348288 27349145 27348288 ID=MS.gene56507.t1.exon1;Parent=MS.gene56507.t1
chr4.2 CDS 27348288 27349145 27348288 ID=cds.MS.gene56507.t1;Parent=MS.gene56507.t1
Gene Sequence

>MS.gene56507

ATGGCTCCAAAAATCTGGGATCTTCTCTATGAATCAAACGTCATAATAAATTCTCAACCTGGTCACTACCTCACTCTTTCCCTCATCTTCCTCCTTCCCCTCTCTTTCCTCTCCCTCATCTACCAACTCATGCTCAAAGACCTTCAACACAACCCACCCACCATTACCAACCCCACCACAATCATCTTTTTGTTTATCCTCCTCTTCCTTACCTCTTCCATCTTCTCTTATAGTGCCATCATCACCATCACCTACAGCGTTTACAACGCCTTCTTTAATCAACCTGTCAAACTCAAAGAAGCCATCAAATCCATCACCACTTCCTTCTTCCCCCTCCTCGCCACCTCCGCCGTCACTTTCACTCTCTACTTCTTCTTTTCATTTCTCTTTATGTTTCTCATTGGACTTGTATTGCTTTTCATCATTTTTATATTAGGCCATATCGACTTCATGACTAACCCTAACTTTGTTTTGTTATATTTCATGGTTTCAATGATTCTTATAGTCCCACTTGTGGTTTATTTGGACGTTTACATGATTTTGGTGAAAGTGATTGTAGTGGTGGAATCACGTTGGGGTTTGGAACCATTAAGGAGAAGCTGGAAACTGGTGAAAGGAATGAAAAGGTTGGCTTTTTCAACCTTGTTTTTGGCTGCGTTGCAAGGGATGTTGACATCGATTAGTGGTTATAGTTGGGTTATGATTTTCGTGGTTTCTCCTATACTTGCGGTGCTTTCACTTTACAGTATTGCGGTTTATACATTGTTGTACATATACTGCAAAGAGAAACATGATGAAGTTGAAGAAGTGGAATTTGGGAAGGAAAAGGACGAGGCTAAATTGTCCTTAATTCCATAA

Protein sequence

>MS.gene56507.t1

MAPKIWDLLYESNVIINSQPGHYLTLSLIFLLPLSFLSLIYQLMLKDLQHNPPTITNPTTIIFLFILLFLTSSIFSYSAIITITYSVYNAFFNQPVKLKEAIKSITTSFFPLLATSAVTFTLYFFFSFLFMFLIGLVLLFIIFILGHIDFMTNPNFVLLYFMVSMILIVPLVVYLDVYMILVKVIVVVESRWGLEPLRRSWKLVKGMKRLAFSTLFLAALQGMLTSISGYSWVMIFVVSPILAVLSLYSIAVYTLLYIYCKEKHDEVEEVEFGKEKDEAKLSLIP