AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene51794


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene51794.t1 MTR_2g029260 91.525 118 10 0 2 119 1 118 1.08e-60 182
MS.gene51794.t1 MTR_1g031930 56.552 145 54 2 6 141 106 250 3.70e-39 134
MS.gene51794.t1 MTR_1g031930 56.552 145 54 2 6 141 167 311 4.54e-38 132
MS.gene51794.t1 MTR_6g069870 38.947 95 51 2 13 107 160 247 3.69e-13 65.5
MS.gene51794.t1 MTR_6g069870 38.947 95 51 2 13 107 160 247 3.79e-13 65.5
MS.gene51794.t1 MTR_6g069870 38.947 95 51 2 13 107 160 247 5.54e-13 64.7
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 44 sgRNAs with CRISPR-Local

Find 110 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GTAATGGCATCGATTACTTT+TGG 0.271813 3.4:-15802653 None:intergenic
CATTTATCATTTGGATGATC+CGG 0.369645 3.4:+15801599 None:intergenic
TTTCTCGCAGTTAAAGCAAC+TGG 0.436705 3.4:+15802596 MS.gene51794:CDS
CGCCATTCCTAGCCAACAAC+AGG 0.438442 3.4:-15802406 None:intergenic
GGCACAAGCTATCCTGTTGT+TGG 0.441454 3.4:+15802394 MS.gene51794:intron
GCCATTACCATGCTGGTGTC+AGG 0.443156 3.4:+15802668 MS.gene51794:CDS
GAGGAGGGTGGTGCATTTGA+AGG 0.446466 3.4:-15802497 None:intergenic
CACAGCACACAGAAAAGTTC+AGG 0.446504 3.4:+15802445 MS.gene51794:CDS
CGCGTAGAAGATGGTAAGTT+GGG 0.452743 3.4:-15802018 None:intergenic
TCGCATACTGGTGCACAGTC+AGG 0.473936 3.4:+15802548 MS.gene51794:CDS
GTATCTATTTCATCGCATAC+TGG 0.486436 3.4:+15802536 MS.gene51794:CDS
TCAAATGCACCACCCTCCTC+TGG 0.491435 3.4:+15802500 MS.gene51794:CDS
AAGAGAGATACCTTGTCAGC+AGG 0.494472 3.4:-15802068 None:intergenic
AAGCTATCCTGTTGTTGGCT+AGG 0.504599 3.4:+15802399 MS.gene51794:CDS
ACCTGACACCAGCATGGTAA+TGG 0.513597 3.4:-15802669 None:intergenic
GCATTTGAAGGTTGACTCAC+GGG 0.518410 3.4:-15802485 None:intergenic
CACAGAAAAGTTCAGGCACC+TGG 0.524123 3.4:+15802452 MS.gene51794:CDS
GACAGTACCCGCGTAGAAGA+TGG 0.529249 3.4:-15802027 None:intergenic
CCGCGTAGAAGATGGTAAGT+TGG 0.530718 3.4:-15802019 None:intergenic
CAACTTACCATCTTCTACGC+GGG 0.531973 3.4:+15802020 MS.gene51794:CDS
ATCCTGTTGTTGGCTAGGAA+TGG 0.535261 3.4:+15802404 MS.gene51794:CDS
CTCACGGGCACACCGTCACC+AGG 0.540218 3.4:-15802470 None:intergenic
TCAGGCTCGGAAATCATCCT+TGG 0.543668 3.4:+15802847 MS.gene51794:CDS
GGCATTGCTAACAGAAGTGG+TGG 0.550160 3.4:-15802624 None:intergenic
AGTTGGGAAGAATGCAGAGA+TGG 0.555952 3.4:-15802002 None:intergenic
TGCATTTGAAGGTTGACTCA+CGG 0.556932 3.4:-15802486 None:intergenic
AATCGATGCCATTACCATGC+TGG 0.562603 3.4:+15802661 MS.gene51794:CDS
GTATGCGATGAAATAGATAC+AGG 0.564795 3.4:-15802533 None:intergenic
TTGCAGCGATACCTCAGGCT+CGG 0.566768 3.4:+15802834 MS.gene51794:intron
CAATGACATCCCTGCTGACA+AGG 0.569187 3.4:+15802058 MS.gene51794:CDS
AGAGAGATACCTTGTCAGCA+GGG 0.569662 3.4:-15802067 None:intergenic
ACTGGTGCACAGTCAGGCAG+TGG 0.578273 3.4:+15802554 MS.gene51794:CDS
AAAGTTCAGGCACCTGGTGA+CGG 0.580555 3.4:+15802458 MS.gene51794:CDS
GGCTAGGAATGGCGTATCAG+TGG 0.588783 3.4:+15802415 MS.gene51794:CDS
CTCGGCATTGCTAACAGAAG+TGG 0.595488 3.4:-15802627 None:intergenic
GATGAAATAGATACAGGACT+TGG 0.619496 3.4:-15802527 None:intergenic
AAGGATGATTTCCGAGCCTG+AGG 0.631439 3.4:-15802845 None:intergenic
AGGACTTGGATGACCAGAGG+AGG 0.643414 3.4:-15802513 None:intergenic
GGACTTGGATGACCAGAGGA+GGG 0.651250 3.4:-15802512 None:intergenic
CAACATACCTGACACCAGCA+TGG 0.665960 3.4:-15802675 None:intergenic
TACAGGACTTGGATGACCAG+AGG 0.680767 3.4:-15802516 None:intergenic
CTTGGATGACCAGAGGAGGG+TGG 0.682495 3.4:-15802509 None:intergenic
CCAACTTACCATCTTCTACG+CGG 0.690002 3.4:+15802019 MS.gene51794:CDS
GCATTGCTAACAGAAGTGGT+GGG 0.734105 3.4:-15802623 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! ATTATTTTATTTTAGTTTGA+GGG - chr3.4:15801685-15801704 None:intergenic 10.0%
!!! TATTATTTTATTTTAGTTTG+AGG - chr3.4:15801686-15801705 None:intergenic 10.0%
!! AATTAAATTAGAATACCAAT+CGG - chr3.4:15801636-15801655 None:intergenic 15.0%
!! AATTTATTAAATGTGTCAAA+TGG - chr3.4:15802799-15802818 None:intergenic 15.0%
!!! TAATTTTATGATTCACTTTT+AGG + chr3.4:15801907-15801926 MS.gene51794:intron 15.0%
!! CCTATAAATAAATGAATACA+AGG + chr3.4:15802108-15802127 MS.gene51794:intron 20.0%
!! CCTTGTATTCATTTATTTAT+AGG - chr3.4:15802111-15802130 None:intergenic 20.0%
!! TAAATGAATACAAGGTAAAA+AGG + chr3.4:15802116-15802135 MS.gene51794:intron 20.0%
!! TTGTTTATTGAAATCTTGTT+TGG + chr3.4:15802733-15802752 MS.gene51794:intron 20.0%
!!! TGTTTATTGAAATCTTGTTT+GGG + chr3.4:15802734-15802753 MS.gene51794:intron 20.0%
!!! TTTTTCGTTAACCAAATTAT+TGG - chr3.4:15802327-15802346 None:intergenic 20.0%
!! GTTTATTGAAATCTTGTTTG+GGG + chr3.4:15802735-15802754 MS.gene51794:intron 25.0%
CAGTTACAAAATGATTCATC+GGG - chr3.4:15801781-15801800 None:intergenic 30.0%
CCAATTGCAATAATGAGAAA+TGG - chr3.4:15802707-15802726 None:intergenic 30.0%
CCATTTCTCATTATTGCAAT+TGG + chr3.4:15802704-15802723 MS.gene51794:intron 30.0%
GCAGTTACAAAATGATTCAT+CGG - chr3.4:15801782-15801801 None:intergenic 30.0%
! ATGAATCATTTTGTAACTGC+TGG + chr3.4:15801782-15801801 MS.gene51794:intron 30.0%
AAAAATGGTTGAGACTTGAG+AGG + chr3.4:15802229-15802248 MS.gene51794:intron 35.0%
ACTAGGACCAATGTAATGTT+TGG - chr3.4:15802152-15802171 None:intergenic 35.0%
ATCTTCACATCATGTTGTAC+AGG - chr3.4:15801710-15801729 None:intergenic 35.0%
CAGTTCACCAAACATTACAT+TGG + chr3.4:15802142-15802161 MS.gene51794:intron 35.0%
GATGAAATAGATACAGGACT+TGG - chr3.4:15802530-15802549 None:intergenic 35.0%
GTATCTATTTCATCGCATAC+TGG + chr3.4:15802536-15802555 MS.gene51794:CDS 35.0%
GTATGCGATGAAATAGATAC+AGG - chr3.4:15802536-15802555 None:intergenic 35.0%
TGAAACTGAATTCGCTTGAT+TGG - chr3.4:15801744-15801763 None:intergenic 35.0%
! ATGTAATGTTTGGTGAACTG+TGG - chr3.4:15802142-15802161 None:intergenic 35.0%
!!! GTAATGGCATCGATTACTTT+TGG - chr3.4:15802656-15802675 None:intergenic 35.0%
ACCATAGTCAAGCTTAACTG+TGG + chr3.4:15802358-15802377 MS.gene51794:intron 40.0%
GGTATCGCTGCAAAAAAGAT+TGG - chr3.4:15802827-15802846 None:intergenic 40.0%
GGTGGATCACACCAATAATT+TGG + chr3.4:15802313-15802332 MS.gene51794:intron 40.0%
GTTAAGCTTGACTATGGTCA+AGG - chr3.4:15802356-15802375 None:intergenic 40.0%
TACATTGGTCCTAGTGAAAC+TGG + chr3.4:15802157-15802176 MS.gene51794:intron 40.0%
TTTCTCGCAGTTAAAGCAAC+TGG + chr3.4:15802596-15802615 MS.gene51794:CDS 40.0%
! AACTGTGGCACTATTTCTTC+AGG + chr3.4:15802373-15802392 MS.gene51794:intron 40.0%
! AGACTAGTCATCAGCAAAGT+CGG + chr3.4:15802292-15802311 MS.gene51794:intron 40.0%
! TGCATTTGAAGGTTGACTCA+CGG - chr3.4:15802489-15802508 None:intergenic 40.0%
!! ATCGATTACTTTTGGAGGCT+CGG - chr3.4:15802648-15802667 None:intergenic 40.0%
!! CTGATGACTAGTCTCTGTTT+GGG - chr3.4:15802286-15802305 None:intergenic 40.0%
!!! ATGGCATCGATTACTTTTGG+AGG - chr3.4:15802653-15802672 None:intergenic 40.0%
AAGAGAGATACCTTGTCAGC+AGG - chr3.4:15802071-15802090 None:intergenic 45.0%
AATCGATGCCATTACCATGC+TGG + chr3.4:15802661-15802680 MS.gene51794:CDS 45.0%
ACTGCTGGTCAGAACATGAA+TGG + chr3.4:15801797-15801816 MS.gene51794:intron 45.0%
AGAGAGATACCTTGTCAGCA+GGG - chr3.4:15802070-15802089 None:intergenic 45.0%
AGTTGGGAAGAATGCAGAGA+TGG - chr3.4:15802005-15802024 None:intergenic 45.0%
CAACTTACCATCTTCTACGC+GGG + chr3.4:15802020-15802039 MS.gene51794:CDS 45.0%
CAATCAACTCTTCCCACCAT+TGG + chr3.4:15801841-15801860 MS.gene51794:intron 45.0%
CACAGCACACAGAAAAGTTC+AGG + chr3.4:15802445-15802464 MS.gene51794:CDS 45.0%
CCAACTTACCATCTTCTACG+CGG + chr3.4:15802019-15802038 MS.gene51794:CDS 45.0%
CCTTGTGGATGGGGAAAAAA+TGG + chr3.4:15802214-15802233 MS.gene51794:intron 45.0%
CGATTCAGTCATTCCAGCAA+CGG - chr3.4:15801869-15801888 None:intergenic 45.0%
CGCGTAGAAGATGGTAAGTT+GGG - chr3.4:15802021-15802040 None:intergenic 45.0%
GCATTGCTAACAGAAGTGGT+GGG - chr3.4:15802626-15802645 None:intergenic 45.0%
GCCACAGTTAAGCTTGACTA+TGG - chr3.4:15802362-15802381 None:intergenic 45.0%
! AAGCTATCCTGTTGTTGGCT+AGG + chr3.4:15802399-15802418 MS.gene51794:CDS 45.0%
! ATCCTGTTGTTGGCTAGGAA+TGG + chr3.4:15802404-15802423 MS.gene51794:CDS 45.0%
! ATGGTGGGAAGAGTTGATTG+AGG - chr3.4:15801841-15801860 None:intergenic 45.0%
! CCAATCGGATTAGAACACAC+CGG - chr3.4:15801621-15801640 None:intergenic 45.0%
! GCATTTGAAGGTTGACTCAC+GGG - chr3.4:15802488-15802507 None:intergenic 45.0%
!! GCTGATGACTAGTCTCTGTT+TGG - chr3.4:15802287-15802306 None:intergenic 45.0%
!!! CCATTTTTTCCCCATCCACA+AGG - chr3.4:15802217-15802236 None:intergenic 45.0%
!!! CTTTTTTGCAGCGATACCTC+AGG + chr3.4:15802829-15802848 MS.gene51794:intron 45.0%
AAAGTTCAGGCACCTGGTGA+CGG + chr3.4:15802458-15802477 MS.gene51794:CDS 50.0%
AAGGATGATTTCCGAGCCTG+AGG - chr3.4:15802848-15802867 None:intergenic 50.0%
ACCTGACACCAGCATGGTAA+TGG - chr3.4:15802672-15802691 None:intergenic 50.0%
AGGATAGACCCTACTGAAGG+TGG + chr3.4:15802249-15802268 MS.gene51794:intron 50.0%
ATGGCTGACCACCTTCAGTA+GGG - chr3.4:15802260-15802279 None:intergenic 50.0%
CAACATACCTGACACCAGCA+TGG - chr3.4:15802678-15802697 None:intergenic 50.0%
CAATGACATCCCTGCTGACA+AGG + chr3.4:15802058-15802077 MS.gene51794:CDS 50.0%
CACAGAAAAGTTCAGGCACC+TGG + chr3.4:15802452-15802471 MS.gene51794:CDS 50.0%
CCGCGTAGAAGATGGTAAGT+TGG - chr3.4:15802022-15802041 None:intergenic 50.0%
CCGGTGTGTTCTAATCCGAT+TGG + chr3.4:15801618-15801637 MS.gene51794:intron 50.0%
CTAGTCATCAGCAAAGTCGG+TGG + chr3.4:15802295-15802314 MS.gene51794:intron 50.0%
CTAGTCTCTGTTTGGGAGCA+TGG - chr3.4:15802279-15802298 None:intergenic 50.0%
CTCGGCATTGCTAACAGAAG+TGG - chr3.4:15802630-15802649 None:intergenic 50.0%
GAATCCGAGACCTGGCATAA+GGG - chr3.4:15802191-15802210 None:intergenic 50.0%
GAGAGGATAGACCCTACTGA+AGG + chr3.4:15802246-15802265 MS.gene51794:intron 50.0%
GGCACAAGCTATCCTGTTGT+TGG + chr3.4:15802394-15802413 MS.gene51794:intron 50.0%
GGCATTGCTAACAGAAGTGG+TGG - chr3.4:15802627-15802646 None:intergenic 50.0%
GGTCCTAGTGAAACTGGACT+CGG + chr3.4:15802163-15802182 MS.gene51794:intron 50.0%
GTCCTAGTGAAACTGGACTC+GGG + chr3.4:15802164-15802183 MS.gene51794:intron 50.0%
TACAGGACTTGGATGACCAG+AGG - chr3.4:15802519-15802538 None:intergenic 50.0%
TCAGGCTCGGAAATCATCCT+TGG + chr3.4:15802847-15802866 MS.gene51794:CDS 50.0%
! CATGCTGGTGTCAGGTATGT+TGG + chr3.4:15802676-15802695 MS.gene51794:intron 50.0%
AGGACTTGGATGACCAGAGG+AGG - chr3.4:15802516-15802535 None:intergenic 55.0%
CATGGCTGACCACCTTCAGT+AGG - chr3.4:15802261-15802280 None:intergenic 55.0%
CATTCCAGCAACGGCACCAA+TGG - chr3.4:15801860-15801879 None:intergenic 55.0%
CGAATCCGAGACCTGGCATA+AGG - chr3.4:15802192-15802211 None:intergenic 55.0%
CGCCATTCCTAGCCAACAAC+AGG - chr3.4:15802409-15802428 None:intergenic 55.0%
GACAGTACCCGCGTAGAAGA+TGG - chr3.4:15802030-15802049 None:intergenic 55.0%
GACCCGAGTCCAGTTTCACT+AGG - chr3.4:15802169-15802188 None:intergenic 55.0%
GAGGAGGGTGGTGCATTTGA+AGG - chr3.4:15802500-15802519 None:intergenic 55.0%
GCCATTACCATGCTGGTGTC+AGG + chr3.4:15802668-15802687 MS.gene51794:CDS 55.0%
GGACTTGGATGACCAGAGGA+GGG - chr3.4:15802515-15802534 None:intergenic 55.0%
GGCTAGGAATGGCGTATCAG+TGG + chr3.4:15802415-15802434 MS.gene51794:CDS 55.0%
TCAAATGCACCACCCTCCTC+TGG + chr3.4:15802500-15802519 MS.gene51794:CDS 55.0%
TCGCATACTGGTGCACAGTC+AGG + chr3.4:15802548-15802567 MS.gene51794:CDS 55.0%
TTGCAGCGATACCTCAGGCT+CGG + chr3.4:15802834-15802853 MS.gene51794:intron 55.0%
! CGGATTCGAGCCTTGTGGAT+GGG + chr3.4:15802204-15802223 MS.gene51794:intron 55.0%
! GGATTCGAGCCTTGTGGATG+GGG + chr3.4:15802205-15802224 MS.gene51794:intron 55.0%
! TCGGATTCGAGCCTTGTGGA+TGG + chr3.4:15802203-15802222 MS.gene51794:intron 55.0%
ACTGGTGCACAGTCAGGCAG+TGG + chr3.4:15802554-15802573 MS.gene51794:CDS 60.0%
CAAGGCTCGAATCCGAGACC+TGG - chr3.4:15802199-15802218 None:intergenic 60.0%
CCAGCAACGGCACCAATGGT+GGG - chr3.4:15801856-15801875 None:intergenic 60.0%
CTTGGATGACCAGAGGAGGG+TGG - chr3.4:15802512-15802531 None:intergenic 60.0%
GGGTCCCTTATGCCAGGTCT+CGG + chr3.4:15802184-15802203 MS.gene51794:intron 60.0%
GGTCTCGGATTCGAGCCTTG+TGG + chr3.4:15802199-15802218 MS.gene51794:intron 60.0%
TCCAGCAACGGCACCAATGG+TGG - chr3.4:15801857-15801876 None:intergenic 60.0%
GGACTCGGGTCCCTTATGCC+AGG + chr3.4:15802178-15802197 MS.gene51794:intron 65.0%
!! CCCACCATTGGTGCCGTTGC+TGG + chr3.4:15801853-15801872 MS.gene51794:intron 65.0%
CTCACGGGCACACCGTCACC+AGG - chr3.4:15802473-15802492 None:intergenic 70.0%


Chromosome Type Strat End Strand Name
chr3.4 gene 15801613 15802874 15801613 ID=MS.gene51794
chr3.4 mRNA 15801613 15802874 15801613 ID=MS.gene51794.t1;Parent=MS.gene51794
chr3.4 exon 15801613 15801620 15801613 ID=MS.gene51794.t1.exon1;Parent=MS.gene51794.t1
chr3.4 CDS 15801613 15801620 15801613 ID=cds.MS.gene51794.t1;Parent=MS.gene51794.t1
chr3.4 exon 15801992 15802079 15801992 ID=MS.gene51794.t1.exon2;Parent=MS.gene51794.t1
chr3.4 CDS 15801992 15802079 15801992 ID=cds.MS.gene51794.t1;Parent=MS.gene51794.t1
chr3.4 exon 15802395 15802689 15802395 ID=MS.gene51794.t1.exon3;Parent=MS.gene51794.t1
chr3.4 CDS 15802395 15802689 15802395 ID=cds.MS.gene51794.t1;Parent=MS.gene51794.t1
chr3.4 exon 15802840 15802874 15802840 ID=MS.gene51794.t1.exon4;Parent=MS.gene51794.t1
chr3.4 CDS 15802840 15802874 15802840 ID=cds.MS.gene51794.t1;Parent=MS.gene51794.t1
Gene Sequence

>MS.gene51794

ATGATCCGGTGTGTTCTAATCCGATTGGTATTCTAATTTAATTCAATTTTTTGTAGTATATTAATTAAACCCTCAAACTAAAATAAAATAATATCCTGTACAACATGATGTGAAGATGTTTTCACTTTCCAATCAAGCGAATTCAGTTTCATCGACGAGCTCATTCCCGATGAATCATTTTGTAACTGCTGGTCAGAACATGAATGGTAATCATATGTTACAGCACCTCAATCAACTCTTCCCACCATTGGTGCCGTTGCTGGAATGACTGAATCGTAGTAATTTTACTAATTCTAATTTTATGATTCACTTTTAGGTGTATAGTGCACAAACTTGTTTGTATTTCGTTTCTCTTACAATTGATTTTATTTTGATACAGCAATGTGAAACCATCTCTGCATTCTTCCCAACTTACCATCTTCTACGCGGGTACTGTCAATGTCTTCAATGACATCCCTGCTGACAAGGTATCTCTCTTTGTTTATATTTCTTCTGCCTATAAATAAATGAATACAAGGTAAAAAGGCCACAGTTCACCAAACATTACATTGGTCCTAGTGAAACTGGACTCGGGTCCCTTATGCCAGGTCTCGGATTCGAGCCTTGTGGATGGGGAAAAAATGGTTGAGACTTGAGAGGATAGACCCTACTGAAGGTGGTCAGCCATGCTCCCAAACAGAGACTAGTCATCAGCAAAGTCGGTGGATCACACCAATAATTTGGTTAACGAAAAAACTTAGCCTTGACCATAGTCAAGCTTAACTGTGGCACTATTTCTTCAGGCACAAGCTATCCTGTTGTTGGCTAGGAATGGCGTATCAGTGGCTTCTAACACAGCACACAGAAAAGTTCAGGCACCTGGTGACGGTGTGCCCGTGAGTCAACCTTCAAATGCACCACCCTCCTCTGGTCATCCAAGTCCTGTATCTATTTCATCGCATACTGGTGCACAGTCAGGCAGTGGCTCAACTAGCACTGATGAATTTCTCGCAGTTAAAGCAACTGGTGTTCCCACCACTTCTGTTAGCAATGCCGAGCCTCCAAAAGTAATCGATGCCATTACCATGCTGGTGTCAGGTATGTTGGAAGTACCATTTCTCATTATTGCAATTGGATTATTTTGTTTATTGAAATCTTGTTTGGGGATATTTGTCTACATTTTACACATTGAAGAGAAACAAATCCATTTGACACATTTAATAAATTCACTACCAATCTTTTTTGCAGCGATACCTCAGGCTCGGAAATCATCCTTGGCTTGA

Protein sequence

>MS.gene51794.t1

MIRNVKPSLHSSQLTIFYAGTVNVFNDIPADKAQAILLLARNGVSVASNTAHRKVQAPGDGVPVSQPSNAPPSSGHPSPVSISSHTGAQSGSGSTSTDEFLAVKATGVPTTSVSNAEPPKVIDAITMLVSAIPQARKSSLA