AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene063283

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene063283.t1 MTR_1g047060 60.204 98 32 2 56 153 3 93 3.17e-33 113
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 31 sgRNAs with CRISPR-Local

Find 85 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GACACTGCAGGACCGGATTC+TGG 0.279523 1.4:-3978637 MS.gene063283:CDS
GACCGGATTCTGGAGGAAAA+AGG 0.317490 1.4:-3978627 MS.gene063283:CDS
ATGGATCTGGATGCTGAGTT+TGG 0.391512 1.4:-3978314 MS.gene063283:CDS
TCAGCATCCAGATCCATCTT+TGG 0.442178 1.4:+3978320 None:intergenic
GTTAGTTCTGATAGCAGTGT+TGG 0.458231 1.4:+3978523 None:intergenic
TTAGTTCTGATAGCAGTGTT+GGG 0.461166 1.4:+3978524 None:intergenic
CTGCCCACCAAAGATGGATC+TGG 0.482322 1.4:-3978327 MS.gene063283:CDS
ACACTGCTATCAGAACTAAC+TGG 0.486063 1.4:-3978520 MS.gene063283:CDS
TGGAGTTACTCAGAAACCTA+TGG 0.490884 1.4:-3978231 MS.gene063283:CDS
TGGTGCTGGTAATGTTGTGT+TGG 0.499495 1.4:-3978585 MS.gene063283:CDS
AAAACACGACAAATGACAAA+AGG 0.501966 1.4:+3978353 None:intergenic
GAGAGAAGACACTGCAGGAC+CGG 0.504565 1.4:-3978644 MS.gene063283:CDS
GATAATGTATGAGCATGCTT+TGG 0.511387 1.4:-3978498 MS.gene063283:CDS
GGTGCTGGTAATGTTGTGTT+GGG 0.514976 1.4:-3978584 MS.gene063283:CDS
GACTCTGCTGACAAGATGAA+TGG 0.517567 1.4:-3978251 MS.gene063283:CDS
GCATCCAGATCCATCTTTGG+TGG 0.546474 1.4:+3978323 None:intergenic
GTTCAAGACATCACTGGTGC+TGG 0.556036 1.4:-3978599 MS.gene063283:CDS
GCGTTATCCAAGGTTGATGA+AGG 0.556534 1.4:-3978290 MS.gene063283:CDS
ACAATCACCTTCATCAACCT+TGG 0.559369 1.4:+3978283 None:intergenic
GGAGTTACTCAGAAACCTAT+GGG 0.559803 1.4:-3978230 MS.gene063283:CDS
ACTAGTGTTGCTGCTGAGCA+AGG 0.563406 1.4:-3978188 MS.gene063283:CDS
TAGTTCTGATAGCAGTGTTG+GGG 0.568976 1.4:+3978525 None:intergenic
CATCCAGATCCATCTTTGGT+GGG 0.591585 1.4:+3978324 None:intergenic
GGAGCTGTTCAAGACATCAC+TGG 0.599122 1.4:-3978605 MS.gene063283:CDS
TGAGTTTGGAGCGTTATCCA+AGG 0.615415 1.4:-3978300 MS.gene063283:CDS
AGTTCTGATAGCAGTGTTGG+GGG 0.663335 1.4:+3978526 None:intergenic
ACTGCAGGACCGGATTCTGG+AGG 0.686245 1.4:-3978634 MS.gene063283:CDS
GAGTTACTCAGAAACCTATG+GGG 0.687052 1.4:-3978229 MS.gene063283:CDS
AGTGTTGCTGCTGAGCAAGG+CGG 0.699580 1.4:-3978185 MS.gene063283:CDS
ACATTGAGAGAAGACACTGC+AGG 0.700620 1.4:-3978649 MS.gene063283:CDS
AGTTACTCAGAAACCTATGG+GGG 0.734801 1.4:-3978228 MS.gene063283:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TTTAAATTTTAAAATATTAA+TGG - chr1.4:3978305-3978324 MS.gene063283:CDS 0.0%
!! AATAATAGTAATTGTAAAAT+AGG - chr1.4:3978466-3978485 MS.gene063283:intron 10.0%
!! AATTAATCATCAATGATTTA+AGG + chr1.4:3977873-3977892 None:intergenic 15.0%
!! TAATGGAAATTATTGATATA+TGG - chr1.4:3978322-3978341 MS.gene063283:CDS 15.0%
!! TTATAAACAAAATATTGTCA+AGG - chr1.4:3978347-3978366 MS.gene063283:CDS 15.0%
!!! TTTTCTTTCAATTATTTTGT+AGG - chr1.4:3977916-3977935 MS.gene063283:intron 15.0%
!! ATTTATTACTAGAGAAAAGA+AGG + chr1.4:3978449-3978468 None:intergenic 20.0%
!! TGCAAGATAAAAAATAAACA+GGG + chr1.4:3977744-3977763 None:intergenic 20.0%
!! TTAATAAAGAGAGATCAAAA+TGG + chr1.4:3978184-3978203 None:intergenic 20.0%
!! TTGCAAGATAAAAAATAAAC+AGG + chr1.4:3977745-3977764 None:intergenic 20.0%
!! TTTATTACTAGAGAAAAGAA+GGG + chr1.4:3978448-3978467 None:intergenic 20.0%
! ACGAGAAAAATTATAAACTG+CGG + chr1.4:3978696-3978715 None:intergenic 25.0%
! ATCAATGATTTAAGGAATCA+AGG + chr1.4:3977865-3977884 None:intergenic 25.0%
! CTGCGGAAATAAAAAAAAAA+AGG + chr1.4:3978679-3978698 None:intergenic 25.0%
! TCAATGATTTAAGGAATCAA+GGG + chr1.4:3977864-3977883 None:intergenic 25.0%
!! TCAAATTTCACAGATTTTGA+AGG - chr1.4:3978136-3978155 MS.gene063283:intron 25.0%
!! TTTTCAAATACACACTTTCA+AGG + chr1.4:3978580-3978599 None:intergenic 25.0%
AAAACACGACAAATGACAAA+AGG + chr1.4:3977944-3977963 None:intergenic 30.0%
CATAGCTGTGAAAATTTGAT+TGG - chr1.4:3978603-3978622 MS.gene063283:CDS 30.0%
GTACGATCAACAACATTAAT+TGG + chr1.4:3978207-3978226 None:intergenic 30.0%
TTTATCACTAACCAAGTGTT+GGG - chr1.4:3978511-3978530 MS.gene063283:CDS 30.0%
! ATGGAATATATTTTACCTGC+AGG + chr1.4:3978165-3978184 None:intergenic 30.0%
! GAAAGAGATAATTTTGCGTT+TGG + chr1.4:3977622-3977641 None:intergenic 30.0%
! TGGAATATATTTTACCTGCA+GGG + chr1.4:3978164-3978183 None:intergenic 30.0%
! TTTTATCACTAACCAAGTGT+TGG - chr1.4:3978510-3978529 MS.gene063283:CDS 30.0%
AATAAAAAGAGCGGAAAGAC+GGG - chr1.4:3978412-3978431 MS.gene063283:intron 35.0%
AGTAGAAAGAGAGAACAAAC+GGG + chr1.4:3978229-3978248 None:intergenic 35.0%
CAATAAAAAGAGCGGAAAGA+CGG - chr1.4:3978411-3978430 MS.gene063283:intron 35.0%
CAGTAGAAAGAGAGAACAAA+CGG + chr1.4:3978230-3978249 None:intergenic 35.0%
CGTTAGTGCAATAAAAAGAG+CGG - chr1.4:3978403-3978422 MS.gene063283:intron 35.0%
GATAATGTATGAGCATGCTT+TGG - chr1.4:3977796-3977815 MS.gene063283:intron 35.0%
GATTTAAGGAATCAAGGGAA+TGG + chr1.4:3977859-3977878 None:intergenic 35.0%
TACATTAATGACCCAACACT+TGG + chr1.4:3978525-3978544 None:intergenic 35.0%
TTCAAAAAGTCCCATACTTG+AGG + chr1.4:3977830-3977849 None:intergenic 35.0%
! AAAATTTGATTGGCCACGTT+TGG - chr1.4:3978613-3978632 MS.gene063283:CDS 35.0%
! AGTGTTGGGTCATTAATGTA+TGG - chr1.4:3978525-3978544 MS.gene063283:CDS 35.0%
! GTTTGGCTCAATGATATCAT+TGG - chr1.4:3978630-3978649 MS.gene063283:CDS 35.0%
! TGATTTTGCTTCGTTGTCAT+GGG - chr1.4:3978552-3978571 MS.gene063283:CDS 35.0%
! TTGATTTTGCTTCGTTGTCA+TGG - chr1.4:3978551-3978570 MS.gene063283:CDS 35.0%
!! TTAGTTCTGATAGCAGTGTT+GGG + chr1.4:3977773-3977792 None:intergenic 35.0%
ACAATCACCTTCATCAACCT+TGG + chr1.4:3978014-3978033 None:intergenic 40.0%
ACACTGCTATCAGAACTAAC+TGG - chr1.4:3977774-3977793 MS.gene063283:intron 40.0%
AGTTACTCAGAAACCTATGG+GGG - chr1.4:3978066-3978085 MS.gene063283:intron 40.0%
GAGTTACTCAGAAACCTATG+GGG - chr1.4:3978065-3978084 MS.gene063283:intron 40.0%
GGAGTTACTCAGAAACCTAT+GGG - chr1.4:3978064-3978083 MS.gene063283:intron 40.0%
TAAGGAATCAAGGGAATGGT+GGG + chr1.4:3977855-3977874 None:intergenic 40.0%
TGATATCATTGAGCCAAACG+TGG + chr1.4:3978629-3978648 None:intergenic 40.0%
TGGAGTTACTCAGAAACCTA+TGG - chr1.4:3978063-3978082 MS.gene063283:intron 40.0%
TTAAGGAATCAAGGGAATGG+TGG + chr1.4:3977856-3977875 None:intergenic 40.0%
!! GTTAGTTCTGATAGCAGTGT+TGG + chr1.4:3977774-3977793 None:intergenic 40.0%
!! TAGTTCTGATAGCAGTGTTG+GGG + chr1.4:3977772-3977791 None:intergenic 40.0%
ACATTGAGAGAAGACACTGC+AGG - chr1.4:3977645-3977664 MS.gene063283:intron 45.0%
ATGGATCTGGATGCTGAGTT+TGG - chr1.4:3977980-3977999 MS.gene063283:intron 45.0%
CATCCAGATCCATCTTTGGT+GGG + chr1.4:3977973-3977992 None:intergenic 45.0%
GACTCTGCTGACAAGATGAA+TGG - chr1.4:3978043-3978062 MS.gene063283:intron 45.0%
TCAGCATCCAGATCCATCTT+TGG + chr1.4:3977977-3977996 None:intergenic 45.0%
! ACCGGATTCTGGAGGAAAAA+GGG - chr1.4:3977668-3977687 MS.gene063283:intron 45.0%
! AGTTCTGATAGCAGTGTTGG+GGG + chr1.4:3977771-3977790 None:intergenic 45.0%
! TCCCTTTTTCCTCCAGAATC+CGG + chr1.4:3977672-3977691 None:intergenic 45.0%
! TGAGTTTGGAGCGTTATCCA+AGG - chr1.4:3977994-3978013 MS.gene063283:intron 45.0%
!! GCGTTATCCAAGGTTGATGA+AGG - chr1.4:3978004-3978023 MS.gene063283:intron 45.0%
!! GGTGCTGGTAATGTTGTGTT+GGG - chr1.4:3977710-3977729 MS.gene063283:intron 45.0%
!! TGGTGCTGGTAATGTTGTGT+TGG - chr1.4:3977709-3977728 MS.gene063283:intron 45.0%
!! TTTTGACTGCCCACCAAAGA+TGG - chr1.4:3977961-3977980 MS.gene063283:intron 45.0%
GCATCCAGATCCATCTTTGG+TGG + chr1.4:3977974-3977993 None:intergenic 50.0%
GGAGCTGTTCAAGACATCAC+TGG - chr1.4:3977689-3977708 MS.gene063283:intron 50.0%
GGCTGACAAGCCTCAAGTAT+GGG - chr1.4:3977817-3977836 MS.gene063283:intron 50.0%
GTTCAAGACATCACTGGTGC+TGG - chr1.4:3977695-3977714 MS.gene063283:intron 50.0%
TGGCTGACAAGCCTCAAGTA+TGG - chr1.4:3977816-3977835 MS.gene063283:intron 50.0%
! ACTAGTGTTGCTGCTGAGCA+AGG - chr1.4:3978106-3978125 MS.gene063283:intron 50.0%
! GACCGGATTCTGGAGGAAAA+AGG - chr1.4:3977667-3977686 MS.gene063283:intron 50.0%
!!! AGATTTTGAAGGCACCCTGC+AGG - chr1.4:3978147-3978166 MS.gene063283:intron 50.0%
ACTCAGAAACCTATGGGGGC+TGG - chr1.4:3978070-3978089 MS.gene063283:intron 55.0%
CTCAGAAACCTATGGGGGCT+GGG - chr1.4:3978071-3978090 MS.gene063283:intron 55.0%
CTGCCCACCAAAGATGGATC+TGG - chr1.4:3977967-3977986 MS.gene063283:intron 55.0%
GAGAGAAGACACTGCAGGAC+CGG - chr1.4:3977650-3977669 MS.gene063283:intron 55.0%
TCAGAAACCTATGGGGGCTG+GGG - chr1.4:3978072-3978091 MS.gene063283:intron 55.0%
! AGTGTTGCTGCTGAGCAAGG+CGG - chr1.4:3978109-3978128 MS.gene063283:intron 55.0%
AAACCTATGGGGGCTGGGGA+TGG - chr1.4:3978076-3978095 MS.gene063283:intron 60.0%
AACCTATGGGGGCTGGGGAT+GGG - chr1.4:3978077-3978096 MS.gene063283:intron 60.0%
ACTGCAGGACCGGATTCTGG+AGG - chr1.4:3977660-3977679 MS.gene063283:intron 60.0%
GACACTGCAGGACCGGATTC+TGG - chr1.4:3977657-3977676 MS.gene063283:intron 60.0%
ACCTATGGGGGCTGGGGATG+GGG - chr1.4:3978078-3978097 MS.gene063283:intron 65.0%
ATGGGGGCTGGGGATGGGGC+TGG - chr1.4:3978082-3978101 MS.gene063283:intron 75.0%
GCCCCATCCCCAGCCCCCAT+AGG + chr1.4:3978082-3978101 None:intergenic 75.0%


Chromosome Type Strat End Strand Name
chr1.4 gene 3977590 3978726 3977590 ID=MS.gene063283
chr1.4 mRNA 3977590 3978726 3977590 ID=MS.gene063283.t1;Parent=MS.gene063283
chr1.4 exon 3978484 3978726 3978484 ID=MS.gene063283.t1.exon1;Parent=MS.gene063283.t1
chr1.4 CDS 3978484 3978726 3978484 ID=cds.MS.gene063283.t1;Parent=MS.gene063283.t1
chr1.4 exon 3978148 3978378 3978148 ID=MS.gene063283.t1.exon2;Parent=MS.gene063283.t1
chr1.4 CDS 3978148 3978378 3978148 ID=cds.MS.gene063283.t1;Parent=MS.gene063283.t1
chr1.4 exon 3977590 3977592 3977590 ID=MS.gene063283.t1.exon3;Parent=MS.gene063283.t1
chr1.4 CDS 3977590 3977592 3977590 ID=cds.MS.gene063283.t1;Parent=MS.gene063283.t1
Gene Sequence

>MS.gene063283

ATGAAGGATGTTCATACTCAATCTCAATGCCAAACGCAAAATTATCTCTTTCAACACATTGAGAGAAGACACTGCAGGACCGGATTCTGGAGGAAAAAGGGAGCTGTTCAAGACATCACTGGTGCTGGTAATGTTGTGTTGGGCAAGAAGACCCTGTTTATTTTTTATCTTGCAAGTTCCCCCAACACTGCTATCAGAACTAACTGGATAATGTATGAGCATGCTTTGGCTGACAAGCCTCAAGTATGGGACTTTTTGAAAACCCACCATTCCCTTGATTCCTTAAATCATTGATGATTAATTAATGTATTCATAACTACTAACTATTTTCTTTCAATTATTTTGTAGGCTCCTTTTGTCATTTGTCGTGTTTTTGACTGCCCACCAAAGATGGATCTGGATGCTGAGTTTGGAGCGTTATCCAAGGTTGATGAAGGTGATTGTGCTAGAGATGACTCTGCTGACAAGATGAATGGAGTTACTCAGAAACCTATGGGGGCTGGGGATGGGGCTGGTACTAGTGTTGCTGCTGAGCAAGGCGGTGCTTCAAATTTCACAGATTTTGAAGGCACCCTGCAGGTAAAATATATTCCATTTTGATCTCTCTTTATTAACCAATTAATGTTGTTGATCGTACCCGTTTGTTCTCTCTTTCTACTGCGCTAACGCATGTGATTATTTTATTATGTTTGTTTGTATAATTTTGATTAAAACTTTTAAATTTTAAAATATTAATGGAAATTATTGATATATGGATTTATAAACAAAATATTGTCAAGGCATATAACAATTATTTATGAACTCAACAATTAACGTTAGTGCAATAAAAAGAGCGGAAAGACGGGCACGTGAGTGCCCTTCTTTTCTCTAGTAATAAATAATAGTAATTGTAAAATAGGTGTAAAAGTATATAATTTTGTTTTTATCACTAACCAAGTGTTGGGTCATTAATGTATGGTAGTTGATTTTGCTTCGTTGTCATGGGTTCCTTGAAAGTGTGTATTTGAAAAATTCATAGCTGTGAAAATTTGATTGGCCACGTTTGGCTCAATGATATCATTGGTGCATGATATTTCAAGTTCATTTCCTTTTTTTTTTTATTTCCGCAGTTTATAATTTTTCTCGTCTTTGAAGTAG
Protein sequence

>MS.gene063283.t1

MKDVHTQSQCQTQNYLFQHIERRHCRTGFWRKKGAVQDITGAGNVVLGKKTLFIFYLASSPNTAIRTNWIMYEHALADKPQAPFVICRVFDCPPKMDLDAEFGALSKVDEGDCARDDSADKMNGVTQKPMGAGDGAGTSVAAEQGGASNFTDFEGTLQ