AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene89057

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene89057.t1 MTR_2g103290 87.293 181 21 2 1 179 1 181 5.45e-111 314
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 30 sgRNAs with CRISPR-Local

Find 84 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GCTGAGTCTTAATCCTCATA+TGG 0.366307 2.4:+2157136 None:intergenic
TCTGCTGCTGCTACAACTAA+TGG 0.397952 2.4:-2155722 MS.gene89057:CDS
GCCATGTGCATAGTTGCATT+GGG 0.419796 2.4:+2157071 None:intergenic
TGAACATAATGAAGAGGTAG+AGG 0.427658 2.4:+2156943 None:intergenic
TCATTCGTCTCTATGCTGAT+TGG 0.440080 2.4:-2155544 MS.gene89057:CDS
AACGACCTCAGAACAGCAAC+AGG 0.451715 2.4:-2157045 MS.gene89057:CDS
AAAATTCACAAACCCATATG+AGG 0.470113 2.4:-2157149 MS.gene89057:CDS
ACTACCTCTTTACATAAGAA+TGG 0.478765 2.4:-2155614 MS.gene89057:CDS
ATGAACATTCTACAGAATCT+TGG 0.480970 2.4:+2157021 None:intergenic
AGCCATGTGCATAGTTGCAT+TGG 0.488645 2.4:+2157070 None:intergenic
CTGAGTCTTAATCCTCATAT+GGG 0.496970 2.4:+2157137 None:intergenic
CATAAGAATGGACCGTATGC+TGG 0.500563 2.4:-2155602 MS.gene89057:CDS
CGGTCCATTCTTATGTAAAG+AGG 0.523765 2.4:+2155610 None:intergenic
ACATAATGAAGAGGTAGAGG+AGG 0.543147 2.4:+2156946 None:intergenic
GTAGAGGAGGAGTTGCATGA+AGG 0.548027 2.4:+2156959 None:intergenic
TGATACAAAATGCAGAATGC+AGG 0.549025 2.4:-2155757 MS.gene89057:CDS
TTGGTCCTGTTGCTGTTCTG+AGG 0.555812 2.4:+2157040 None:intergenic
ATGGCTGAGGTATTTGTAGC+AGG 0.556435 2.4:+2155647 None:intergenic
CCCCAATGCAACTATGCACA+TGG 0.558064 2.4:-2157072 MS.gene89057:CDS
GTGTCCGTAGCTACAATGTC+TGG 0.558270 2.4:+2156993 None:intergenic
CACACCAGACATTGTAGCTA+CGG 0.572650 2.4:-2156997 MS.gene89057:CDS
TTGCATTGGGGTGCAACAAG+AGG 0.590171 2.4:+2157084 None:intergenic
GATAAGGATTTACCAGCATA+CGG 0.594337 2.4:+2155590 None:intergenic
TGAGGATGAACATAATGAAG+AGG 0.648497 2.4:+2156937 None:intergenic
AGTTGCCACTGTGATGGCTG+AGG 0.653448 2.4:+2155634 None:intergenic
CCATGTGCATAGTTGCATTG+GGG 0.656451 2.4:+2157072 None:intergenic
AGAGGTAGTTGCCACTGTGA+TGG 0.670611 2.4:+2155628 None:intergenic
CTATGCAAAAGATTCATGCA+AGG 0.677580 2.4:-2157114 MS.gene89057:CDS
AGTTTGTGAATGCAGAACCA+GGG 0.757579 2.4:-2155781 MS.gene89057:intron
AAATACCTCAGCCATCACAG+TGG 0.797236 2.4:-2155639 MS.gene89057:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AATAAGCTAAAAACAATTTA+TGG + chr2.4:2156648-2156667 None:intergenic 15.0%
!! TTAATTAATAAGTAATGTCT+CGG - chr2.4:2156297-2156316 MS.gene89057:intron 15.0%
!! ACATAAACACTTATATGATA+TGG - chr2.4:2156763-2156782 MS.gene89057:intron 20.0%
!! TCTTAGTATTAGAACAAAAA+GGG - chr2.4:2155891-2155910 MS.gene89057:intron 20.0%
!! TTCTTAGTATTAGAACAAAA+AGG - chr2.4:2155890-2155909 MS.gene89057:intron 20.0%
!!! CAATTTTCTACTAAATATCA+TGG - chr2.4:2156546-2156565 MS.gene89057:intron 20.0%
!!! TTTATAGGTTTTATGTAATC+TGG - chr2.4:2156036-2156055 MS.gene89057:intron 20.0%
! AAACAACAAACACATAATGT+TGG - chr2.4:2156250-2156269 MS.gene89057:intron 25.0%
! AATAGAATATAGAACTGTGT+TGG - chr2.4:2156877-2156896 MS.gene89057:intron 25.0%
! AGTAGAAAATTGTCAAATAG+CGG + chr2.4:2156538-2156557 None:intergenic 25.0%
! TAAATGGAAAAAATGTGCAT+CGG - chr2.4:2156332-2156351 MS.gene89057:intron 25.0%
! TAATTAAGCAACCTCATAAT+CGG + chr2.4:2156284-2156303 None:intergenic 25.0%
AAAATTCACAAACCCATATG+AGG - chr2.4:2155554-2155573 MS.gene89057:CDS 30.0%
ACTACCTCTTTACATAAGAA+TGG - chr2.4:2157089-2157108 MS.gene89057:CDS 30.0%
AGAAGTTGAAGAAAAATACG+TGG + chr2.4:2155826-2155845 None:intergenic 30.0%
AGCTTTCATGGAAATCATAT+TGG + chr2.4:2156846-2156865 None:intergenic 30.0%
ATGAACATTCTACAGAATCT+TGG + chr2.4:2155685-2155704 None:intergenic 30.0%
TGAATCACAAAAAGCTTTCA+TGG + chr2.4:2156858-2156877 None:intergenic 30.0%
! GACTTCAGTTTATCTTTTGT+TGG - chr2.4:2156727-2156746 MS.gene89057:intron 30.0%
!! ACTACACTAACACTACTTTT+TGG - chr2.4:2155853-2155872 MS.gene89057:intron 30.0%
!! CATTGTGTTTTTGTCAGATA+AGG + chr2.4:2157132-2157151 None:intergenic 30.0%
AAATAGACCCTAACTCATAG+GGG + chr2.4:2156368-2156387 None:intergenic 35.0%
ATCATATTGGACCTGGAATA+AGG + chr2.4:2156833-2156852 None:intergenic 35.0%
ATTAAGCTGTTTACCCAAAC+AGG - chr2.4:2156806-2156825 MS.gene89057:intron 35.0%
CAAATAGACCCTAACTCATA+GGG + chr2.4:2156369-2156388 None:intergenic 35.0%
CTATGCAAAAGATTCATGCA+AGG - chr2.4:2155589-2155608 MS.gene89057:CDS 35.0%
CTGACAAAAACACAATGCAA+AGG - chr2.4:2157135-2157154 MS.gene89057:CDS 35.0%
CTGAGTCTTAATCCTCATAT+GGG + chr2.4:2155569-2155588 None:intergenic 35.0%
GATAAGGATTTACCAGCATA+CGG + chr2.4:2157116-2157135 None:intergenic 35.0%
GCTGTTTGTATAAGCTATCA+TGG + chr2.4:2156683-2156702 None:intergenic 35.0%
TCAAATAGACCCTAACTCAT+AGG + chr2.4:2156370-2156389 None:intergenic 35.0%
TGAACATAATGAAGAGGTAG+AGG + chr2.4:2155763-2155782 None:intergenic 35.0%
TGAAGAAAAATACGTGGTTG+TGG + chr2.4:2155820-2155839 None:intergenic 35.0%
TGAGGATGAACATAATGAAG+AGG + chr2.4:2155769-2155788 None:intergenic 35.0%
TGATACAAAATGCAGAATGC+AGG - chr2.4:2156946-2156965 MS.gene89057:CDS 35.0%
! ATGCTCTCAATTTTGAATCG+CGG - chr2.4:2156466-2156485 MS.gene89057:intron 35.0%
! CAATTTTGAATCGCGGAAAT+TGG - chr2.4:2156473-2156492 MS.gene89057:intron 35.0%
! TCGGATTCGAGTCTTATAAA+TGG - chr2.4:2156316-2156335 MS.gene89057:intron 35.0%
! TGTTTGTGTTGGTGCTTTAT+AGG - chr2.4:2156021-2156040 MS.gene89057:intron 35.0%
ACATAATGAAGAGGTAGAGG+AGG + chr2.4:2155760-2155779 None:intergenic 40.0%
AGTTTGTGAATGCAGAACCA+GGG - chr2.4:2156922-2156941 MS.gene89057:CDS 40.0%
CATGGAAATCATATTGGACC+TGG + chr2.4:2156840-2156859 None:intergenic 40.0%
CGGTCCATTCTTATGTAAAG+AGG + chr2.4:2157096-2157115 None:intergenic 40.0%
GCTGAGTCTTAATCCTCATA+TGG + chr2.4:2155570-2155589 None:intergenic 40.0%
GCTTAATCAGTTATGGCATG+TGG - chr2.4:2156185-2156204 MS.gene89057:intron 40.0%
TCATTCGTCTCTATGCTGAT+TGG - chr2.4:2157159-2157178 MS.gene89057:CDS 40.0%
TGTGGTGAATTTAGCTAGGA+TGG - chr2.4:2156203-2156222 MS.gene89057:intron 40.0%
! ATGATTTGCCCCTATGAGTT+AGG - chr2.4:2156357-2156376 MS.gene89057:intron 40.0%
! GCAGCTTGCTTAATCAGTTA+TGG - chr2.4:2156178-2156197 MS.gene89057:intron 40.0%
! TAAAGCACCAACACAAACAC+CGG + chr2.4:2156020-2156039 None:intergenic 40.0%
! TCTGCATTTTGTATCATCCC+TGG + chr2.4:2156942-2156961 None:intergenic 40.0%
! TGATTTGCCCCTATGAGTTA+GGG - chr2.4:2156358-2156377 MS.gene89057:intron 40.0%
! TTTTGAATCGCGGAAATTGG+CGG - chr2.4:2156476-2156495 MS.gene89057:intron 40.0%
!!! TGTTGTTTTGTGCAGAAGAG+TGG + chr2.4:2157007-2157026 None:intergenic 40.0%
AAATACCTCAGCCATCACAG+TGG - chr2.4:2157064-2157083 MS.gene89057:CDS 45.0%
ACCTGGAATAAGGTCCTGTT+TGG + chr2.4:2156823-2156842 None:intergenic 45.0%
AGCCATGTGCATAGTTGCAT+TGG + chr2.4:2155636-2155655 None:intergenic 45.0%
ATAGTGTCACCATAGCGTAG+TGG + chr2.4:2156592-2156611 None:intergenic 45.0%
CACACCAGACATTGTAGCTA+CGG - chr2.4:2155706-2155725 MS.gene89057:CDS 45.0%
CATAAGAATGGACCGTATGC+TGG - chr2.4:2157101-2157120 MS.gene89057:CDS 45.0%
CATTCGATCAGTGTTGTGTC+CGG - chr2.4:2155998-2156017 MS.gene89057:intron 45.0%
CCATGTGCATAGTTGCATTG+GGG + chr2.4:2155634-2155653 None:intergenic 45.0%
CCTGGAATAAGGTCCTGTTT+GGG + chr2.4:2156822-2156841 None:intergenic 45.0%
GAGTTTGTGAATGCAGAACC+AGG - chr2.4:2156921-2156940 MS.gene89057:CDS 45.0%
GCCATGTGCATAGTTGCATT+GGG + chr2.4:2155635-2155654 None:intergenic 45.0%
GGCATGTGGTGAATTTAGCT+AGG - chr2.4:2156199-2156218 MS.gene89057:intron 45.0%
GTTCGAATTCCACTACGCTA+TGG - chr2.4:2156580-2156599 MS.gene89057:intron 45.0%
TAGCGGCGTTGTAGCATTAT+AGG + chr2.4:2156521-2156540 None:intergenic 45.0%
TCTGCTGCTGCTACAACTAA+TGG - chr2.4:2156981-2157000 MS.gene89057:CDS 45.0%
! ATGGCTGAGGTATTTGTAGC+AGG + chr2.4:2157059-2157078 None:intergenic 45.0%
! TGGTTCTTCTGCCGATTATG+AGG - chr2.4:2156270-2156289 MS.gene89057:intron 45.0%
!!! TTTTGTTATTAAAATAAAAT+GGG - chr2.4:2156088-2156107 MS.gene89057:intron 5.0%
!!! TTTTTGTTATTAAAATAAAA+TGG - chr2.4:2156087-2156106 MS.gene89057:intron 5.0%
AACGACCTCAGAACAGCAAC+AGG - chr2.4:2155658-2155677 MS.gene89057:CDS 50.0%
AGAGGTAGTTGCCACTGTGA+TGG + chr2.4:2157078-2157097 None:intergenic 50.0%
CCCAAACAGGACCTTATTCC+AGG - chr2.4:2156819-2156838 MS.gene89057:intron 50.0%
CCCCAATGCAACTATGCACA+TGG - chr2.4:2155631-2155650 MS.gene89057:CDS 50.0%
GTAGAGGAGGAGTTGCATGA+AGG + chr2.4:2155747-2155766 None:intergenic 50.0%
GTGTCCGTAGCTACAATGTC+TGG + chr2.4:2155713-2155732 None:intergenic 50.0%
GTTGTGTCCGGTGTTTGTGT+TGG - chr2.4:2156010-2156029 MS.gene89057:intron 50.0%
TTGCATTGGGGTGCAACAAG+AGG + chr2.4:2155622-2155641 None:intergenic 50.0%
! TTGGTCCTGTTGCTGTTCTG+AGG + chr2.4:2155666-2155685 None:intergenic 50.0%
AGTTGCCACTGTGATGGCTG+AGG + chr2.4:2157072-2157091 None:intergenic 55.0%
TCATGCTGCTGCTGCTGCTG+AGG + chr2.4:2155787-2155806 None:intergenic 60.0%


Chromosome Type Strat End Strand Name
chr2.4 gene 2155538 2157187 2155538 ID=MS.gene89057
chr2.4 mRNA 2155538 2157187 2155538 ID=MS.gene89057.t1;Parent=MS.gene89057
chr2.4 exon 2156899 2157187 2156899 ID=MS.gene89057.t1.exon1;Parent=MS.gene89057.t1
chr2.4 CDS 2156899 2157187 2156899 ID=cds.MS.gene89057.t1;Parent=MS.gene89057.t1
chr2.4 exon 2155538 2155788 2155538 ID=MS.gene89057.t1.exon2;Parent=MS.gene89057.t1
chr2.4 CDS 2155538 2155788 2155538 ID=cds.MS.gene89057.t1;Parent=MS.gene89057.t1
Gene Sequence

>MS.gene89057

ATGGATTCAGAAGCTGAAAATTCACAAACCCATATGAGGATTAAGACTCAGCTATGCAAAAGATTCATGCAAGGAACGTGTCCTCTTGTTGCACCCCAATGCAACTATGCACATGGCTACAACGACCTCAGAACAGCAACAGGACCAAGATTCTGTAGAATGTTCATGCACACCAGACATTGTAGCTACGGACACAACTGTCGTTTCCTTCATGCAACTCCTCCTCTACCTCTTCATTATGTTCATCCTCAGCAGCAGCAGCAGCATGAGAACTTTTCTCCACAACCACGTATTTTTCTTCAACTTCTTTCATTTACTACACTAACACTACTTTTTGGTCTTGTTTGTTCATTTCTTAGTATTAGAACAAAAAGGGTTTTCTTTTCTGTAGCATCGACACATTTGATCAAAAGTGTGTTTGTCAGTTCTTAAACAAACACAACACTGACAAATGTGAATACATTCGATCAGTGTTGTGTCCGGTGTTTGTGTTGGTGCTTTATAGGTTTTATGTAATCTGGTGAATTTTGTGCTTGTTTAATAATTTTTTTTTTGTTATTAAAATAAAATGGGTTTTTTATTTTTTTTCTAAACATTATTACTTGAACTGTGAAATTGTGTTATTGTATGATCTAGTTCTGCAGCTTGCTTAATCAGTTATGGCATGTGGTGAATTTAGCTAGGATGGCATACTGTTAAAATATTTCAATAAAAACAACAAACACATAATGTTGGTTCTTCTGCCGATTATGAGGTTGCTTAATTAATAAGTAATGTCTCGGATTCGAGTCTTATAAATGGAAAAAATGTGCATCGGAGATGATTTGCCCCTATGAGTTAGGGTCTATTTGAATTGACTTATTTGAGTTTATTTACTGACATAAAATATCGTGAGATTGTTTGTAAGAGTTTATGAAAACAAATTAAAATGCTCTCAATTTTGAATCGCGGAAATTGGCGGTCTGTTCAATTTCTGCTATCCTATAATGCTACAACGCCGCTATTTGACAATTTTCTACTAAATATCATGGAACAATAGTTTGTTCGAATTCCACTACGCTATGGTGACACTATAACTGCTATTTGACAACACTGTTTATGACATATCCATAAATTGTTTTTAGCTTATTTTTATAAGCTCTCCATGATAGCTTATACAAACAGCTTATAGTATATATGAAAACAATTTGACTTCAGTTTATCTTTTGTTGGAAAAATAGCTTATACATAAACACTTATATGATATGGACTTATGCTATGAGTGTTTAATTAAGCTGTTTACCCAAACAGGACCTTATTCCAGGTCCAATATGATTTCCATGAAAGCTTTTTGTGATTCAATAGAATATAGAACTGTGTTGGTGTAAGTAAATTTTGACTTGAGAGTTTGTGAATGCAGAACCAGGGATGATACAAAATGCAGAATGCAGGATCATGCAAACTTCTGCTGCTGCTACAACTAATGGCCACTCTTCTGCACAAAACAACACAACGCAATTGCAAACTTATAGCTCTACTCCTGCTACAAATACCTCAGCCATCACAGTGGCAACTACCTCTTTACATAAGAATGGACCGTATGCTGGTAAATCCTTATCTGACAAAAACACAATGCAAAGGATCATTCGTCTCTATGCTGATTGGATTTAA
Protein sequence

>MS.gene89057.t1

MDSEAENSQTHMRIKTQLCKRFMQGTCPLVAPQCNYAHGYNDLRTATGPRFCRMFMHTRHCSYGHNCRFLHATPPLPLHYVHPQQQQQHENFSPQPQPGMIQNAECRIMQTSAAATTNGHSSAQNNTTQLQTYSSTPATNTSAITVATTSLHKNGPYAGKSLSDKNTMQRIIRLYADWI