AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene038852

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene038852.t1 MTR_2g054750 89.286 140 3 1 1 140 1 128 2.84e-86 248
MS.gene038852.t1 MTR_4g113840 77.857 140 31 0 1 140 1 140 3.55e-80 233
MS.gene038852.t1 MTR_4g011190 45.139 144 60 2 6 134 5 144 3.74e-36 121
MS.gene038852.t1 MTR_3g107610 35.758 165 60 4 6 134 5 159 2.78e-28 102
MS.gene038852.t1 MTR_3g107610 34.014 147 47 4 6 114 5 139 1.34e-19 80.1
MS.gene038852.t1 MTR_3g107610 43.617 94 42 4 50 136 5 94 1.02e-13 65.1
MS.gene038852.t1 MTR_6g069400 28.358 134 74 4 1 134 265 376 5.81e-11 59.3
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene038852.t1 AT2G26695 67.626 139 42 2 1 138 1 137 2.14e-64 193
MS.gene038852.t1 AT2G26695 67.626 139 42 2 1 138 1 137 2.14e-64 193
MS.gene038852.t1 AT5G25490 38.182 165 65 5 6 137 5 165 3.47e-32 112
MS.gene038852.t1 AT5G25490 38.182 165 65 5 6 137 5 165 3.47e-32 112
MS.gene038852.t1 AT3G15680 40.909 154 68 6 6 136 5 158 2.38e-30 107
MS.gene038852.t1 AT3G15680 40.909 154 68 6 6 136 5 158 2.38e-30 107
MS.gene038852.t1 AT2G17975 31.544 149 72 6 6 130 7 149 6.87e-14 67.0
MS.gene038852.t1 AT2G17975 31.507 146 84 6 2 140 125 261 7.32e-11 58.5
MS.gene038852.t1 AT2G17975 31.724 145 83 6 3 140 96 231 2.88e-11 59.3

Find 37 sgRNAs with CRISPR-Local

Find 94 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TCTTAGGGTATCCACAATTT+TGG 0.169674 2.1:+36842567 None:intergenic
CAGTTATATCTATAGGTTTC+TGG 0.204139 2.1:+36842530 None:intergenic
GGATCAGGGCCTCCAATCTT+AGG 0.228355 2.1:+36842551 None:intergenic
ACATTTCATACCAAAACTTT+TGG 0.233482 2.1:+36841725 None:intergenic
AATGGTTACTCTTGTGGATT+TGG 0.299384 2.1:-36842407 MS.gene038852:CDS
ATGGATGCCTCTGGTGGATA+TGG 0.313642 2.1:-36842377 MS.gene038852:CDS
TATCTATAGGTTTCTGGATC+AGG 0.325728 2.1:+36842536 None:intergenic
TGCAAAACACCCAAAAGTTT+TGG 0.338060 2.1:-36841735 MS.gene038852:intron
CAGAAACCTATAGATATAAC+TGG 0.359021 2.1:-36842529 MS.gene038852:CDS
TTCAGTCCAGTTATATCTAT+AGG 0.364972 2.1:+36842523 None:intergenic
TCTTCTTGAAATTTATATGC+TGG 0.441540 2.1:+36842600 None:intergenic
AATTGTGGATACCCTAAGAT+TGG 0.457887 2.1:-36842563 MS.gene038852:CDS
TGAGCTGGTCAGGAGGAGAT+TGG 0.487008 2.1:-36842637 MS.gene038852:CDS
ATCTATAGGTTTCTGGATCA+GGG 0.490676 2.1:+36842537 None:intergenic
GGTGGGAACATGGATGCCTC+TGG 0.491282 2.1:-36842386 MS.gene038852:CDS
ATATAACTGGACTGAAACCT+TGG 0.499509 2.1:-36842516 MS.gene038852:CDS
AACTGGACTGAAACCTTGGC+AGG 0.503471 2.1:-36842512 MS.gene038852:CDS
GATCAGGGCCTCCAATCTTA+GGG 0.508242 2.1:+36842552 None:intergenic
CTGAAACCTTGGCAGGGGAC+TGG 0.517119 2.1:-36842505 MS.gene038852:CDS
CTGGATGGAAAACTGGTGAC+TGG 0.527330 2.1:-36842334 MS.gene038852:CDS
AGCATATAAATTTCAAGAAG+AGG 0.527814 2.1:-36842598 MS.gene038852:CDS
TTGTGGATTTGGTGGGAACA+TGG 0.541127 2.1:-36842396 MS.gene038852:CDS
GGTTACTCTTGTGGATTTGG+TGG 0.558743 2.1:-36842404 MS.gene038852:CDS
GCATATAAATTTCAAGAAGA+GGG 0.572289 2.1:-36842597 MS.gene038852:CDS
CTGGTGACTGGATATGCACT+AGG 0.573750 2.1:-36842322 MS.gene038852:intron
TGTGGATACCCTAAGATTGG+AGG 0.581161 2.1:-36842560 MS.gene038852:CDS
AGGGATGCATGCCAAAATTG+TGG 0.584842 2.1:-36842578 MS.gene038852:CDS
TCATGTATCAGATATGGCTG+TGG 0.590303 2.1:-36841795 MS.gene038852:intron
GTTACTCTTGTGGATTTGGT+GGG 0.590561 2.1:-36842403 MS.gene038852:CDS
GGGAACATGGATGCCTCTGG+TGG 0.591219 2.1:-36842383 MS.gene038852:CDS
ACTGGACTGAAACCTTGGCA+GGG 0.594678 2.1:-36842511 MS.gene038852:CDS
GCAGGGGACTGGTATTGCAG+TGG 0.597750 2.1:-36842494 MS.gene038852:CDS
GCAATACCAGTCCCCTGCCA+AGG 0.605697 2.1:+36842499 None:intergenic
CTGGACTGAAACCTTGGCAG+GGG 0.627405 2.1:-36842510 MS.gene038852:CDS
AGAACAAGCTGTTATAGATG+TGG 0.633263 2.1:-36842440 MS.gene038852:CDS
ATCAGATCCATATCCACCAG+AGG 0.683350 2.1:+36842370 None:intergenic
TATTGCAGTGGTATGAACTG+TGG 0.711677 2.1:-36842482 MS.gene038852:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AATTAATTATATAAGCATCA+TGG + chr2.1:36842617-36842636 None:intergenic 15.0%
!! ATATAATTAATTCCTATTTC+AGG - chr2.1:36842625-36842644 MS.gene038852:CDS 15.0%
!! TAATTACAAAATATGTGATA+GGG + chr2.1:36842180-36842199 None:intergenic 15.0%
!! TTAATTACAAAATATGTGAT+AGG + chr2.1:36842181-36842200 None:intergenic 15.0%
!!! ATCTCATATTTTGTAATTGA+GGG - chr2.1:36841984-36842003 MS.gene038852:intron 20.0%
! AGCATATAAATTTCAAGAAG+AGG - chr2.1:36841673-36841692 MS.gene038852:intron 25.0%
! CGATAAATTTCAAATCTTCT+CGG + chr2.1:36842339-36842358 None:intergenic 25.0%
! GCATATAAATTTCAAGAAGA+GGG - chr2.1:36841674-36841693 MS.gene038852:intron 25.0%
! GCATATACTTTAAGTAATGA+AGG + chr2.1:36842576-36842595 None:intergenic 25.0%
! TAATTAATTCCTATTTCAGG+TGG - chr2.1:36842628-36842647 MS.gene038852:CDS 25.0%
! TCTTCTTGAAATTTATATGC+TGG + chr2.1:36841674-36841693 None:intergenic 25.0%
!! ACATTTCATACCAAAACTTT+TGG + chr2.1:36842549-36842568 None:intergenic 25.0%
!! CATCTCATATTTTGTAATTG+AGG - chr2.1:36841983-36842002 MS.gene038852:intron 25.0%
!! CATTTCATACCAAAACTTTT+GGG + chr2.1:36842548-36842567 None:intergenic 25.0%
!! CGAGAAGATTTGAAATTTAT+CGG - chr2.1:36842337-36842356 MS.gene038852:CDS 25.0%
!! TCTCATATTTTGTAATTGAG+GGG - chr2.1:36841985-36842004 MS.gene038852:intron 25.0%
!! TGCATTTTGTAATTAGACTT+GGG - chr2.1:36842254-36842273 MS.gene038852:intron 25.0%
CAGAAACCTATAGATATAAC+TGG - chr2.1:36841742-36841761 MS.gene038852:CDS 30.0%
CAGTTATATCTATAGGTTTC+TGG + chr2.1:36841744-36841763 None:intergenic 30.0%
TCTTGTGTAAAAACAGGTTA+AGG - chr2.1:36842080-36842099 MS.gene038852:intron 30.0%
TTCAGTCCAGTTATATCTAT+AGG + chr2.1:36841751-36841770 None:intergenic 30.0%
TTGAAAAATGGTTACTCTTG+TGG - chr2.1:36841858-36841877 MS.gene038852:intron 30.0%
TTGTAATTAGACTTGGGAAA+CGG - chr2.1:36842260-36842279 MS.gene038852:intron 30.0%
! CTGCATTTTGTAATTAGACT+TGG - chr2.1:36842253-36842272 MS.gene038852:intron 30.0%
!!! TTAACCTGTTTTTACACAAG+AGG + chr2.1:36842081-36842100 None:intergenic 30.0%
AATGGTTACTCTTGTGGATT+TGG - chr2.1:36841864-36841883 MS.gene038852:intron 35.0%
AATTGTGGATACCCTAAGAT+TGG - chr2.1:36841708-36841727 MS.gene038852:intron 35.0%
AGAACAAGCTGTTATAGATG+TGG - chr2.1:36841831-36841850 MS.gene038852:intron 35.0%
AGATGTGGTGCATTGAAAAA+TGG - chr2.1:36841846-36841865 MS.gene038852:intron 35.0%
ATATAACTGGACTGAAACCT+TGG - chr2.1:36841755-36841774 MS.gene038852:CDS 35.0%
TGCTTCTCATGTATCAGATA+TGG - chr2.1:36842470-36842489 MS.gene038852:CDS 35.0%
! ATCTATAGGTTTCTGGATCA+GGG + chr2.1:36841737-36841756 None:intergenic 35.0%
! TATCTATAGGTTTCTGGATC+AGG + chr2.1:36841738-36841757 None:intergenic 35.0%
! TGCAAAACACCCAAAAGTTT+TGG - chr2.1:36842536-36842555 MS.gene038852:CDS 35.0%
!! TCTTAGGGTATCCACAATTT+TGG + chr2.1:36841707-36841726 None:intergenic 35.0%
!! TGTTTTGCACTTGAAGCATT+CGG + chr2.1:36842525-36842544 None:intergenic 35.0%
ACAGCCTCTTGTGTAAAAAC+AGG - chr2.1:36842074-36842093 MS.gene038852:intron 40.0%
CAATCTGAACCACCTGAAAT+AGG + chr2.1:36842640-36842659 None:intergenic 40.0%
CGTACAATACACCAAATGGT+GGG - chr2.1:36842106-36842125 MS.gene038852:intron 40.0%
GTTGTTGTCATGTGACTGTA+AGG - chr2.1:36842030-36842049 MS.gene038852:intron 40.0%
TAAGCATCATGGATCTGATG+AGG + chr2.1:36842606-36842625 None:intergenic 40.0%
TATTGCAGTGGTATGAACTG+TGG - chr2.1:36841789-36841808 MS.gene038852:intron 40.0%
TCATGTATCAGATATGGCTG+TGG - chr2.1:36842476-36842495 MS.gene038852:CDS 40.0%
TTGTAATTGAGGGGTAACCT+TGG - chr2.1:36841994-36842013 MS.gene038852:intron 40.0%
! AAATATGTGATAGGGCATCC+CGG + chr2.1:36842172-36842191 None:intergenic 40.0%
! GTTACTCTTGTGGATTTGGT+GGG - chr2.1:36841868-36841887 MS.gene038852:intron 40.0%
!! GTTATTTTATGTCAGCGCAG+AGG + chr2.1:36842387-36842406 None:intergenic 40.0%
AGGGATGCATGCCAAAATTG+TGG - chr2.1:36841693-36841712 MS.gene038852:intron 45.0%
ATCAGATCCATATCCACCAG+AGG + chr2.1:36841904-36841923 None:intergenic 45.0%
GCGTACAATACACCAAATGG+TGG - chr2.1:36842105-36842124 MS.gene038852:intron 45.0%
GCTGCGTACAATACACCAAA+TGG - chr2.1:36842102-36842121 MS.gene038852:intron 45.0%
GGTTACTCTTGTGGATTTGG+TGG - chr2.1:36841867-36841886 MS.gene038852:intron 45.0%
GTCATGTGACTGTAAGGTCA+CGG - chr2.1:36842036-36842055 MS.gene038852:intron 45.0%
TCATGTGACTGTAAGGTCAC+GGG - chr2.1:36842037-36842056 MS.gene038852:intron 45.0%
TGTGGATACCCTAAGATTGG+AGG - chr2.1:36841711-36841730 MS.gene038852:intron 45.0%
! AGTCACCAGTTTTCCATCCA+GGG + chr2.1:36841938-36841957 None:intergenic 45.0%
! TTACACAAGAGGCTGTTTCC+AGG + chr2.1:36842070-36842089 None:intergenic 45.0%
!! TTGTGGATTTGGTGGGAACA+TGG - chr2.1:36841875-36841894 MS.gene038852:intron 45.0%
AACTGGACTGAAACCTTGGC+AGG - chr2.1:36841759-36841778 MS.gene038852:CDS 50.0%
ACTGGACTGAAACCTTGGCA+GGG - chr2.1:36841760-36841779 MS.gene038852:CDS 50.0%
ATTGCAATTACCCCCCTGGA+TGG - chr2.1:36841922-36841941 MS.gene038852:intron 50.0%
CTGGATGGAAAACTGGTGAC+TGG - chr2.1:36841937-36841956 MS.gene038852:intron 50.0%
CTGGTGACTGGATATGCACT+AGG - chr2.1:36841949-36841968 MS.gene038852:intron 50.0%
GATCAGGGCCTCCAATCTTA+GGG + chr2.1:36841722-36841741 None:intergenic 50.0%
TCTGATTGCAATTACCCCCC+TGG - chr2.1:36841918-36841937 MS.gene038852:intron 50.0%
! ATGGATGCCTCTGGTGGATA+TGG - chr2.1:36841894-36841913 MS.gene038852:intron 50.0%
! CAGTCACCAGTTTTCCATCC+AGG + chr2.1:36841939-36841958 None:intergenic 50.0%
! GTCACCAGTTTTCCATCCAG+GGG + chr2.1:36841937-36841956 None:intergenic 50.0%
! TCACCAGTTTTCCATCCAGG+GGG + chr2.1:36841936-36841955 None:intergenic 50.0%
AAGGTCACGGGTTCAAGTCC+TGG - chr2.1:36842049-36842068 MS.gene038852:intron 55.0%
CAACTTTGCCAGTTGCGCCA+AGG + chr2.1:36842014-36842033 None:intergenic 55.0%
CATACGCAGGGTTTGGGAAG+GGG + chr2.1:36842133-36842152 None:intergenic 55.0%
CTGGACTGAAACCTTGGCAG+GGG - chr2.1:36841761-36841780 MS.gene038852:CDS 55.0%
CTTCCCAAACCCTGCGTATG+CGG - chr2.1:36842133-36842152 MS.gene038852:intron 55.0%
GCATACGCAGGGTTTGGGAA+GGG + chr2.1:36842134-36842153 None:intergenic 55.0%
GGATCAGGGCCTCCAATCTT+AGG + chr2.1:36841723-36841742 None:intergenic 55.0%
TACCCCCCTGGATGGAAAAC+TGG - chr2.1:36841930-36841949 MS.gene038852:intron 55.0%
TGAGCTGGTCAGGAGGAGAT+TGG - chr2.1:36841634-36841653 MS.gene038852:intron 55.0%
TTCCCAAACCCTGCGTATGC+GGG - chr2.1:36842134-36842153 MS.gene038852:intron 55.0%
! CACCAGTTTTCCATCCAGGG+GGG + chr2.1:36841935-36841954 None:intergenic 55.0%
ACTGAAGCTCCCGCATACGC+AGG + chr2.1:36842146-36842165 None:intergenic 60.0%
AGGGGTAACCTTGGCGCAAC+TGG - chr2.1:36842003-36842022 MS.gene038852:intron 60.0%
ATGCGGGAGCTTCAGTGCAC+CGG - chr2.1:36842150-36842169 MS.gene038852:intron 60.0%
CGCATACGCAGGGTTTGGGA+AGG + chr2.1:36842135-36842154 None:intergenic 60.0%
CTCCCGCATACGCAGGGTTT+GGG + chr2.1:36842139-36842158 None:intergenic 60.0%
CTGAAACCTTGGCAGGGGAC+TGG - chr2.1:36841766-36841785 MS.gene038852:CDS 60.0%
CTGAAGCTCCCGCATACGCA+GGG + chr2.1:36842145-36842164 None:intergenic 60.0%
GCAATACCAGTCCCCTGCCA+AGG + chr2.1:36841775-36841794 None:intergenic 60.0%
GGGAACATGGATGCCTCTGG+TGG - chr2.1:36841888-36841907 MS.gene038852:intron 60.0%
GGTGGGAACATGGATGCCTC+TGG - chr2.1:36841885-36841904 MS.gene038852:intron 60.0%
TGGGAAGGGGTCCCACCATT+TGG + chr2.1:36842120-36842139 None:intergenic 60.0%
! GCAGGGGACTGGTATTGCAG+TGG - chr2.1:36841777-36841796 MS.gene038852:CDS 60.0%
GCTCCCGCATACGCAGGGTT+TGG + chr2.1:36842140-36842159 None:intergenic 65.0%
TGCGGGAGCTTCAGTGCACC+GGG - chr2.1:36842151-36842170 MS.gene038852:intron 65.0%


Chromosome Type Strat End Strand Name
chr2.1 gene 36841633 36842660 36841633 ID=MS.gene038852
chr2.1 mRNA 36841633 36842660 36841633 ID=MS.gene038852.t1;Parent=MS.gene038852
chr2.1 exon 36842323 36842660 36842323 ID=MS.gene038852.t1.exon1;Parent=MS.gene038852.t1
chr2.1 CDS 36842323 36842660 36842323 ID=cds.MS.gene038852.t1;Parent=MS.gene038852.t1
chr2.1 exon 36841736 36841806 36841736 ID=MS.gene038852.t1.exon2;Parent=MS.gene038852.t1
chr2.1 CDS 36841736 36841806 36841736 ID=cds.MS.gene038852.t1;Parent=MS.gene038852.t1
chr2.1 exon 36841633 36841646 36841633 ID=MS.gene038852.t1.exon3;Parent=MS.gene038852.t1
chr2.1 CDS 36841633 36841646 36841633 ID=cds.MS.gene038852.t1;Parent=MS.gene038852.t1
Gene Sequence

>MS.gene038852

ATGAGCTGGTCAGGAGGAGATTGGATGTGCAATGCTTGCCAGCATATAAATTTCAAGAAGAGGGATGCATGCCAAAATTGTGGATACCCTAAGATTGGAGGCCCTGATCCAGAAACCTATAGATATAACTGGACTGAAACCTTGGCAGGGGACTGGTATTGCAGTGGTATGAACTGTGGAGCTCACAATTATGCTAGCAGAACAAGCTGTTATAGATGTGGTGCATTGAAAAATGGTTACTCTTGTGGATTTGGTGGGAACATGGATGCCTCTGGTGGATATGGATCTGATTGCAATTACCCCCCTGGATGGAAAACTGGTGACTGGATATGCACTAGGTATTTTCACATCATCTCATATTTTGTAATTGAGGGGTAACCTTGGCGCAACTGGCAAAGTTGTTGTCATGTGACTGTAAGGTCACGGGTTCAAGTCCTGGAAACAGCCTCTTGTGTAAAAACAGGTTAAGGCTGCGTACAATACACCAAATGGTGGGACCCCTTCCCAAACCCTGCGTATGCGGGAGCTTCAGTGCACCGGGATGCCCTATCACATATTTTGTAATTAACTTCACTAAAATATGCTGCTAAAATATGCTGCATTTTCATGTACTGAAGTTGCTGCATTTTGTAATTAGACTTGGGAAACGGAGAAATTATTATTAATAAGAATGATGACACTAATGACAGTTTTGCAATTGTCTCCGAGAAGATTTGAAATTTATCGGTTAAAACTACAAAGTCAACTCTCACCTCTGCGCTGACATAAAATAACTCGTTTCATTGTATTACATAAAAAGAAATATGAAATATCATAGAAATACATTTTTATTTTCTTTGCTTCTCATGTATCAGATATGGCTGTGGAGTGCACAATTATGCTAGCAGAGCCGAATGCTTCAAGTGCAAAACACCCAAAAGTTTTGGTATGAAATGTTTATCCTTCATTACTTAAAGTATATGCTATTCAACCTCATCAGATCCATGATGCTTATATAATTAATTCCTATTTCAGGTGGTTCAGATTGA
Protein sequence

>MS.gene038852.t1

MSWSGGDWMCNACQHINFKKRDACQNCGYPKIGGPDPETYRYNWTETLAGDWYCSGMNCGAHNYASRTSCYRCGALKNGYSCGFGGNMDASGGYGSDCNYPPGWKTGDWICTRYGCGVHNYASRAECFKCKTPKSFGGSD