AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene69926


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene69926.t1 MTR_1g081280 86.555 238 20 2 1 226 1 238 3.09e-151 420
MS.gene69926.t1 MTR_1g081280 75.314 239 20 3 1 200 1 239 1.42e-122 348
MS.gene69926.t1 MTR_8g028545 30.519 154 90 4 70 220 85 224 6.71e-20 85.1
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene69926.t1 AT3G04890 59.429 175 66 2 50 219 33 207 5.71e-67 206
MS.gene69926.t1 AT3G04890 59.429 175 66 2 50 219 37 211 1.35e-66 205
MS.gene69926.t1 AT3G04890 54.037 161 69 2 50 205 33 193 9.22e-53 169
MS.gene69926.t1 AT3G04890 54.037 161 69 2 50 205 37 197 1.20e-52 169
MS.gene69926.t1 AT2G46100 31.638 177 105 6 54 220 60 230 1.85e-20 86.7

Find 36 sgRNAs with CRISPR-Local

Find 98 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ACATCATCAATACTTGAAAC+TGG 0.314009 1.4:+65958408 None:intergenic
GATCCAACTATTAAATTTAG+TGG 0.322543 1.4:-65958131 MS.gene69926:intron
GCATAGATACCTTGTTTGTT+GGG 0.356498 1.4:+65958778 None:intergenic
AGGCCTCTGATTGCTATTGA+TGG 0.367080 1.4:-65957538 MS.gene69926:CDS
GGCATAGATACCTTGTTTGT+TGG 0.370365 1.4:+65958777 None:intergenic
TGCGTGCATCTTGGAAATTA+AGG 0.376993 1.4:-65957664 MS.gene69926:intron
TTACCACTAAATTTAATAGT+TGG 0.387007 1.4:+65958128 None:intergenic
TGATGTTCTAATCATCATAA+AGG 0.421681 1.4:-65958391 MS.gene69926:CDS
TGGAAGTGTAAGGCTATTGT+AGG 0.430972 1.4:+65959075 None:intergenic
GGACCAACTTAAAACTTCCT+TGG 0.437814 1.4:-65957561 MS.gene69926:CDS
ATAATGCAGGATGTTGAATC+TGG 0.446617 1.4:-65957698 MS.gene69926:intron
CGCCATGACATTCAACCACC+TGG 0.479324 1.4:+65957320 None:intergenic
GATCTTTAGTAGTCTAATTG+AGG 0.482759 1.4:+65957813 None:intergenic
GGAAGTGTAAGGCTATTGTA+GGG 0.518951 1.4:+65959076 None:intergenic
AGATACCTTGTTTGTTGGGG+AGG 0.519985 1.4:+65958782 None:intergenic
AATTGAGGCACAGTCGAAGA+AGG 0.520587 1.4:+65957828 None:intergenic
CCAACTTAAAACTTCCTTGG+AGG 0.532999 1.4:-65957558 MS.gene69926:CDS
TAGACTACTAAAGATCGAAA+AGG 0.538132 1.4:-65957806 MS.gene69926:intron
CATAGATACCTTGTTTGTTG+GGG 0.538359 1.4:+65958779 None:intergenic
AGACATTTATTACCTGGGAG+TGG 0.539869 1.4:+65959055 None:intergenic
CATCATCAATACTTGAAACT+GGG 0.541779 1.4:+65958409 None:intergenic
GGGGAGGAGAGAAAAGCCTC+AGG 0.553407 1.4:+65958798 None:intergenic
TCGTTCGGCATATTGAGAGT+TGG 0.563467 1.4:-65957391 MS.gene69926:CDS
AGCCTTACACTTCCACTCCC+AGG 0.566168 1.4:-65959067 MS.gene69926:intron
AGAAAGAAATGAAACCCCTC+AGG 0.569312 1.4:-65958855 MS.gene69926:CDS
TCTCTCCTCCCCAACAAACA+AGG 0.591145 1.4:-65958787 MS.gene69926:intron
ATAGCAATCAGAGGCCTCCA+AGG 0.592160 1.4:+65957544 None:intergenic
GACTTGTGCAATTTATAACA+TGG 0.596814 1.4:-65958882 MS.gene69926:CDS
TACCTGGGAGTGGAAGTGTA+AGG 0.601591 1.4:+65959065 None:intergenic
GCGGAGTGACTGAGCTCCTG+AGG 0.601635 1.4:-65958814 MS.gene69926:CDS
ATTGAGGCACAGTCGAAGAA+GGG 0.608103 1.4:+65957829 None:intergenic
ATCATCAATACTTGAAACTG+GGG 0.643651 1.4:+65958410 None:intergenic
GCACAAGTCTTTCTACTACA+CGG 0.651194 1.4:+65958896 None:intergenic
GAAGTGTAAGGCTATTGTAG+GGG 0.673629 1.4:+65959077 None:intergenic
CTTCCATCAATAGCAATCAG+AGG 0.678084 1.4:+65957535 None:intergenic
GTTCTGAAAATTGCAGTGAG+CGG 0.681587 1.4:-65958833 MS.gene69926:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ATTATATAAATTAATAATGC+AGG - chr1.4:65958728-65958747 MS.gene69926:intron 10.0%
!! ATGAAAAAATATTTGATAAG+AGG + chr1.4:65958132-65958151 None:intergenic 15.0%
!! GTAATTTAAGAAAATAAAAG+TGG + chr1.4:65957822-65957841 None:intergenic 15.0%
!! TGAAAAAATATTTGATAAGA+GGG + chr1.4:65958131-65958150 None:intergenic 15.0%
!! AACACTGCATATTAATAAAT+TGG + chr1.4:65957990-65958009 None:intergenic 20.0%
!! AATAAAGACATTTATTACCT+GGG + chr1.4:65957392-65957411 None:intergenic 20.0%
!! TTACCACTAAATTTAATAGT+TGG + chr1.4:65958314-65958333 None:intergenic 20.0%
!!! ATTATGAGTGGAAAATTTTA+AGG + chr1.4:65958977-65958996 None:intergenic 20.0%
!!! TTAAAGATTTGAAACATCTA+GGG + chr1.4:65958457-65958476 None:intergenic 20.0%
!!! TTTAAAGATTTGAAACATCT+AGG + chr1.4:65958458-65958477 None:intergenic 20.0%
! AAATGTTTGTGCTACATAAA+TGG + chr1.4:65957686-65957705 None:intergenic 25.0%
! AGACTAGCATAAGTTATTAT+AGG + chr1.4:65958352-65958371 None:intergenic 25.0%
! ATTTCAAATCACATTATGAG+TGG + chr1.4:65958989-65959008 None:intergenic 25.0%
! GAATAAAGACATTTATTACC+TGG + chr1.4:65957393-65957412 None:intergenic 25.0%
! GATCCAACTATTAAATTTAG+TGG - chr1.4:65958308-65958327 MS.gene69926:intron 25.0%
! TGATGTTCTAATCATCATAA+AGG - chr1.4:65958048-65958067 MS.gene69926:intron 25.0%
! TTTATATAATGAGTGAAGCA+CGG + chr1.4:65958718-65958737 None:intergenic 25.0%
!! CTTACTTTGTTTGAGATTTA+GGG - chr1.4:65958243-65958262 MS.gene69926:intron 25.0%
!! TCTTACTTTGTTTGAGATTT+AGG - chr1.4:65958242-65958261 MS.gene69926:intron 25.0%
!!! ATTTTCAAGTTTGAAAAACC+AGG - chr1.4:65959101-65959120 MS.gene69926:CDS 25.0%
AAACAACTGTAAGAGCTAAA+AGG - chr1.4:65958476-65958495 MS.gene69926:intron 30.0%
ACATCATCAATACTTGAAAC+TGG + chr1.4:65958034-65958053 None:intergenic 30.0%
ATCATCAATACTTGAAACTG+GGG + chr1.4:65958032-65958051 None:intergenic 30.0%
ATTAACATGCTTAATGAGCA+AGG + chr1.4:65958807-65958826 None:intergenic 30.0%
CATCATCAATACTTGAAACT+GGG + chr1.4:65958033-65958052 None:intergenic 30.0%
GACTTGTGCAATTTATAACA+TGG - chr1.4:65957557-65957576 MS.gene69926:CDS 30.0%
GATCTTTAGTAGTCTAATTG+AGG + chr1.4:65958629-65958648 None:intergenic 30.0%
TAGACTACTAAAGATCGAAA+AGG - chr1.4:65958633-65958652 MS.gene69926:intron 30.0%
TCTATGATGAATGATCATAC+AGG - chr1.4:65958550-65958569 MS.gene69926:intron 30.0%
TTGAAATCCATGTTAACTAG+TGG - chr1.4:65959002-65959021 MS.gene69926:intron 30.0%
TTTAGATTACATGCCAGAAA+TGG + chr1.4:65958218-65958237 None:intergenic 30.0%
!! TTTTTGTTTGACAGATCGTT+CGG - chr1.4:65959033-65959052 MS.gene69926:intron 30.0%
ACTACTAAAGATCGAAAAGG+TGG - chr1.4:65958636-65958655 MS.gene69926:intron 35.0%
ATAATGCAGGATGTTGAATC+TGG - chr1.4:65958741-65958760 MS.gene69926:intron 35.0%
CAACATTGACGCTTAAACAT+TGG + chr1.4:65957776-65957795 None:intergenic 35.0%
CTGAATCTCTTGTTAAGACT+AGG - chr1.4:65957472-65957491 MS.gene69926:intron 35.0%
CTTTATTATCCCTCAATCTC+AGG - chr1.4:65958857-65958876 MS.gene69926:CDS 35.0%
GATGAATGATCATACAGGTA+GGG - chr1.4:65958555-65958574 MS.gene69926:intron 35.0%
TGATGAATGATCATACAGGT+AGG - chr1.4:65958554-65958573 MS.gene69926:intron 35.0%
TTCAACCTCATTTCCATTTC+TGG - chr1.4:65958202-65958221 MS.gene69926:intron 35.0%
! CATAGATACCTTGTTTGTTG+GGG + chr1.4:65957663-65957682 None:intergenic 35.0%
! GAAGCAAAAAAGTGTAGTTC+AGG + chr1.4:65958683-65958702 None:intergenic 35.0%
! GCATAGATACCTTGTTTGTT+GGG + chr1.4:65957664-65957683 None:intergenic 35.0%
! TTCAAGTTTGAAAAACCAGG+TGG - chr1.4:65959104-65959123 MS.gene69926:CDS 35.0%
ACATGCCAGAAATGGAAATG+AGG + chr1.4:65958210-65958229 None:intergenic 40.0%
AGAAAGAAATGAAACCCCTC+AGG - chr1.4:65957584-65957603 MS.gene69926:intron 40.0%
AGACATTTATTACCTGGGAG+TGG + chr1.4:65957387-65957406 None:intergenic 40.0%
CCAACTTAAAACTTCCTTGG+AGG - chr1.4:65958881-65958900 MS.gene69926:CDS 40.0%
CTTCCATCAATAGCAATCAG+AGG + chr1.4:65958907-65958926 None:intergenic 40.0%
GAAGTGTAAGGCTATTGTAG+GGG + chr1.4:65957365-65957384 None:intergenic 40.0%
GCACAAGTCTTTCTACTACA+CGG + chr1.4:65957546-65957565 None:intergenic 40.0%
GGACCAACTTAAAACTTCCT+TGG - chr1.4:65958878-65958897 MS.gene69926:CDS 40.0%
GTAGCAACCACTAGTTAACA+TGG + chr1.4:65959012-65959031 None:intergenic 40.0%
TGCGTGCATCTTGGAAATTA+AGG - chr1.4:65958775-65958794 MS.gene69926:intron 40.0%
TGTGTATGTGTAAGAGGTAG+TGG - chr1.4:65957874-65957893 MS.gene69926:intron 40.0%
TTTCAGAGTGAAGACGTCTT+TGG - chr1.4:65957703-65957722 MS.gene69926:intron 40.0%
! ACTGCAATTTTCAGAACCTG+AGG + chr1.4:65957603-65957622 None:intergenic 40.0%
! CAAATTTTCTGCGTGCATCT+TGG - chr1.4:65958766-65958785 MS.gene69926:intron 40.0%
! CTGCAATTTTCAGAACCTGA+GGG + chr1.4:65957602-65957621 None:intergenic 40.0%
! GCAAAAACATGCTGCTTCAA+CGG - chr1.4:65957334-65957353 MS.gene69926:CDS 40.0%
! GCATAAGTTGACGATTAGTG+AGG + chr1.4:65957939-65957958 None:intergenic 40.0%
! GGAAGTGTAAGGCTATTGTA+GGG + chr1.4:65957366-65957385 None:intergenic 40.0%
! GGCATAGATACCTTGTTTGT+TGG + chr1.4:65957665-65957684 None:intergenic 40.0%
! TGCAATTTTCAGAACCTGAG+GGG + chr1.4:65957601-65957620 None:intergenic 40.0%
! TGGAAGTGTAAGGCTATTGT+AGG + chr1.4:65957367-65957386 None:intergenic 40.0%
!! GTTCTGAAAATTGCAGTGAG+CGG - chr1.4:65957606-65957625 MS.gene69926:intron 40.0%
!! TAAGTTGGTCCTGAGATTGA+GGG + chr1.4:65958869-65958888 None:intergenic 40.0%
!! TTAAGTTGGTCCTGAGATTG+AGG + chr1.4:65958870-65958889 None:intergenic 40.0%
!!! CCTCCAAGGAAGTTTTAAGT+TGG + chr1.4:65958884-65958903 None:intergenic 40.0%
AATTGAGGCACAGTCGAAGA+AGG + chr1.4:65958614-65958633 None:intergenic 45.0%
ACGTGTCAAGTGTACGACAT+TGG + chr1.4:65957743-65957762 None:intergenic 45.0%
ATTGAGGCACAGTCGAAGAA+GGG + chr1.4:65958613-65958632 None:intergenic 45.0%
GACGCTTAAACATTGGCCAA+TGG + chr1.4:65957769-65957788 None:intergenic 45.0%
GCTTAAACATTGGCCAATGG+CGG + chr1.4:65957766-65957785 None:intergenic 45.0%
GGTGCATGTGTATGTGTAAG+AGG - chr1.4:65957868-65957887 MS.gene69926:CDS 45.0%
TCGTTCGGCATATTGAGAGT+TGG - chr1.4:65959048-65959067 MS.gene69926:intron 45.0%
! AGATACCTTGTTTGTTGGGG+AGG + chr1.4:65957660-65957679 None:intergenic 45.0%
! AGGCCTCTGATTGCTATTGA+TGG - chr1.4:65958901-65958920 MS.gene69926:CDS 45.0%
! GAGGTAGTGGTTCATGTTGT+TGG - chr1.4:65957887-65957906 MS.gene69926:intron 45.0%
!! TGTTGTTTCCGCAACTGCAA+GGG + chr1.4:65957504-65957523 None:intergenic 45.0%
!!! GACAGCGCTTATTTTGTCAC+AGG - chr1.4:65958079-65958098 MS.gene69926:intron 45.0%
ATAGCAATCAGAGGCCTCCA+AGG + chr1.4:65958898-65958917 None:intergenic 50.0%
ATGCATATTGCCCTGGCAGT+TGG + chr1.4:65957915-65957934 None:intergenic 50.0%
GTGAGGAATGCATATTGCCC+TGG + chr1.4:65957922-65957941 None:intergenic 50.0%
GTTGTTGGAACCAACTGCCA+GGG - chr1.4:65957902-65957921 MS.gene69926:intron 50.0%
TACCAGTGTCGTGTCATGTC+TGG - chr1.4:65957842-65957861 MS.gene69926:CDS 50.0%
TCTCTCCTCCCCAACAAACA+AGG - chr1.4:65957652-65957671 MS.gene69926:intron 50.0%
TGTTGTTGGAACCAACTGCC+AGG - chr1.4:65957901-65957920 MS.gene69926:intron 50.0%
! TACCTGGGAGTGGAAGTGTA+AGG + chr1.4:65957377-65957396 None:intergenic 50.0%
!! GTGTTGTTTCCGCAACTGCA+AGG + chr1.4:65957505-65957524 None:intergenic 50.0%
ACACTTGACACGTCCGCCAT+TGG - chr1.4:65957750-65957769 MS.gene69926:intron 55.0%
AGCCTTACACTTCCACTCCC+AGG - chr1.4:65957372-65957391 MS.gene69926:CDS 55.0%
GACCAGACATGACACGACAC+TGG + chr1.4:65957847-65957866 None:intergenic 55.0%
GTGTCGTGTCATGTCTGGTC+TGG - chr1.4:65957847-65957866 MS.gene69926:CDS 55.0%
TGTTTCCGCAACTGCAAGGG+TGG + chr1.4:65957501-65957520 None:intergenic 55.0%
GGGGAGGAGAGAAAAGCCTC+AGG + chr1.4:65957644-65957663 None:intergenic 60.0%
GCGGAGTGACTGAGCTCCTG+AGG - chr1.4:65957625-65957644 MS.gene69926:intron 65.0%
GGACGCCACCCTTGCAGTTG+CGG - chr1.4:65957493-65957512 MS.gene69926:intron 65.0%


Chromosome Type Strat End Strand Name
chr1.4 gene 65957331 65959130 65957331 ID=MS.gene69926
chr1.4 mRNA 65957331 65959130 65957331 ID=MS.gene69926.t1;Parent=MS.gene69926
chr1.4 exon 65959068 65959130 65959068 ID=MS.gene69926.t1.exon1;Parent=MS.gene69926.t1
chr1.4 CDS 65959068 65959130 65959068 ID=cds.MS.gene69926.t1;Parent=MS.gene69926.t1
chr1.4 exon 65958788 65958951 65958788 ID=MS.gene69926.t1.exon2;Parent=MS.gene69926.t1
chr1.4 CDS 65958788 65958951 65958788 ID=cds.MS.gene69926.t1;Parent=MS.gene69926.t1
chr1.4 exon 65958361 65958455 65958361 ID=MS.gene69926.t1.exon3;Parent=MS.gene69926.t1
chr1.4 CDS 65958361 65958455 65958361 ID=cds.MS.gene69926.t1;Parent=MS.gene69926.t1
chr1.4 exon 65958132 65958197 65958132 ID=MS.gene69926.t1.exon4;Parent=MS.gene69926.t1
chr1.4 CDS 65958132 65958197 65958132 ID=cds.MS.gene69926.t1;Parent=MS.gene69926.t1
chr1.4 exon 65957807 65957889 65957807 ID=MS.gene69926.t1.exon5;Parent=MS.gene69926.t1
chr1.4 CDS 65957807 65957889 65957807 ID=cds.MS.gene69926.t1;Parent=MS.gene69926.t1
chr1.4 exon 65957665 65957711 65957665 ID=MS.gene69926.t1.exon6;Parent=MS.gene69926.t1
chr1.4 CDS 65957665 65957711 65957665 ID=cds.MS.gene69926.t1;Parent=MS.gene69926.t1
chr1.4 exon 65957504 65957582 65957504 ID=MS.gene69926.t1.exon7;Parent=MS.gene69926.t1
chr1.4 CDS 65957504 65957582 65957504 ID=cds.MS.gene69926.t1;Parent=MS.gene69926.t1
chr1.4 exon 65957331 65957414 65957331 ID=MS.gene69926.t1.exon8;Parent=MS.gene69926.t1
chr1.4 CDS 65957331 65957414 65957331 ID=cds.MS.gene69926.t1;Parent=MS.gene69926.t1
Gene Sequence

>MS.gene69926

ATGGCAAAAACATGCTGCTTCAACGGAAAATCCCCTACAATAGCCTTACACTTCCACTCCCAGGTAATAAATGTCTTTATTCTGAGATGAGTTATTTATTTGTAAAGTGATCAAAGTGAATTATTTATATGAAGAAGTTCACTGAATCTCTTGTTAAGACTAGGACGCCACCCTTGCAGTTGCGGAAACAACACTGCTCAAAAAGTTACACACCGTGTAGTAGAAAGACTTGTGCAATTTATAACATGGTAAAAGAAAGAAATGAAACCCCTCAGGTTCTGAAAATTGCAGTGAGCGGAGTGACTGAGCTCCTGAGGCTTTTCTCTCCTCCCCAACAAACAAGGTATCTATGCCATTTATGTAGCACAAACATTTCAGAGTGAAGACGTCTTTGGTACTCAAACACATGCCAATGTCGTACACTTGACACGTCCGCCATTGGCCAATGTTTAAGCGTCAATGTTGTGTCTAGTATCTGTATGTGTCAACCACTTTTATTTTCTTAAATTACTACCAGTGTCGTGTCATGTCTGGTCTGGTGCATGTGTATGTGTAAGAGGTAGTGGTTCATGTTGTTGGAACCAACTGCCAGGGCAATATGCATTCCTCACTAATCGTCAACTTATGCGTTTATAAATCGTTGAGTGAATCATACTCCAATTTATTAATATGCAGTGTTTTAAGCAGTAATGTTTACTCCCCAGTTTCAAGTATTGATGATGTTCTAATCATCATAAAGGATGATTATGACAGCGCTTATTTTGTCACAGGTAGCTTGTTTTTCTTTCTTTCAATTTCCCTCTTATCAAATATTTTTTCATGACATTGCTCTTACTTGCTAATTTAGCATCTTTTTGCTATTTGTTTTTAATTCAACCTCATTTCCATTTCTGGCATGTAATCTAAAATTGTCTTACTTTGTTTGAGATTTAGGGAACTTCACTTCTTCAATTTACGCAGAAAATTGCATCTTTGAAGATCCAACTATTAAATTTAGTGGTAAGAATCATGACTTTTACCTATAATAACTTATGCTAGTCTTTCTCTCGCAATTTTTTAATTGATCTTCTTCATCATCAACTTAATTGATCAATAGCTAAAAGTTACACATTGCTCTTGTTCTCCCTAGATGTTTCAAATCTTTAAAACAACTGTAAGAGCTAAAAGGAGAAAAAAAAAGTGCTATCAGTTTGAAAATGTGTCAATTAGCTGAACTGAATCTATGATGAATGATCATACAGGTAGGGACTTATATGCGCGCAACTTGAAATTACTCGTTCCCTTCTTCGACTGTGCCTCAATTAGACTACTAAAGATCGAAAAGGTGGATATTCTTCGTAAATTAACATCCTGAACTACACTTTTTTGCTTCAAAGAAACAGCGCCGTGCTTCACTCATTATATAAATTAATAATGCAGGATGTTGAATCTGGCACAAATTTTCTGCGTGCATCTTGGAAATTAAGGTGCTTACCTTGCTCATTAAGCATGTTAATATGTAACATCTGAGTTAATTTTTTGAAACGCTTTATTATCCCTCAATCTCAGGACCAACTTAAAACTTCCTTGGAGGCCTCTGATTGCTATTGATGGAAGCACTTCTTATGAATTGAATGAAGATTTCAAAGTCAGAATCAATTTTGCCTTAAAATTTTCCACTCATAATGTGATTTGAAATCCATGTTAACTAGTGGTTGCTACATTTTTGTTTGACAGATCGTTCGGCATATTGAGAGTTGGAATGTTTCTGCACTTGAAGCAGTTTTGCAGATTTTCAAGTTTGAAAAACCAGGTGGTTGA

Protein sequence

>MS.gene69926.t1

MAKTCCFNGKSPTIALHFHSQLRKQHCSKSYTPCSRKTCAIYNMVKERNETPQVLKIAVSGVTELLRLFSPPQQTSVLSSNVYSPVSSIDDVLIIIKDDYDSAYFVTGNFTSSIYAENCIFEDPTIKFSGRDLYARNLKLLVPFFDCASIRLLKIEKDVESGTNFLRASWKLRTNLKLPWRPLIAIDGSTSYELNEDFKIVRHIESWNVSALEAVLQIFKFEKPGG