AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene040928

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene040928.t1 MTR_1g032880 94.611 167 7 1 1 167 1 165 1.93e-114 321
MS.gene040928.t1 MTR_8g105930 40.816 196 70 2 16 165 46 241 1.42e-41 139
MS.gene040928.t1 MTR_8g097310 31.788 151 73 4 27 159 13 151 1.90e-13 64.7
MS.gene040928.t1 MTR_2g055210 40.230 87 46 2 27 113 147 227 1.49e-12 64.7
MS.gene040928.t1 MTR_4g094680 38.202 89 52 2 26 112 66 153 4.92e-12 62.4
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene040928.t1 AT2G01818 43.956 91 48 2 25 113 58 147 8.63e-17 74.7
MS.gene040928.t1 AT2G01818 41.975 81 44 2 35 113 4 83 3.72e-12 61.2
MS.gene040928.t1 AT3G60670 40.909 88 47 2 26 113 51 133 4.39e-12 62.4
MS.gene040928.t1 AT4G17900 31.206 141 82 4 27 162 80 210 2.05e-11 60.5
MS.gene040928.t1 AT2G12646 40.230 87 47 2 26 112 47 128 2.58e-11 60.5
MS.gene040928.t1 AT2G12646 40.230 87 47 2 26 112 50 131 2.83e-11 60.5
MS.gene040928.t1 AT2G12646 40.230 87 47 2 26 112 50 131 2.83e-11 60.5
MS.gene040928.t1 AT4G17900 31.429 140 81 4 27 161 66 195 2.90e-11 59.7
MS.gene040928.t1 AT1G31040 35.632 87 50 2 26 112 63 143 5.42e-11 59.7

Find 21 sgRNAs with CRISPR-Local

Find 69 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ATGACTCAGCCTCTGAATTT+TGG 0.202823 1.2:-17428696 None:intergenic
AAACTAGAGATAGATCTTAT+AGG 0.311632 1.2:-17428790 None:intergenic
TACCAAATGGAAAAGAAGAT+TGG 0.357613 1.2:+17427210 MS.gene040928:CDS
TGTTGTTACCTTGCATTTGA+TGG 0.360512 1.2:-17428312 None:intergenic
TGTCTTTGCTACTGCTAGTC+GGG 0.379634 1.2:-17428210 None:intergenic
ACCCTTTCAATAGATTCATT+TGG 0.386727 1.2:-17428736 None:intergenic
TAGATCACAATTGAGGAGCT+TGG 0.458055 1.2:+17428655 MS.gene040928:intron
ATGTCTTTGCTACTGCTAGT+CGG 0.459833 1.2:-17428211 None:intergenic
GTGAAGCGTAGTTTACCAAA+TGG 0.503152 1.2:+17427197 MS.gene040928:CDS
ACCAAATGAATCTATTGAAA+GGG 0.508734 1.2:+17428735 MS.gene040928:CDS
AACCAAATGAATCTATTGAA+AGG 0.511364 1.2:+17428734 MS.gene040928:CDS
ATCTCATTCTCTTCATCGAA+AGG 0.512601 1.2:+17427349 MS.gene040928:CDS
GTATTGTTAGATCACAATTG+AGG 0.574373 1.2:+17428648 MS.gene040928:intron
AGCAATCAAAATACTTGAGT+AGG 0.578161 1.2:-17427418 None:intergenic
TGAATCTCAGAAAGCGTCCA+AGG 0.581640 1.2:+17428758 MS.gene040928:CDS
ACATCTCAAAAGCAAGCTGG+TGG 0.603751 1.2:+17428236 MS.gene040928:CDS
TCAACATCTCAAAAGCAAGC+TGG 0.604147 1.2:+17428233 MS.gene040928:CDS
GTCTTTGCTACTGCTAGTCG+GGG 0.609471 1.2:-17428209 None:intergenic
ATTCTGTTCCATCAAATGCA+AGG 0.622156 1.2:+17428304 MS.gene040928:CDS
AAATGATCACCAAAATTCAG+AGG 0.644619 1.2:+17428687 MS.gene040928:CDS
GGTGGAATCTGTGAAGAATG+TGG 0.716936 1.2:+17428254 MS.gene040928:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAAATTTATATATTCATCAA+TGG - chr1.2:17427805-17427824 None:intergenic 10.0%
!! TTCACATTAAATTAAAATAT+AGG - chr1.2:17428593-17428612 None:intergenic 10.0%
!!! GAATATATAAATTTTTTAAG+TGG + chr1.2:17427810-17427829 MS.gene040928:intron 10.0%
!!! TTTTTTTTTCAAATTATTAG+CGG - chr1.2:17427955-17427974 None:intergenic 10.0%
!! TCTATTTATATGAGAAAATT+GGG - chr1.2:17427581-17427600 None:intergenic 15.0%
!! TTCTATTTATATGAGAAAAT+TGG - chr1.2:17427582-17427601 None:intergenic 15.0%
!!! TAATTAACACTTTTTTGTTT+TGG - chr1.2:17428535-17428554 None:intergenic 15.0%
!!! TCAATATAAATAAATTTTGC+AGG - chr1.2:17428471-17428490 None:intergenic 15.0%
!!! TTTTCTCATATAAATAGAAC+CGG + chr1.2:17427583-17427602 MS.gene040928:intron 20.0%
! AAACTAGAGATAGATCTTAT+AGG - chr1.2:17428793-17428812 None:intergenic 25.0%
! AACCAAATGAATCTATTGAA+AGG + chr1.2:17428734-17428753 MS.gene040928:CDS 25.0%
! ACCAAATGAATCTATTGAAA+GGG + chr1.2:17428735-17428754 MS.gene040928:CDS 25.0%
! GTTTCTTAATTGTAATCTGA+TGG + chr1.2:17427721-17427740 MS.gene040928:intron 25.0%
!! AAATCCATATGTTACTTCTA+CGG - chr1.2:17428091-17428110 None:intergenic 25.0%
!! GAATTGATTCACTCAATAAA+TGG - chr1.2:17427700-17427719 None:intergenic 25.0%
!! TCTCATTAAACTTTTCTTTG+TGG - chr1.2:17427277-17427296 None:intergenic 25.0%
!!! TATTGATCTAATTTGCTCTT+AGG + chr1.2:17427674-17427693 MS.gene040928:intron 25.0%
!!! TTTTGATTGCTCATATATTC+AGG + chr1.2:17427430-17427449 MS.gene040928:CDS 25.0%
AAATGATCACCAAAATTCAG+AGG + chr1.2:17428687-17428706 MS.gene040928:CDS 30.0%
ACCCTTTCAATAGATTCATT+TGG - chr1.2:17428739-17428758 None:intergenic 30.0%
AGCAATCAAAATACTTGAGT+AGG - chr1.2:17427421-17427440 None:intergenic 30.0%
AGGACTACAACAAAACTATA+AGG + chr1.2:17428508-17428527 MS.gene040928:intron 30.0%
ATGAAATCAATTACTACCTC+CGG - chr1.2:17427605-17427624 None:intergenic 30.0%
CACGTTGTAAGTACAAATTT+AGG - chr1.2:17428136-17428155 None:intergenic 30.0%
GGATAGTTTATGCTACATTA+TGG + chr1.2:17427742-17427761 MS.gene040928:intron 30.0%
GTATTGTTAGATCACAATTG+AGG + chr1.2:17428648-17428667 MS.gene040928:intron 30.0%
TACCAAATGGAAAAGAAGAT+TGG + chr1.2:17427210-17427229 MS.gene040928:CDS 30.0%
! AATCCATATGTTACTTCTAC+GGG - chr1.2:17428090-17428109 None:intergenic 30.0%
! ATTGTGGAATCAGTTTTTGT+AGG + chr1.2:17427315-17427334 MS.gene040928:intron 30.0%
! CAGTTTTTGTAGGTATGATA+AGG + chr1.2:17427325-17427344 MS.gene040928:intron 30.0%
! TGAAACTGATTCAAAATGTG+AGG + chr1.2:17428488-17428507 MS.gene040928:intron 30.0%
! TTCAAATTATTAGCGGATAC+CGG - chr1.2:17427948-17427967 None:intergenic 30.0%
! TTGATGCACTTTTGATAGAT+AGG + chr1.2:17427234-17427253 MS.gene040928:CDS 30.0%
!! CTGAATTTTGGTGATCATTT+TGG - chr1.2:17428687-17428706 None:intergenic 30.0%
!! TGAGAAGAATGTGTTTTGTT+TGG + chr1.2:17427292-17427311 MS.gene040928:intron 30.0%
!!! AATGTGTTTTGTTTGGATTG+TGG + chr1.2:17427299-17427318 MS.gene040928:intron 30.0%
!!! GATGGTTTTAAACACAAACA+CGG + chr1.2:17427893-17427912 MS.gene040928:intron 30.0%
ACCATCAAGACTATGACTAA+TGG - chr1.2:17427879-17427898 None:intergenic 35.0%
ATCTCATTCTCTTCATCGAA+AGG + chr1.2:17427349-17427368 MS.gene040928:CDS 35.0%
ATTCTGTTCCATCAAATGCA+AGG + chr1.2:17428304-17428323 MS.gene040928:CDS 35.0%
GCACATACATTCCTTGAATT+AGG - chr1.2:17428055-17428074 None:intergenic 35.0%
TATATGTATCAGTGTCGTGT+CGG + chr1.2:17427994-17428013 MS.gene040928:intron 35.0%
TCTCATATAAATAGAACCGG+AGG + chr1.2:17427586-17427605 MS.gene040928:intron 35.0%
TGTTGTTACCTTGCATTTGA+TGG - chr1.2:17428315-17428334 None:intergenic 35.0%
! AGCCAATCTTCTTTTCCATT+TGG - chr1.2:17427215-17427234 None:intergenic 35.0%
! GCACTTTTGATAGATAGGTT+TGG + chr1.2:17427239-17427258 MS.gene040928:intron 35.0%
! TCCATTAGTCATAGTCTTGA+TGG + chr1.2:17427875-17427894 MS.gene040928:intron 35.0%
!! TGTTGACTTAACTTTCTCTG+AGG - chr1.2:17427505-17427524 None:intergenic 35.0%
ATGTCTTTGCTACTGCTAGT+CGG - chr1.2:17428214-17428233 None:intergenic 40.0%
CAACCCGTAGAAGTAACATA+TGG + chr1.2:17428084-17428103 MS.gene040928:intron 40.0%
GTGAAGCGTAGTTTACCAAA+TGG + chr1.2:17427197-17427216 MS.gene040928:CDS 40.0%
TAGATCACAATTGAGGAGCT+TGG + chr1.2:17428655-17428674 MS.gene040928:intron 40.0%
TCAACATCTCAAAAGCAAGC+TGG + chr1.2:17428233-17428252 MS.gene040928:CDS 40.0%
! ATGACTCAGCCTCTGAATTT+TGG - chr1.2:17428699-17428718 None:intergenic 40.0%
!!! CTTATAGGAGTGCTTTTCCT+TGG - chr1.2:17428778-17428797 None:intergenic 40.0%
ACATCTCAAAAGCAAGCTGG+TGG + chr1.2:17428236-17428255 MS.gene040928:CDS 45.0%
GGTGGAATCTGTGAAGAATG+TGG + chr1.2:17428254-17428273 MS.gene040928:CDS 45.0%
TGTCTTTGCTACTGCTAGTC+GGG - chr1.2:17428213-17428232 None:intergenic 45.0%
TTGTTTACTACTCCCTCTGC+TGG + chr1.2:17427478-17427497 MS.gene040928:intron 45.0%
!! TGAATCTCAGAAAGCGTCCA+AGG + chr1.2:17428758-17428777 MS.gene040928:CDS 45.0%
!! AATGATAAAAAATAATTATA+AGG - chr1.2:17428399-17428418 None:intergenic 5.0%
AATTAGGCGTGTCCCGATGT+CGG - chr1.2:17428039-17428058 None:intergenic 50.0%
ACACAACGCATGTCCGACAT+CGG + chr1.2:17428023-17428042 MS.gene040928:intron 50.0%
ATCGGGACACGCCTAATTCA+AGG + chr1.2:17428041-17428060 MS.gene040928:intron 50.0%
CAACAAGAACACTGACACGC+CGG + chr1.2:17427926-17427945 MS.gene040928:intron 50.0%
GTCTTTGCTACTGCTAGTCG+GGG - chr1.2:17428212-17428231 None:intergenic 50.0%
! TTTCTCTGAGGACCAGCAGA+GGG - chr1.2:17427493-17427512 None:intergenic 50.0%
CACAACGCATGTCCGACATC+GGG + chr1.2:17428024-17428043 MS.gene040928:intron 55.0%
! CTTTCTCTGAGGACCAGCAG+AGG - chr1.2:17427494-17427513 None:intergenic 55.0%


Chromosome Type Strat End Strand Name
chr1.2 gene 17427194 17428828 17427194 ID=MS.gene040928
chr1.2 mRNA 17427194 17428828 17427194 ID=MS.gene040928.t1;Parent=MS.gene040928
chr1.2 exon 17427194 17427255 17427194 ID=MS.gene040928.t1.exon1;Parent=MS.gene040928.t1
chr1.2 CDS 17427194 17427255 17427194 ID=cds.MS.gene040928.t1;Parent=MS.gene040928.t1
chr1.2 exon 17427337 17427451 17427337 ID=MS.gene040928.t1.exon2;Parent=MS.gene040928.t1
chr1.2 CDS 17427337 17427451 17427337 ID=cds.MS.gene040928.t1;Parent=MS.gene040928.t1
chr1.2 exon 17428170 17428325 17428170 ID=MS.gene040928.t1.exon3;Parent=MS.gene040928.t1
chr1.2 CDS 17428170 17428325 17428170 ID=cds.MS.gene040928.t1;Parent=MS.gene040928.t1
chr1.2 exon 17428658 17428828 17428658 ID=MS.gene040928.t1.exon4;Parent=MS.gene040928.t1
chr1.2 CDS 17428658 17428828 17428658 ID=cds.MS.gene040928.t1;Parent=MS.gene040928.t1
Gene Sequence

>MS.gene040928

ATGGTGAAGCGTAGTTTACCAAATGGAAAAGAAGATTGGCTTGATGCACTTTTGATAGATAGGTTTGGAAATTGCAAAAACCACAAAGAAAAGTTTAATGAGAAGAATGTGTTTTGTTTGGATTGTGGAATCAGTTTTTGTAGGTATGATAAGGAATCTCATTCTCTTCATCGAAAGGTTCAGATATACAGATATTGCTATGTAGATGTTGCAAAATATACTGACCTACTCAAGTATTTTGATTGCTCATATATTCAGGTTCTTTTCTCTCTACTTTGTCGTTATTGTTTACTACTCCCTCTGCTGGTCCTCAGAGAAAGTTAAGTCAACAAAAGTTGATCTAACTTGACTGAATTTTGAATAAGATACATCAATTTTTGTTGACCCAATTTTCTCATATAAATAGAACCGGAGGTAGTAATTGATTTCATTAATATTTTTTGAAATCAATTATGTGTCTTAATGAATTGCAATGTCATTTATTGATCTAATTTGCTCTTAGGCCATTTATTGAGTGAATCAATTCAGTTTCTTAATTGTAATCTGATGGATAGTTTATGCTACATTATGGTTGATTTATTTTGCTCGTATGATTGTGTGAATGATAACCATTGATGAATATATAAATTTTTTAAGTGGTTTAAATTGTTGAAATGAATTGTGCTGTTCTATTAACTATTCTCCATTAGTCATAGTCTTGATGGTTTTAAACACAAACACGGACATCAGACACAACAAGAACACTGACACGCCGGTATCCGCTAATAATTTGAAAAAAAAATCACATAATTCAATGTAACTATATGTATCAGTGTCGTGTCGGTGTCAAACACAACGCATGTCCGACATCGGGACACGCCTAATTCAAGGAATGTATGTGCTTCATAGATCAACCCGTAGAAGTAACATATGGATTTATTTGTCTGATTAAATACTTAACCTAAATTTGTACTTACAACGTGACATGATTTTGCAGACTTATATATCAAACAATGACAAGATTGTGCTTATCAAACCCCGACTAGCAGTAGCAAAGACATCAACATCTCAAAAGCAAGCTGGTGGAATCTGTGAAGAATGTGGCAAACAGTTACAAGATAAGCGTAACAGATTCTGTTCCATCAAATGCAAGGTAACAACAACATATATACTTTAGTATGTTTAAATATGTTTTTAGTACTTATAAATATTATACTTTCGATCCTTATAATTATTTTTTATCATTGCAAACTTAAAATTTTACGTTGTTTAGTTCTTATTATTTTGTTTTAGTTCCTGCAAAATTTATTTATATTGAAACTGATTCAAAATGTGAGGACTACAACAAAACTATAAGGACCAAAACAAAAAAGTGTTAATTAGCAGAGACTAAAAATTAAATGAAAACACATTTAAACCTATATTTTAATTTAATGTGAAATTTATTGTTTGCTTAATTTTGTGATTTAAATCGTGTATTGTTAGATCACAATTGAGGAGCTTGGAGTCAACCAAAATGATCACCAAAATTCAGAGGCTGAGTCATCTATCTCTACTGTTGAACCAAATGAATCTATTGAAAGGGTGAATCTCAGAAAGCGTCCAAGGAAAAGCACTCCTATAAGATCTATCTCTAGTTTTGTAAATGATTATTGA
Protein sequence

>MS.gene040928.t1

MVKRSLPNGKEDWLDALLIDRYDKESHSLHRKVQIYRYCYVDVAKYTDLLKYFDCSYIQTYISNNDKIVLIKPRLAVAKTSTSQKQAGGICEECGKQLQDKRNRFCSIKCKITIEELGVNQNDHQNSEAESSISTVEPNESIERVNLRKRPRKSTPIRSISSFVNDY