AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene035503

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene035503.t1 MTR_2g012700 32.979 94 62 1 25 117 12 105 3.56e-12 59.7
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 35 sgRNAs with CRISPR-Local

Find 46 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ATTACTTACCCGAAAATTTC+TGG 0.121099 1.4:+38564162 None:intergenic
TCTTTATCGTTGGGAAATTA+AGG 0.270333 1.4:-38564206 MS.gene035503:CDS
ATCTCCAGTATCTTCCTAAA+AGG 0.283887 1.4:-38564029 MS.gene035503:intron
TTGCGCAGAACAACGTTCAT+TGG 0.370169 1.4:-38564261 MS.gene035503:CDS
TATGTTTGCCCCATTAAAAC+TGG 0.383833 1.4:-38563937 MS.gene035503:CDS
TCAATCACACAGGGTGTTGC+CGG 0.416330 1.4:+38563782 None:intergenic
AGCAAGCTGTTCTTTATCGT+TGG 0.432504 1.4:-38564216 MS.gene035503:CDS
TGTTCGTGACAACGAGTTGA+AGG 0.462873 1.4:-38563866 MS.gene035503:CDS
GCAAGCTGTTCTTTATCGTT+GGG 0.471256 1.4:-38564215 MS.gene035503:CDS
ACGAGTTGAAGGTCAATGAT+AGG 0.471795 1.4:-38563855 MS.gene035503:CDS
AGGATAATCACACGTTGATC+CGG 0.481188 1.4:+38563985 None:intergenic
TCGTGGAGGTTAAAATTCTC+CGG 0.489434 1.4:-38563801 MS.gene035503:CDS
GAGGATAAGTATATCTATGA+AGG 0.529571 1.4:-38563901 MS.gene035503:CDS
ATACTTATCCTCAACACCTC+TGG 0.529619 1.4:+38563912 None:intergenic
TGTGAGGGAGGTGATGCATC+CGG 0.535867 1.4:-38564004 MS.gene035503:CDS
AACTGGTACCAGAGGTGTTG+AGG 0.541872 1.4:-38563920 MS.gene035503:CDS
GGTCACAGAGAGCGTTGCTA+TGG 0.546123 1.4:-38564185 MS.gene035503:CDS
ATCTTCCTAAAAGGTATGTG+AGG 0.553150 1.4:-38564020 MS.gene035503:CDS
ATAAGTATATCTATGAAGGC+TGG 0.555742 1.4:-38563897 MS.gene035503:CDS
CATATTGAAATGCATGTATG+AGG 0.560024 1.4:-38563830 MS.gene035503:CDS
AAAGGTTTCAACGACATGGA+AGG 0.563193 1.4:-38564285 MS.gene035503:intron
CCATGGCAATTTCTTCGAGA+AGG 0.564688 1.4:-38564440 MS.gene035503:intron
CATGTATGAGGTTGAATTCG+TGG 0.565338 1.4:-38563818 MS.gene035503:CDS
AAGGTTTCAACGACATGGAA+GGG 0.580139 1.4:-38564284 MS.gene035503:CDS
TAAACATACTTCAATCACAC+AGG 0.592278 1.4:+38563772 None:intergenic
GTGATTATCCTCTATGATGT+TGG 0.597229 1.4:-38563973 MS.gene035503:CDS
TCCTAAAAGGTATGTGAGGG+AGG 0.598055 1.4:-38564016 MS.gene035503:CDS
CCCATTAAAACTGGTACCAG+AGG 0.609643 1.4:-38563928 MS.gene035503:CDS
TCGTAAAGGTTTCAACGACA+TGG 0.617077 1.4:-38564289 MS.gene035503:intron
TCTTCCTAAAAGGTATGTGA+GGG 0.625158 1.4:-38564019 MS.gene035503:CDS
CCTTCTCGAAGAAATTGCCA+TGG 0.641633 1.4:+38564440 None:intergenic
TGTCTTGACCAACATCATAG+AGG 0.651392 1.4:+38563965 None:intergenic
TTGGATTGACGAAGATACTG+AGG 0.654652 1.4:-38564242 MS.gene035503:CDS
AAACATACTTCAATCACACA+GGG 0.675982 1.4:+38563773 None:intergenic
GTATGAGGTTGAATTCGTGG+AGG 0.713812 1.4:-38563815 MS.gene035503:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
ATAAGTATATCTATGAAGGC+TGG - chr1.4:38564327-38564346 MS.gene035503:intron 30.0%
ATTACTTACCCGAAAATTTC+TGG + chr1.4:38564065-38564084 None:intergenic 30.0%
CATATTGAAATGCATGTATG+AGG - chr1.4:38564394-38564413 MS.gene035503:intron 30.0%
GAGGATAAGTATATCTATGA+AGG - chr1.4:38564323-38564342 MS.gene035503:intron 30.0%
TCTTTATCGTTGGGAAATTA+AGG - chr1.4:38564018-38564037 MS.gene035503:CDS 30.0%
TTTACGACACATTTAGACAA+AGG + chr1.4:38563922-38563941 None:intergenic 30.0%
TTTGTCTAAATGTGTCGTAA+AGG - chr1.4:38563921-38563940 MS.gene035503:CDS 30.0%
!! TTATCTGGCTTATTCTGTTT+TGG - chr1.4:38563817-38563836 MS.gene035503:CDS 30.0%
!!! GAAGGTATTCTGTTTTTATC+TGG - chr1.4:38563802-38563821 MS.gene035503:CDS 30.0%
ATCTCCAGTATCTTCCTAAA+AGG - chr1.4:38564195-38564214 MS.gene035503:CDS 35.0%
GAATGATATCACTTTGACTG+AGG - chr1.4:38564112-38564131 MS.gene035503:intron 35.0%
GTGATTATCCTCTATGATGT+TGG - chr1.4:38564251-38564270 MS.gene035503:CDS 35.0%
TATGTTTGCCCCATTAAAAC+TGG - chr1.4:38564287-38564306 MS.gene035503:intron 35.0%
! ATCTTCCTAAAAGGTATGTG+AGG - chr1.4:38564204-38564223 MS.gene035503:CDS 35.0%
! TCTTCCTAAAAGGTATGTGA+GGG - chr1.4:38564205-38564224 MS.gene035503:CDS 35.0%
! TTGCTATGGCCAGAAATTTT+CGG - chr1.4:38564053-38564072 MS.gene035503:intron 35.0%
!! CATACCTTTTAGGAAGATAC+TGG + chr1.4:38564202-38564221 None:intergenic 35.0%
!!! TGGCTTATTCTGTTTTGGTA+TGG - chr1.4:38563822-38563841 MS.gene035503:CDS 35.0%
AAAGGTTTCAACGACATGGA+AGG - chr1.4:38563939-38563958 MS.gene035503:CDS 40.0%
AAGGTTTCAACGACATGGAA+GGG - chr1.4:38563940-38563959 MS.gene035503:CDS 40.0%
AGCAAGCTGTTCTTTATCGT+TGG - chr1.4:38564008-38564027 MS.gene035503:CDS 40.0%
AGGATAATCACACGTTGATC+CGG + chr1.4:38564242-38564261 None:intergenic 40.0%
ATACTTATCCTCAACACCTC+TGG + chr1.4:38564315-38564334 None:intergenic 40.0%
CATGTATGAGGTTGAATTCG+TGG - chr1.4:38564406-38564425 MS.gene035503:intron 40.0%
GCAAGCTGTTCTTTATCGTT+GGG - chr1.4:38564009-38564028 MS.gene035503:CDS 40.0%
TCGTAAAGGTTTCAACGACA+TGG - chr1.4:38563935-38563954 MS.gene035503:CDS 40.0%
TCGTGGAGGTTAAAATTCTC+CGG - chr1.4:38564423-38564442 MS.gene035503:intron 40.0%
TGTCTTGACCAACATCATAG+AGG + chr1.4:38564262-38564281 None:intergenic 40.0%
TTGGATTGACGAAGATACTG+AGG - chr1.4:38563982-38564001 MS.gene035503:CDS 40.0%
! ACGAGTTGAAGGTCAATGAT+AGG - chr1.4:38564369-38564388 MS.gene035503:intron 40.0%
! CACTTTGACTGAGGTTCTTT+TGG - chr1.4:38564121-38564140 MS.gene035503:intron 40.0%
! TGCTATGGCCAGAAATTTTC+GGG - chr1.4:38564054-38564073 MS.gene035503:intron 40.0%
!! ACCTCTGGTACCAGTTTTAA+TGG + chr1.4:38564300-38564319 None:intergenic 40.0%
!! CCTCTGGTACCAGTTTTAAT+GGG + chr1.4:38564299-38564318 None:intergenic 40.0%
!! CTCTGGTACCAGTTTTAATG+GGG + chr1.4:38564298-38564317 None:intergenic 40.0%
CCCATTAAAACTGGTACCAG+AGG - chr1.4:38564296-38564315 MS.gene035503:intron 45.0%
GTATGAGGTTGAATTCGTGG+AGG - chr1.4:38564409-38564428 MS.gene035503:intron 45.0%
TTGCGCAGAACAACGTTCAT+TGG - chr1.4:38563963-38563982 MS.gene035503:CDS 45.0%
! ACCTCCCTCACATACCTTTT+AGG + chr1.4:38564212-38564231 None:intergenic 45.0%
! TCCTAAAAGGTATGTGAGGG+AGG - chr1.4:38564208-38564227 MS.gene035503:CDS 45.0%
! TGTTCGTGACAACGAGTTGA+AGG - chr1.4:38564358-38564377 MS.gene035503:intron 45.0%
!! ATAAAAAAAACTTAAATTTA+AGG + chr1.4:38564177-38564196 None:intergenic 5.0%
!! TAAAAAAAACTTAAATTTAA+GGG + chr1.4:38564176-38564195 None:intergenic 5.0%
!! AACTGGTACCAGAGGTGTTG+AGG - chr1.4:38564304-38564323 MS.gene035503:intron 50.0%
TGTGAGGGAGGTGATGCATC+CGG - chr1.4:38564220-38564239 MS.gene035503:CDS 55.0%
!! GGTCACAGAGAGCGTTGCTA+TGG - chr1.4:38564039-38564058 MS.gene035503:intron 55.0%


Chromosome Type Strat End Strand Name
chr1.4 gene 38563786 38564460 38563786 ID=MS.gene035503
chr1.4 mRNA 38563786 38564460 38563786 ID=MS.gene035503.t1;Parent=MS.gene035503
chr1.4 exon 38564441 38564460 38564441 ID=MS.gene035503.t1.exon1;Parent=MS.gene035503.t1
chr1.4 CDS 38564441 38564460 38564441 ID=cds.MS.gene035503.t1;Parent=MS.gene035503.t1
chr1.4 exon 38564171 38564303 38564171 ID=MS.gene035503.t1.exon2;Parent=MS.gene035503.t1
chr1.4 CDS 38564171 38564303 38564171 ID=cds.MS.gene035503.t1;Parent=MS.gene035503.t1
chr1.4 exon 38563786 38564043 38563786 ID=MS.gene035503.t1.exon3;Parent=MS.gene035503.t1
chr1.4 CDS 38563786 38564043 38563786 ID=cds.MS.gene035503.t1;Parent=MS.gene035503.t1
Gene Sequence

>MS.gene035503

ATGGCAATTTCTTCGAGAAGGTATTCTGTTTTTATCTGGCTTATTCTGTTTTGGTATGGTAATGTTTAGTTTTCTATCGTCTACTTTCATTAAGAATATTCAATAATCAGATATAAAATGTTTGTATTTTTCTCCTTTGTCTAAATGTGTCGTAAAGGTTTCAACGACATGGAAGGGTTGCGCAGAACAACGTTCATTGGATTGACGAAGATACTGAGGATGAGCAAGCTGTTCTTTATCGTTGGGAAATTAAGGTCACAGAGAGCGTTGCTATGGCCAGAAATTTTCGGGTAAGTAATAGTTGAAAGTATCATGTTTTGATACATGAATGATATCACTTTGACTGAGGTTCTTTTGGTTTTGTTTTGATGTACTCTTTGATTGTTGCCCTTAAATTTAAGTTTTTTTTATCTCCAGTATCTTCCTAAAAGGTATGTGAGGGAGGTGATGCATCCGGATCAACGTGTGATTATCCTCTATGATGTTGGTCAAGACAATACATATGTTTGCCCCATTAAAACTGGTACCAGAGGTGTTGAGGATAAGTATATCTATGAAGGCTGGCGTAAATTTGTTCGTGACAACGAGTTGAAGGTCAATGATAGGCTCATATTGAAATGCATGTATGAGGTTGAATTCGTGGAGGTTAAAATTCTCCGGCAACACCCTGTGTGA
Protein sequence

>MS.gene035503.t1

MAISSRRFQRHGRVAQNNVHWIDEDTEDEQAVLYRWEIKVTESVAMARNFRYLPKRYVREVMHPDQRVIILYDVGQDNTYVCPIKTGTRGVEDKYIYEGWRKFVRDNELKVNDRLILKCMYEVEFVEVKILRQHPV