AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene003848

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene003848.t1 MTR_4g068310 89.899 198 20 0 1 198 1 198 2.15e-128 359
MS.gene003848.t1 MTR_4g068300 57.789 199 63 6 1 180 1 197 4.22e-62 194
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene003848.t1 AT5G18090 28.671 143 97 4 4 144 11 150 9.87e-13 65.9
MS.gene003848.t1 AT5G18000 31.132 106 72 1 4 108 13 118 2.11e-12 64.7
MS.gene003848.t1 AT3G17010 28.402 169 108 5 4 164 14 177 1.92e-11 62.0

Find 41 sgRNAs with CRISPR-Local

Find 71 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CTCTTTCTCTTGGCCACAAT+TGG 0.131130 4.2:+38298058 None:intergenic
ATGTTCAAGGTGGAAATTTA+TGG 0.176554 4.2:-38298136 MS.gene003848:CDS
ACCGAAGATTGTTATGGATT+TGG 0.260147 4.2:-38298341 MS.gene003848:CDS
GAAGAAAGCATCAATTATTC+TGG 0.262336 4.2:-38298305 MS.gene003848:CDS
TGGATTTGGGTGAAGAGTTT+TGG 0.266007 4.2:-38298327 MS.gene003848:CDS
TTCTTTGATGATAGCGAAAA+AGG 0.271206 4.2:+38298868 None:intergenic
CCGAAGATTGTTATGGATTT+GGG 0.289825 4.2:-38298340 MS.gene003848:CDS
AGTGGGACTTGAAGAGTTCT+TGG 0.304248 4.2:-38298182 MS.gene003848:CDS
TTTCCAACGCATACTCTCTT+TGG 0.308501 4.2:+38297938 None:intergenic
CCCTTCTTTGTCACAATTGT+TGG 0.332631 4.2:+38297896 None:intergenic
TCTTTCTCTTGGCCACAATT+GGG 0.346000 4.2:+38298059 None:intergenic
GTGGAAATTTATGGTAAGAA+TGG 0.371009 4.2:-38298127 MS.gene003848:CDS
TTTGTCTTAGCCACAATTGT+TGG 0.398096 4.2:+38297980 None:intergenic
TGGTCTACCCCTCTTTCTCT+TGG 0.402146 4.2:+38298048 None:intergenic
AGTACCACCGAAGATTGTTA+TGG 0.409721 4.2:-38298347 MS.gene003848:CDS
TGGAAATTTATGGTAAGAAT+GGG 0.420098 4.2:-38298126 MS.gene003848:CDS
CTTTCTCTTGGCCACAATTG+GGG 0.448018 4.2:+38298060 None:intergenic
CCCAAATCCATAACAATCTT+CGG 0.452160 4.2:+38298340 None:intergenic
GACATTTATCTGCGAAACAT+TGG 0.475455 4.2:-38298232 MS.gene003848:CDS
ACCAACAATTGTGACAAAGA+AGG 0.484661 4.2:-38297897 MS.gene003848:CDS
TCTACTAAAATAACAGAAAG+AGG 0.490912 4.2:+38297851 None:intergenic
CAATTGTGGCCAAGAGAAAG+AGG 0.520539 4.2:-38298057 MS.gene003848:CDS
CCAACAATTGTGACAAAGAA+GGG 0.536191 4.2:-38297896 MS.gene003848:CDS
TATTGGAGATAACATGTTCA+AGG 0.538893 4.2:-38298149 MS.gene003848:CDS
AAAATAACAGAAAGAGGAGC+AGG 0.548640 4.2:+38297857 None:intergenic
TTTATCTGCGAAACATTGGT+TGG 0.556011 4.2:-38298228 MS.gene003848:CDS
AGTTGTTGCAGCCCCAATTG+TGG 0.571592 4.2:-38298071 MS.gene003848:CDS
AATTGTGGCTAAGACAAAGA+TGG 0.585870 4.2:-38297975 MS.gene003848:CDS
AGAAGCTGCACCAACAATTG+TGG 0.589864 4.2:-38297990 MS.gene003848:CDS
CAAATGAATTACCATGCACT+TGG 0.596053 4.2:+38298835 None:intergenic
TATGCTCTTCGAGTGAGAAG+TGG 0.604662 4.2:-38298282 MS.gene003848:CDS
AGGCTTCAACACCAAGTGCA+TGG 0.605306 4.2:-38298846 MS.gene003848:intron
ATGCTCTTCGAGTGAGAAGT+GGG 0.605893 4.2:-38298281 MS.gene003848:CDS
TTTCTGAAAGACAACTCAGT+GGG 0.610997 4.2:-38298199 MS.gene003848:CDS
AATCCAAAGAGAGTATGCGT+TGG 0.611249 4.2:-38297941 MS.gene003848:CDS
AATTGTGGCCAAGAGAAAGA+GGG 0.618437 4.2:-38298056 MS.gene003848:CDS
TGGAGATAACATGTTCAAGG+TGG 0.674338 4.2:-38298146 MS.gene003848:CDS
CGTTGGAAAACAAAACGCAG+AGG 0.680803 4.2:-38297924 MS.gene003848:CDS
ATTGTGGCCAAGAGAAAGAG+GGG 0.688040 4.2:-38298055 MS.gene003848:CDS
AAATCCATAACAATCTTCGG+TGG 0.712870 4.2:+38298343 None:intergenic
GTTTCTGAAAGACAACTCAG+TGG 0.730659 4.2:-38298200 MS.gene003848:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TTATGACAAAATAAAAAACA+TGG + chr4.2:38298367-38298386 None:intergenic 15.0%
!!! CAATAATATGTTTACTTTTT+TGG - chr4.2:38298214-38298233 MS.gene003848:CDS 15.0%
!! ATTATACATATATATGAACC+CGG - chr4.2:38298132-38298151 MS.gene003848:CDS 20.0%
!! TAGAAAAATGTTATTAAGCT+AGG - chr4.2:38298054-38298073 MS.gene003848:CDS 20.0%
!! TATATATGTATAATCTCTGT+TGG + chr4.2:38298126-38298145 None:intergenic 20.0%
!!! GAAGTTAAAATTTTGAAGAA+AGG - chr4.2:38298484-38298503 MS.gene003848:intron 20.0%
! ATATTATTGAGCTTGATATC+TGG + chr4.2:38298203-38298222 None:intergenic 25.0%
! TCTACTAAAATAACAGAAAG+AGG + chr4.2:38298895-38298914 None:intergenic 25.0%
! TGGAAATTTATGGTAAGAAT+GGG - chr4.2:38298617-38298636 MS.gene003848:intron 25.0%
!!! TACTGAATGAGTTTTAAACT+TGG + chr4.2:38298091-38298110 None:intergenic 25.0%
!!! TTCTTGGTTTTCACATATAT+TGG - chr4.2:38298577-38298596 MS.gene003848:intron 25.0%
ATGTTCAAGGTGGAAATTTA+TGG - chr4.2:38298607-38298626 MS.gene003848:intron 30.0%
GTGGAAATTTATGGTAAGAA+TGG - chr4.2:38298616-38298635 MS.gene003848:intron 30.0%
TATTGGAGATAACATGTTCA+AGG - chr4.2:38298594-38298613 MS.gene003848:intron 30.0%
! TTCTTTGATGATAGCGAAAA+AGG + chr4.2:38297878-38297897 None:intergenic 30.0%
! TTTTTCGCTATCATCAAAGA+AGG - chr4.2:38297877-38297896 MS.gene003848:CDS 30.0%
!! GAAGAAAGCATCAATTATTC+TGG - chr4.2:38298438-38298457 MS.gene003848:intron 30.0%
AAAAAATCCTGCTGATGTCA+AGG - chr4.2:38298720-38298739 MS.gene003848:intron 35.0%
AAAATAACAGAAAGAGGAGC+AGG + chr4.2:38298889-38298908 None:intergenic 35.0%
AAATCCATAACAATCTTCGG+TGG + chr4.2:38298403-38298422 None:intergenic 35.0%
AATTGTGGCTAAGACAAAGA+TGG - chr4.2:38298768-38298787 MS.gene003848:intron 35.0%
ACCAACAATTGTGACAAAGA+AGG - chr4.2:38298846-38298865 MS.gene003848:intron 35.0%
ACCGAAGATTGTTATGGATT+TGG - chr4.2:38298402-38298421 MS.gene003848:intron 35.0%
CAAATGAATTACCATGCACT+TGG + chr4.2:38297911-38297930 None:intergenic 35.0%
CCAACAATTGTGACAAAGAA+GGG - chr4.2:38298847-38298866 MS.gene003848:CDS 35.0%
CCCAAATCCATAACAATCTT+CGG + chr4.2:38298406-38298425 None:intergenic 35.0%
CCGAAGATTGTTATGGATTT+GGG - chr4.2:38298403-38298422 MS.gene003848:intron 35.0%
GACATTTATCTGCGAAACAT+TGG - chr4.2:38298511-38298530 MS.gene003848:intron 35.0%
GAGAAATACCTGTCTTTCTT+TGG - chr4.2:38297984-38298003 MS.gene003848:CDS 35.0%
TTTATCTGCGAAACATTGGT+TGG - chr4.2:38298515-38298534 MS.gene003848:intron 35.0%
TTTGTCTTAGCCACAATTGT+TGG + chr4.2:38298766-38298785 None:intergenic 35.0%
! TTGATGATAGCGAAAAAGGA+TGG + chr4.2:38297874-38297893 None:intergenic 35.0%
! TTTCTGAAAGACAACTCAGT+GGG - chr4.2:38298544-38298563 MS.gene003848:intron 35.0%
!!! ACATCAGCAGGATTTTTTCT+TGG + chr4.2:38298718-38298737 None:intergenic 35.0%
!!! TCTTGCTTTTTCTTGAAGCA+TGG + chr4.2:38298652-38298671 None:intergenic 35.0%
AATTGTGGCCAAGAGAAAGA+GGG - chr4.2:38298687-38298706 MS.gene003848:intron 40.0%
AGTACCACCGAAGATTGTTA+TGG - chr4.2:38298396-38298415 MS.gene003848:intron 40.0%
ATCAGCATCCAAAGAAAGAC+AGG + chr4.2:38297995-38298014 None:intergenic 40.0%
CCCTTCTTTGTCACAATTGT+TGG + chr4.2:38298850-38298869 None:intergenic 40.0%
TCTTTCTCTTGGCCACAATT+GGG + chr4.2:38298687-38298706 None:intergenic 40.0%
TGGAGATAACATGTTCAAGG+TGG - chr4.2:38298597-38298616 MS.gene003848:intron 40.0%
TTTCCAACGCATACTCTCTT+TGG + chr4.2:38298808-38298827 None:intergenic 40.0%
! AATCCAAAGAGAGTATGCGT+TGG - chr4.2:38298802-38298821 MS.gene003848:intron 40.0%
! GTTTCTGAAAGACAACTCAG+TGG - chr4.2:38298543-38298562 MS.gene003848:intron 40.0%
! TAATCTCTGTTGGTGAGCTA+AGG + chr4.2:38298116-38298135 None:intergenic 40.0%
! TGGATTTGGGTGAAGAGTTT+TGG - chr4.2:38298416-38298435 MS.gene003848:intron 40.0%
! TTTTCTTCCTTGACATCAGC+AGG + chr4.2:38298730-38298749 None:intergenic 40.0%
AGAAGCTGCACCAACAATTG+TGG - chr4.2:38298753-38298772 MS.gene003848:intron 45.0%
AGTGGGACTTGAAGAGTTCT+TGG - chr4.2:38298561-38298580 MS.gene003848:intron 45.0%
ATATGAACCCGGATTCCCTA+CGG - chr4.2:38298143-38298162 MS.gene003848:CDS 45.0%
ATGCTCTTCGAGTGAGAAGT+GGG - chr4.2:38298462-38298481 MS.gene003848:intron 45.0%
ATTGTGGCCAAGAGAAAGAG+GGG - chr4.2:38298688-38298707 MS.gene003848:intron 45.0%
CAATTGTGGCCAAGAGAAAG+AGG - chr4.2:38298686-38298705 MS.gene003848:intron 45.0%
CGTTGGAAAACAAAACGCAG+AGG - chr4.2:38298819-38298838 MS.gene003848:intron 45.0%
CTCTTTCTCTTGGCCACAAT+TGG + chr4.2:38298688-38298707 None:intergenic 45.0%
CTTTCTCTTGGCCACAATTG+GGG + chr4.2:38298686-38298705 None:intergenic 45.0%
GATCATCCAATCGAGATGGA+CGG + chr4.2:38298241-38298260 None:intergenic 45.0%
GCTTGCATTGAATGACCGTA+GGG + chr4.2:38298161-38298180 None:intergenic 45.0%
GTCATTCAATGCAAGCAGAC+AGG - chr4.2:38298165-38298184 MS.gene003848:CDS 45.0%
TATGCTCTTCGAGTGAGAAG+TGG - chr4.2:38298461-38298480 MS.gene003848:intron 45.0%
TCGTGATCATCCAATCGAGA+TGG + chr4.2:38298245-38298264 None:intergenic 45.0%
TGCTTGCATTGAATGACCGT+AGG + chr4.2:38298162-38298181 None:intergenic 45.0%
TTGAATGACCGTAGGGAATC+CGG + chr4.2:38298154-38298173 None:intergenic 45.0%
AGGCTTCAACACCAAGTGCA+TGG - chr4.2:38297897-38297916 MS.gene003848:CDS 50.0%
AGTTGTTGCAGCCCCAATTG+TGG - chr4.2:38298672-38298691 MS.gene003848:intron 50.0%
GTGAATGCTTGCAGTCTGCA+GGG - chr4.2:38298280-38298299 MS.gene003848:CDS 50.0%
TGAATGACCGTAGGGAATCC+GGG + chr4.2:38298153-38298172 None:intergenic 50.0%
TGGTCTACCCCTCTTTCTCT+TGG + chr4.2:38298698-38298717 None:intergenic 50.0%
TTTGGACCGTCCATCTCGAT+TGG - chr4.2:38298232-38298251 MS.gene003848:CDS 50.0%
CAGTCTGCAGGGAATTCGAC+TGG - chr4.2:38298291-38298310 MS.gene003848:CDS 55.0%
CGTGAATGCTTGCAGTCTGC+AGG - chr4.2:38298279-38298298 MS.gene003848:CDS 55.0%


Chromosome Type Strat End Strand Name
chr4.2 gene 38297847 38298918 38297847 ID=MS.gene003848
chr4.2 mRNA 38297847 38298918 38297847 ID=MS.gene003848.t1;Parent=MS.gene003848
chr4.2 exon 38298847 38298918 38298847 ID=MS.gene003848.t1.exon1;Parent=MS.gene003848.t1
chr4.2 CDS 38298847 38298918 38298847 ID=cds.MS.gene003848.t1;Parent=MS.gene003848.t1
chr4.2 exon 38297847 38298371 38297847 ID=MS.gene003848.t1.exon2;Parent=MS.gene003848.t1
chr4.2 CDS 38297847 38298371 38297847 ID=cds.MS.gene003848.t1;Parent=MS.gene003848.t1
Gene Sequence

>MS.gene003848

ATGGATCATGAGCAGCAAGACAAGCCATCCTTTTTCGCTATCATCAAAGAAGGCTTCAACACCAAGTGCATGGTAATTCATTTGTACTTTTGTTCTTCATCATCTAATGCATGCTAAAATTTGTAATCTTTGTTAATGAGAAATACCTGTCTTTCTTTGGATGCTGATGAGAAAGTTATAGATATGAAGAATGAAAAAAAAAGTTCATAGAAAAATGTTATTAAGCTAGGTCGTTAGTTTTCCAAGTTTAAAACTCATTCAGTATTCCTTAGCTCACCAACAGAGATTATACATATATATGAACCCGGATTCCCTACGGTCATTCAATGCAAGCAGACAGGAGTTCAGACAATCCAGATATCAAGCTCAATAATATGTTTACTTTTTTGGACCGTCCATCTCGATTGGATGATCACGAATACATCTTGACTGCGTGAATGCTTGCAGTCTGCAGGGAATTCGACTGGTGCATATAACATACATATTTTTAAAAAAAATATTACTTCTTGAGAAGTTACCATGTTTTTTATTTTGTCATAATCTGCAGAAAGTACCACCGAAGATTGTTATGGATTTGGGTGAAGAGTTTTGGAAGAAAGCATCAATTATTCTGGTATGCTCTTCGAGTGAGAAGTGGGAAGTTAAAATTTTGAAGAAAGGAAATGACATTTATCTGCGAAACATTGGTTGGCAAAAGTTTCTGAAAGACAACTCAGTGGGACTTGAAGAGTTCTTGGTTTTCACATATATTGGAGATAACATGTTCAAGGTGGAAATTTATGGTAAGAATGGGTTAGAGAAACCATGCTTCAAGAAAAAGCAAGAAGTTGTTGCAGCCCCAATTGTGGCCAAGAGAAAGAGGGGTAGACCAAGAAAAAATCCTGCTGATGTCAAGGAAGAAAAAGAAGAAGCTGCACCAACAATTGTGGCTAAGACAAAGATGGTACAAAGAAAAAATCCAAAGAGAGTATGCGTTGGAAAACAAAACGCAGAGGTTTCACCAACAATTGTGACAAAGAAGGGTATATCAAGAAAATGTCCTGCTCCTCTTTCTGTTATTTTAGTAGACTGA
Protein sequence

>MS.gene003848.t1

MDHEQQDKPSFFAIIKEGFNTKCMKVPPKIVMDLGEEFWKKASIILVCSSSEKWEVKILKKGNDIYLRNIGWQKFLKDNSVGLEEFLVFTYIGDNMFKVEIYGKNGLEKPCFKKKQEVVAAPIVAKRKRGRPRKNPADVKEEKEEAAPTIVAKTKMVQRKNPKRVCVGKQNAEVSPTIVTKKGISRKCPAPLSVILVD