AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene99704


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene99704.t1 MTR_5g074560 91.781 146 11 1 1 145 1 146 7.51e-96 275
MS.gene99704.t1 MTR_5g074550 75.974 154 25 4 3 145 1 153 7.77e-77 227
MS.gene99704.t1 MTR_7g072270 34.074 135 80 4 20 146 32 165 4.78e-17 75.1
MS.gene99704.t1 MTR_7g072270 34.074 135 80 4 20 146 32 165 4.91e-17 73.9
MS.gene99704.t1 MTR_7g072170 33.088 136 81 5 20 146 33 167 2.14e-15 70.9
MS.gene99704.t1 MTR_7g072140 29.286 140 89 5 20 150 33 171 1.83e-12 62.8
MS.gene99704.t1 MTR_7g072250 34.167 120 64 5 36 146 83 196 3.87e-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.gene99704.t1 AT2G30270 42.069 145 78 3 3 145 1 141 3.47e-22 87.8

Find 38 sgRNAs with CRISPR-Local

Find 104 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ACATGGAACTCCGGCCTCTT+TGG 0.293965 5.2:+62410885 None:intergenic
GTTTGCGACTTAAAAGTTAT+TGG 0.298838 5.2:-62409736 MS.gene99704:CDS
GAGAAATGGTGATGAGAATA+AGG 0.306353 5.2:-62409848 MS.gene99704:CDS
ATTGGAATCAAGCAAGAGTT+TGG 0.352102 5.2:+62410795 None:intergenic
GACATTTGTGTATATTGAAT+AGG 0.354091 5.2:-62409352 None:intergenic
CACCTTGAAAACCATGTTCC+CGG 0.373489 5.2:+62410837 None:intergenic
CATTTCTAAAGACGGTGATT+TGG 0.384432 5.2:-62409689 MS.gene99704:CDS
AAATGGAAACTTCAGAAGAT+TGG 0.396214 5.2:-62410957 MS.gene99704:CDS
TTGGAATCAAGCAAGAGTTT+GGG 0.419781 5.2:+62410796 None:intergenic
ATCAAGCAAGAGTTTGGGAT+TGG 0.427325 5.2:+62410801 None:intergenic
AATGGAAACTTCAGAAGATT+GGG 0.430383 5.2:-62410956 MS.gene99704:CDS
ACAAATGTCATAAACTCATT+TGG 0.432948 5.2:+62409366 None:intergenic
GATTGGGATGTGTTCATCTT+CGG 0.437653 5.2:+62410921 None:intergenic
GGAGAATAGAGGATTATCAT+TGG 0.453902 5.2:+62410777 None:intergenic
TGGAAATGTTACAAGAGAAA+TGG 0.454502 5.2:-62409862 MS.gene99704:CDS
CTAACGTTCACTGATGCATC+CGG 0.465094 5.2:-62410856 MS.gene99704:CDS
CGGATGCATCAGTGAACGTT+AGG 0.475705 5.2:+62410857 None:intergenic
TTGGAACAGAAGAGATCGAT+TGG 0.479549 5.2:+62410904 None:intergenic
TTCTAAAGACGGTGATTTGG+TGG 0.482022 5.2:-62409686 MS.gene99704:CDS
TCAAGCAAGAGTTTGGGATT+GGG 0.489749 5.2:+62410802 None:intergenic
CACTGATGCATCCGGGAACA+TGG 0.502309 5.2:-62410848 MS.gene99704:CDS
ACTAACGTGACGACGGTGGA+TGG 0.504748 5.2:+62410756 None:intergenic
CTCTTCTGTTCCAAAGAGGC+CGG 0.506612 5.2:-62410895 MS.gene99704:CDS
TCAGAAGATTGGGAGTATAC+AGG 0.511784 5.2:-62410946 MS.gene99704:CDS
TGGAACAGAAGAGATCGATT+GGG 0.531250 5.2:+62410905 None:intergenic
AGCAAGAGTTTGGGATTGGG+TGG 0.555142 5.2:+62410805 None:intergenic
AGACGGTGATTTGGTGGCAC+AGG 0.565780 5.2:-62409680 MS.gene99704:intron
CGACGGTGGATGGAGAATAG+AGG 0.586292 5.2:+62410766 None:intergenic
AGCTTGTGTTAAAAGTAAAG+AGG 0.588306 5.2:-62409825 MS.gene99704:CDS
CGATCTCTTCTGTTCCAAAG+AGG 0.591924 5.2:-62410899 MS.gene99704:CDS
TAGGATGCCACATGGAACTC+CGG 0.593109 5.2:+62410876 None:intergenic
TAACGTTCACTGATGCATCC+GGG 0.593676 5.2:-62410855 MS.gene99704:CDS
ATGCTGCATGATCTCATGAA+AGG 0.599728 5.2:+62409709 None:intergenic
AGAGACTAACGTGACGACGG+TGG 0.605276 5.2:+62410752 None:intergenic
TCATGCAGCATTTCTAAAGA+CGG 0.624828 5.2:-62409697 MS.gene99704:CDS
CAGAGAGACTAACGTGACGA+CGG 0.675593 5.2:+62410749 None:intergenic
GTGAACGTTAGGATGCCACA+TGG 0.693955 5.2:+62410868 None:intergenic
AAAGAGGCCGGAGTTCCATG+TGG 0.732945 5.2:-62410883 MS.gene99704:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TGAAATATGTTGTTTTATTT+TGG - chr5.2:62410417-62410436 MS.gene99704:intron 15.0%
!!! TTTTATAAGGTAATTACTAT+TGG - chr5.2:62409880-62409899 MS.gene99704:intron 15.0%
!! ATAAAAAAGGAAAGAAATTG+AGG - chr5.2:62410386-62410405 MS.gene99704:intron 20.0%
!! TAGAAACATAAACATTGATA+TGG - chr5.2:62410756-62410775 MS.gene99704:intron 20.0%
!!! GTCATATTTTAGATTACTAT+CGG - chr5.2:62409854-62409873 MS.gene99704:CDS 20.0%
!!! TAAATATTTTTTCTAGGAGA+TGG + chr5.2:62410367-62410386 None:intergenic 20.0%
!!! TCAATGTTTATGTTTCTAAT+TGG + chr5.2:62410754-62410773 None:intergenic 20.0%
! ACAAATGTCATAAACTCATT+TGG + chr5.2:62410951-62410970 None:intergenic 25.0%
! ATAAATCACATGGAAAAATG+TGG + chr5.2:62409755-62409774 None:intergenic 25.0%
! TACAATGTAATCATATGTGT+CGG - chr5.2:62410153-62410172 MS.gene99704:intron 25.0%
!! CAAGGACATTTAATGTTTTT+GGG + chr5.2:62410892-62410911 None:intergenic 25.0%
!! GATCACTTTAGTGTATTTTA+GGG - chr5.2:62409994-62410013 MS.gene99704:intron 25.0%
!! TGATCACTTTAGTGTATTTT+AGG - chr5.2:62409993-62410012 MS.gene99704:intron 25.0%
!!! AAGGACATTTAATGTTTTTG+GGG + chr5.2:62410891-62410910 None:intergenic 25.0%
!!! ATCAAAGAAGTGTTTAAAGA+TGG - chr5.2:62409793-62409812 MS.gene99704:CDS 25.0%
!!! TCAAAGAAGTGTTTAAAGAT+GGG - chr5.2:62409794-62409813 MS.gene99704:CDS 25.0%
!!! TTACTATCGGTGTTTTTATA+AGG - chr5.2:62409867-62409886 MS.gene99704:CDS 25.0%
!!! TTGTTTTATTTTGGTAGAGT+GGG - chr5.2:62410426-62410445 MS.gene99704:intron 25.0%
!!! TTTTTCGTCAATTAGTCTAT+TGG - chr5.2:62410835-62410854 MS.gene99704:CDS 25.0%
AAATGGAAACTTCAGAAGAT+TGG - chr5.2:62409357-62409376 MS.gene99704:CDS 30.0%
AACATTGATATGGTTAGACT+TGG - chr5.2:62410766-62410785 MS.gene99704:CDS 30.0%
AATGGAAACTTCAGAAGATT+GGG - chr5.2:62409358-62409377 MS.gene99704:CDS 30.0%
AGCTTGTGTTAAAAGTAAAG+AGG - chr5.2:62410489-62410508 MS.gene99704:intron 30.0%
CGTTGAAAAATGTGAAATTG+TGG + chr5.2:62409699-62409718 None:intergenic 30.0%
GTAGTTGTTCTTCATAGTAT+AGG - chr5.2:62410223-62410242 MS.gene99704:intron 30.0%
GTTTGCGACTTAAAAGTTAT+TGG - chr5.2:62410578-62410597 MS.gene99704:intron 30.0%
TCATAGTATGTGATTAAGCA+AGG - chr5.2:62410313-62410332 MS.gene99704:intron 30.0%
TGGAAATGTTACAAGAGAAA+TGG - chr5.2:62410452-62410471 MS.gene99704:intron 30.0%
! ATTTTCAATTTTTCGCTGCA+AGG + chr5.2:62410910-62410929 None:intergenic 30.0%
! GCAAGGACATTTAATGTTTT+TGG + chr5.2:62410893-62410912 None:intergenic 30.0%
!!! AAGTTAGAAGTGTTTTTTGC+TGG - chr5.2:62410536-62410555 MS.gene99704:intron 30.0%
!!! GGAACATGTTTTAGTTGTAA+TGG - chr5.2:62410787-62410806 MS.gene99704:CDS 30.0%
!!! GTTGTTTTATTTTGGTAGAG+TGG - chr5.2:62410425-62410444 MS.gene99704:intron 30.0%
ACATGTAATTACATGCGTCT+TGG + chr5.2:62409828-62409847 None:intergenic 35.0%
ATTGGAATCAAGCAAGAGTT+TGG + chr5.2:62409522-62409541 None:intergenic 35.0%
CTCTTAGATTAGATATGTCC+TGG + chr5.2:62410204-62410223 None:intergenic 35.0%
GGAGAATAGAGGATTATCAT+TGG + chr5.2:62409540-62409559 None:intergenic 35.0%
TCACTGCTACATAAATCACA+TGG + chr5.2:62409765-62409784 None:intergenic 35.0%
TCTGCTATCCATGTTTGTAT+GGG - chr5.2:62409926-62409945 MS.gene99704:intron 35.0%
TTGGAATCAAGCAAGAGTTT+GGG + chr5.2:62409521-62409540 None:intergenic 35.0%
! CATTTCTAAAGACGGTGATT+TGG - chr5.2:62410625-62410644 MS.gene99704:intron 35.0%
! GAAGTGTTTAAAGATGGGTT+TGG - chr5.2:62409799-62409818 MS.gene99704:CDS 35.0%
! GAGAAATGGTGATGAGAATA+AGG - chr5.2:62410466-62410485 MS.gene99704:intron 35.0%
! TCATGCAGCATTTCTAAAGA+CGG - chr5.2:62410617-62410636 MS.gene99704:intron 35.0%
!! GTAATGGATAAGCTTCTGTA+TGG - chr5.2:62410803-62410822 MS.gene99704:CDS 35.0%
ACGATCGAGTGACTTTAATG+AGG - chr5.2:62409959-62409978 MS.gene99704:intron 40.0%
ATGCTGCATGATCTCATGAA+AGG + chr5.2:62410608-62410627 None:intergenic 40.0%
CGATCGAGTGACTTTAATGA+GGG - chr5.2:62409960-62409979 MS.gene99704:intron 40.0%
GATTAGATATGTCCTGGTGT+CGG + chr5.2:62410198-62410217 None:intergenic 40.0%
GATTGGGATGTGTTCATCTT+CGG + chr5.2:62409396-62409415 None:intergenic 40.0%
GTCTGCTATCCATGTTTGTA+TGG - chr5.2:62409925-62409944 MS.gene99704:intron 40.0%
TGGAACAGAAGAGATCGATT+GGG + chr5.2:62409412-62409431 None:intergenic 40.0%
TTCATAGTATAGGCGAGAGA+TGG - chr5.2:62410233-62410252 MS.gene99704:intron 40.0%
TTGGAACAGAAGAGATCGAT+TGG + chr5.2:62409413-62409432 None:intergenic 40.0%
! AAACTCATTTGGTAGCTGCA+AGG + chr5.2:62410940-62410959 None:intergenic 40.0%
! ATCAAGCAAGAGTTTGGGAT+TGG + chr5.2:62409516-62409535 None:intergenic 40.0%
! GTAATCATATGTGTCGGTGT+TGG - chr5.2:62410159-62410178 MS.gene99704:intron 40.0%
! TACTATGAAGCACTACGACA+AGG + chr5.2:62410301-62410320 None:intergenic 40.0%
! TCAAGCAAGAGTTTGGGATT+GGG + chr5.2:62409515-62409534 None:intergenic 40.0%
! TCAGAAGATTGGGAGTATAC+AGG - chr5.2:62409368-62409387 MS.gene99704:CDS 40.0%
! TTCTAAAGACGGTGATTTGG+TGG - chr5.2:62410628-62410647 MS.gene99704:intron 40.0%
!!! TATTTTGGTAGAGTGGGACT+TGG - chr5.2:62410432-62410451 MS.gene99704:intron 40.0%
ACAAGGAATGGGTGACTTTG+TGG + chr5.2:62410284-62410303 None:intergenic 45.0%
AGACACACGACATTGACACA+TGG + chr5.2:62409909-62409928 None:intergenic 45.0%
CACCTTGAAAACCATGTTCC+CGG + chr5.2:62409480-62409499 None:intergenic 45.0%
CATGATATGTATCCGACACC+AGG - chr5.2:62410183-62410202 MS.gene99704:intron 45.0%
CGATCTCTTCTGTTCCAAAG+AGG - chr5.2:62409415-62409434 MS.gene99704:intron 45.0%
CTAACGTTCACTGATGCATC+CGG - chr5.2:62409458-62409477 MS.gene99704:intron 45.0%
TAACGTTCACTGATGCATCC+GGG - chr5.2:62409459-62409478 MS.gene99704:intron 45.0%
TCGAACTCGCAATTCTCTAC+TGG + chr5.2:62410861-62410880 None:intergenic 45.0%
! ATCCGGGAACATGGTTTTCA+AGG - chr5.2:62409475-62409494 MS.gene99704:intron 45.0%
! GAAGCACTACGACAAGGAAT+GGG + chr5.2:62410295-62410314 None:intergenic 45.0%
! TCGAAGCACCCATACAAACA+TGG + chr5.2:62409937-62409956 None:intergenic 45.0%
! TGAAGCACTACGACAAGGAA+TGG + chr5.2:62410296-62410315 None:intergenic 45.0%
!! GTGATTAAGCAAGGTGTCGT+AGG - chr5.2:62410322-62410341 MS.gene99704:intron 45.0%
!! AGAAAAAATATTTATAAAAA+AGG - chr5.2:62410373-62410392 MS.gene99704:intron 5.0%
!!! TTTTTATAAATATTTTTTCT+AGG + chr5.2:62410373-62410392 None:intergenic 5.0%
AGGAATGGGTGACTTTGTGG+AGG + chr5.2:62410281-62410300 None:intergenic 50.0%
ATCTATGACCGACCGTGTGT+GGG + chr5.2:62410094-62410113 None:intergenic 50.0%
CAGAGAGACTAACGTGACGA+CGG + chr5.2:62409568-62409587 None:intergenic 50.0%
CGGATGCATCAGTGAACGTT+AGG + chr5.2:62409460-62409479 None:intergenic 50.0%
CTCAACCGAATCAACCGTCT+CGG + chr5.2:62409624-62409643 None:intergenic 50.0%
CTCTTCTGTTCCAAAGAGGC+CGG - chr5.2:62409419-62409438 MS.gene99704:intron 50.0%
GGAATGGGTGACTTTGTGGA+GGG + chr5.2:62410280-62410299 None:intergenic 50.0%
GGTGTGGTGCGTGTAAAAGA+AGG + chr5.2:62409601-62409620 None:intergenic 50.0%
GTGAACGTTAGGATGCCACA+TGG + chr5.2:62409449-62409468 None:intergenic 50.0%
TAGGATGCCACATGGAACTC+CGG + chr5.2:62409441-62409460 None:intergenic 50.0%
TATCTATGACCGACCGTGTG+TGG + chr5.2:62410095-62410114 None:intergenic 50.0%
TCAACCGAATCAACCGTCTC+GGG + chr5.2:62409623-62409642 None:intergenic 50.0%
TGAGCTATGAAGCCCACACA+CGG - chr5.2:62410079-62410098 MS.gene99704:intron 50.0%
! AGCAAGAGTTTGGGATTGGG+TGG + chr5.2:62409512-62409531 None:intergenic 50.0%
!! AGCAAGGTGTCGTAGGTGTA+AGG - chr5.2:62410329-62410348 MS.gene99704:intron 50.0%
AAAGAGGCCGGAGTTCCATG+TGG - chr5.2:62409431-62409450 MS.gene99704:intron 55.0%
ACACCCCGAGACGGTTGATT+CGG - chr5.2:62409616-62409635 MS.gene99704:intron 55.0%
ACATGGAACTCCGGCCTCTT+TGG + chr5.2:62409432-62409451 None:intergenic 55.0%
ACTAACGTGACGACGGTGGA+TGG + chr5.2:62409561-62409580 None:intergenic 55.0%
AGAGACTAACGTGACGACGG+TGG + chr5.2:62409565-62409584 None:intergenic 55.0%
CAACCGAATCAACCGTCTCG+GGG + chr5.2:62409622-62409641 None:intergenic 55.0%
CACTGATGCATCCGGGAACA+TGG - chr5.2:62409466-62409485 MS.gene99704:intron 55.0%
CGACGGTGGATGGAGAATAG+AGG + chr5.2:62409551-62409570 None:intergenic 55.0%
CTATGAAGCCCACACACGGT+CGG - chr5.2:62410083-62410102 MS.gene99704:intron 55.0%
!! AGACGGTGATTTGGTGGCAC+AGG - chr5.2:62410634-62410653 MS.gene99704:intron 55.0%
GAATCAACCGTCTCGGGGTG+TGG + chr5.2:62409617-62409636 None:intergenic 60.0%
ACACGCACCACACCCCGAGA+CGG - chr5.2:62409607-62409626 MS.gene99704:intron 65.0%


Chromosome Type Strat End Strand Name
chr5.2 gene 62409353 62410983 62409353 ID=MS.gene99704
chr5.2 mRNA 62409353 62410983 62409353 ID=MS.gene99704.t1;Parent=MS.gene99704
chr5.2 exon 62410762 62410983 62410762 ID=MS.gene99704.t1.exon1;Parent=MS.gene99704.t1
chr5.2 CDS 62410762 62410983 62410762 ID=cds.MS.gene99704.t1;Parent=MS.gene99704.t1
chr5.2 exon 62409681 62409893 62409681 ID=MS.gene99704.t1.exon2;Parent=MS.gene99704.t1
chr5.2 CDS 62409681 62409893 62409681 ID=cds.MS.gene99704.t1;Parent=MS.gene99704.t1
chr5.2 exon 62409353 62409391 62409353 ID=MS.gene99704.t1.exon3;Parent=MS.gene99704.t1
chr5.2 CDS 62409353 62409391 62409353 ID=cds.MS.gene99704.t1;Parent=MS.gene99704.t1
Gene Sequence

>MS.gene99704

ATGGAAATGGAAACTTCAGAAGATTGGGAGTATACAGGCACCGAAGATGAACACATCCCAATCGATCTCTTCTGTTCCAAAGAGGCCGGAGTTCCATGTGGCATCCTAACGTTCACTGATGCATCCGGGAACATGGTTTTCAAGGTGCAACATCAACCACCCAATCCCAAACTCTTGCTTGATTCCAATGATAATCCTCTATTCTCCATCCACCGTCGTCACGTTAGTCTCTCTGTCTAATGATTCCTTCTTTTACACGCACCACACCCCGAGACGGTTGATTCGGTTGAGTAGATGATTAATTTAATTATCAATCAAAATTTTGTTTAATTCAATTGATTAACCACAATTTCACATTTTTCAACGCGTTTAAATTGACTATCTATTCAACTTAAACAACCACATTTTTCCATGTGATTTATGTAGCAGTGACACTTTTGATCAAAGAAGTGTTTAAAGATGGGTTTGGTGTCCAAGACGCATGTAATTACATGTAATTATGTCATATTTTAGATTACTATCGGTGTTTTTATAAGGTAATTACTATTGGTGTCCATGTGTCAATGTCGTGTGTCTGCTATCCATGTTTGTATGGGTGCTTCGACAACGATCGAGTGACTTTAATGAGGGAAAGTTATTATGATCACTTTAGTGTATTTTAGGGTGTTTTATGACAGAGAAAGATGAAAGAGAAATGAGTTTTAAGCTGAGAGATAGAGTAATACATGAGCTATGAAGCCCACACACGGTCGGTCATAGATACGTACGTCAACAACGATAATAATGAGAAAATAACAAAATACAATGTAATCATATGTGTCGGTGTTGGACATGATATGTATCCGACACCAGGACATATCTAATCTAAGAGTAGTTGTTCTTCATAGTATAGGCGAGAGATGGAGAGAAAGTCATAATGACTGACCCTCCACAAAGTCACCCATTCCTTGTCGTAGTGCTTCATAGTATGTGATTAAGCAAGGTGTCGTAGGTGTAAGGAAAATTGTACGTCCATCTCCTAGAAAAAATATTTATAAAAAAGGAAAGAAATTGAGGCAAGTTTTTGAAATATGTTGTTTTATTTTGGTAGAGTGGGACTTGGAAATGTTACAAGAGAAATGGTGATGAGAATAAGGAGCTTGTGTTAAAAGTAAAGAGGACTGTGAAAACAATTTCTAGAGTTAAGTTAGAAGTGTTTTTTGCTGGTGAGAGATTAAACAAAGACGTTTGCGACTTAAAAGTTATTGGTTCTCCTTTCATGAGATCATGCAGCATTTCTAAAGACGGTGATTTGGTGGCACAGGTACATAAATTGAAGTTTACTATCAGTTTATTTATGTTCAAGTACAGATGTATACTGAGATTGTTTTGATTCAAGTATGTTACAACTTTTAAAGACCAATTAGAAACATAAACATTGATATGGTTAGACTTGGAACATGTTTTAGTTGTAATGGATAAGCTTCTGTATGGTTGTGTTTTTTTTTCGTCAATTAGTCTATTGGCCAGTAGAGAATTGCGAGTTCGAAACTACACCCCAAAAACATTAAATGTCCTTGCAGCGAAAAATTGAAAATATAATGTCCTTGCAGCTACCAAATGAGTTTATGACATTTGTGTATATTGAATAG

Protein sequence

>MS.gene99704.t1

MEMETSEDWEYTGTEDEHIPIDLFCSKEAGVPCGILTFTDASGNMVFKVQHQPPNPKLLLDSNDNPLFSIHRRHSGTWKCYKRNGDENKELVLKVKRTVKTISRVKLEVFFAGERLNKDVCDLKVIGSPFMRSCSISKDGDLVAQLPNEFMTFVYIE