AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene71529


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene71529.t1 MTR_3g083080 68.966 203 21 4 1 170 1 194 2.96e-88 258
MS.gene71529.t1 MTR_3g083030 44.954 218 57 5 1 161 1 212 9.50e-49 159
MS.gene71529.t1 MTR_3g083050 47.692 195 62 4 1 161 1 189 1.45e-47 155
MS.gene71529.t1 MTR_3g082340 30.144 209 95 8 1 161 1 206 1.69e-17 77.8
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 44 sgRNAs with CRISPR-Local

Find 97 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTCGGTTGCAATCCCGTTAC+AGG 0.190009 3.4:-78255762 None:intergenic
CCGGAAAACTGTGATGAAAA+AGG 0.252165 3.4:+78255732 MS.gene71529:CDS
AATCTGAGCCTTATTCTTAT+AGG 0.253945 3.4:-78255898 None:intergenic
CGCCCACACATAAACATAAA+AGG 0.266595 3.4:-78255870 None:intergenic
TCATATTTCTTTCTCCGTTT+CGG 0.317369 3.4:-78255780 None:intergenic
GCGATTTACCTATAAGAATA+AGG 0.398069 3.4:+78255890 MS.gene71529:CDS
TCTTGTTTCATACTTGTGCT+TGG 0.413432 3.4:-78256226 None:intergenic
ATAAATGCTAACAGGTCATT+AGG 0.415829 3.4:+78256372 MS.gene71529:intron
TATGGATTTACTACTCAAAC+CGG 0.438570 3.4:-78256409 None:intergenic
TTAGGCCTGTGCAAAATAAC+CGG 0.445160 3.4:+78256390 MS.gene71529:CDS
GAAAATTATAGCAGAGATGT+TGG 0.447031 3.4:-78256204 None:intergenic
CGGCGTCACCCAACCTTCTC+CGG 0.453638 3.4:+78255713 MS.gene71529:CDS
AACGGAGAAAGAAATATGAA+TGG 0.461826 3.4:+78255784 MS.gene71529:CDS
AAAGGGAATCAACCTGTAAC+GGG 0.471848 3.4:+78255750 MS.gene71529:CDS
TGCAGAGGGGAGTGAGTTCA+AGG 0.477142 3.4:-78255965 None:intergenic
CACGACGGCGGCAAAATATG+TGG 0.492216 3.4:+78256881 MS.gene71529:CDS
CGGAGAAGGTTGGGTGACGC+CGG 0.498648 3.4:-78255712 None:intergenic
TTCTTGTTCGTGTGCTTGAA+AGG 0.503496 3.4:-78256162 None:intergenic
AATGTCGATGGAATTCAATA+CGG 0.514369 3.4:+78255683 None:intergenic
GGAGAAGGTTGGGTGACGCC+GGG 0.516300 3.4:-78255711 None:intergenic
TAACGGGATTGCAACCGAAA+CGG 0.516954 3.4:+78255766 MS.gene71529:CDS
ACGGAGAAAGAAATATGAAT+GGG 0.520163 3.4:+78255785 MS.gene71529:CDS
CAAGTACAATGCTGAGAACC+AGG 0.527031 3.4:+78256001 MS.gene71529:CDS
ATACATACAACCAGGTCTCC+AGG 0.532645 3.4:-78256132 None:intergenic
AAGATCATCGGTTAAGTCGA+TGG 0.533943 3.4:-78255940 None:intergenic
GAATTCAATACGGTTTCGCC+CGG 0.538537 3.4:+78255693 MS.gene71529:CDS
TTGACATTGTGAAGACAACC+TGG 0.541774 3.4:+78256114 MS.gene71529:CDS
TTTGCCGCCGTCGTGCAAAG+AGG 0.560812 3.4:-78256873 None:intergenic
AAAAGGGAATCAACCTGTAA+CGG 0.561384 3.4:+78255749 MS.gene71529:CDS
GTCTAACACAAACTTGCAGA+GGG 0.571934 3.4:-78255979 None:intergenic
ATTATAGCAGAGATGTTGGA+AGG 0.576865 3.4:-78256200 None:intergenic
AGATCATCGGTTAAGTCGAT+GGG 0.584455 3.4:-78255939 None:intergenic
GAGTTCAAGGCAAAGATCAT+CGG 0.594092 3.4:-78255952 None:intergenic
GTGAAGACAACCTGGAGACC+TGG 0.604519 3.4:+78256122 MS.gene71529:CDS
TCCGTGTTACAGAATGTCGA+TGG 0.606334 3.4:+78255671 None:intergenic
GACGACAGAAGCTTTGCGCA+CGG 0.608634 3.4:+78256839 MS.gene71529:CDS
ATAACCTCTTTGCACGACGG+CGG 0.614814 3.4:+78256869 MS.gene71529:CDS
GTTGACAGAAACTTTGCTCA+CGG 0.614889 3.4:+78256815 MS.gene71529:CDS
ACGGCGGCAAAATATGTGGA+TGG 0.637748 3.4:+78256885 MS.gene71529:CDS
TGTCTAACACAAACTTGCAG+AGG 0.637970 3.4:-78255980 None:intergenic
GATATAACCTCTTTGCACGA+CGG 0.649315 3.4:+78256866 MS.gene71529:CDS
GTAATGTAATACATACAACC+AGG 0.734534 3.4:-78256140 None:intergenic
GACAGAAGCTTTGCGCACGG+CGG 0.747493 3.4:+78256842 MS.gene71529:CDS
TCTAACACAAACTTGCAGAG+GGG 0.776478 3.4:-78255978 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! ATATTTGGTTTTAAAATTTA+TGG - chr3.4:78256462-78256481 None:intergenic 10.0%
!!! AAAAATTGGTAATAGTTTTT+TGG - chr3.4:78256553-78256572 None:intergenic 15.0%
!!! AAAATTGGTAATAGTTTTTT+GGG - chr3.4:78256552-78256571 None:intergenic 15.0%
!!! AATTTATGGTTATTTTAGAA+TGG - chr3.4:78256448-78256467 None:intergenic 15.0%
! ATCAACCAAACCATTTAAAA+TGG + chr3.4:78256480-78256499 MS.gene71529:intron 25.0%
!! ACTAATTTTTCTCCTGATTT+AGG + chr3.4:78256073-78256092 MS.gene71529:intron 25.0%
!! CATCATGTTTAATCTTTTCT+TGG + chr3.4:78256343-78256362 MS.gene71529:intron 25.0%
!! CTAATTTTTCTCCTGATTTA+GGG + chr3.4:78256074-78256093 MS.gene71529:intron 25.0%
!! TATAACCGATCCATTTTAAA+TGG - chr3.4:78256493-78256512 None:intergenic 25.0%
!!! TAAATGGTTTGGTTGATATT+TGG - chr3.4:78256477-78256496 None:intergenic 25.0%
!!! TGGTTATTTTAGAATGGTTA+CGG - chr3.4:78256442-78256461 None:intergenic 25.0%
!!! TTTTGGGCTTTTTCTTTTTA+GGG - chr3.4:78256536-78256555 None:intergenic 25.0%
!!! TTTTTCTTTTTAGGGATAAC+CGG - chr3.4:78256528-78256547 None:intergenic 25.0%
!!! TTTTTGGGCTTTTTCTTTTT+AGG - chr3.4:78256537-78256556 None:intergenic 25.0%
AACGGAGAAAGAAATATGAA+TGG + chr3.4:78255784-78255803 MS.gene71529:CDS 30.0%
ACGGAGAAAGAAATATGAAT+GGG + chr3.4:78255785-78255804 MS.gene71529:CDS 30.0%
ATAAATGCTAACAGGTCATT+AGG + chr3.4:78256372-78256391 MS.gene71529:intron 30.0%
GAAAATTATAGCAGAGATGT+TGG - chr3.4:78256207-78256226 None:intergenic 30.0%
GCGATTTACCTATAAGAATA+AGG + chr3.4:78255890-78255909 MS.gene71529:CDS 30.0%
GGAGATTTATAAATGCTAAC+AGG + chr3.4:78256364-78256383 MS.gene71529:intron 30.0%
GGTTATAAACCATTGTTAAC+CGG + chr3.4:78256506-78256525 MS.gene71529:intron 30.0%
GTAATGTAATACATACAACC+AGG - chr3.4:78256143-78256162 None:intergenic 30.0%
TATGGATTTACTACTCAAAC+CGG - chr3.4:78256412-78256431 None:intergenic 30.0%
TCATATTTCTTTCTCCGTTT+CGG - chr3.4:78255783-78255802 None:intergenic 30.0%
! AAGCCTTTTATGTTTATGTG+TGG + chr3.4:78255867-78255886 MS.gene71529:CDS 30.0%
! AGCCTTTTATGTTTATGTGT+GGG + chr3.4:78255868-78255887 MS.gene71529:CDS 30.0%
! CCAAACCATTTAAAATGGAT+CGG + chr3.4:78256485-78256504 MS.gene71529:intron 30.0%
! TGAGTTGAAAGCAGAAAAAT+TGG - chr3.4:78256567-78256586 None:intergenic 30.0%
!! AATCTGAGCCTTATTCTTAT+AGG - chr3.4:78255901-78255920 None:intergenic 30.0%
!! TTCTTGTAATTTGTTGAACC+TGG - chr3.4:78256022-78256041 None:intergenic 30.0%
!!! GGTTATTTTAGAATGGTTAC+GGG - chr3.4:78256441-78256460 None:intergenic 30.0%
AAAAGGGAATCAACCTGTAA+CGG + chr3.4:78255749-78255768 MS.gene71529:CDS 35.0%
AAGCACAAGTATGAAACAAG+AGG + chr3.4:78256228-78256247 MS.gene71529:intron 35.0%
ATTATAGCAGAGATGTTGGA+AGG - chr3.4:78256203-78256222 None:intergenic 35.0%
CAAAATTTGCACCCTAAATC+AGG - chr3.4:78256088-78256107 None:intergenic 35.0%
CGGAAAACTGTGATGAAAAA+GGG + chr3.4:78255733-78255752 MS.gene71529:CDS 35.0%
! CCGATCCATTTTAAATGGTT+TGG - chr3.4:78256488-78256507 None:intergenic 35.0%
! TCTTGTTTCATACTTGTGCT+TGG - chr3.4:78256229-78256248 None:intergenic 35.0%
!! CCTTTTTCATCACAGTTTTC+CGG - chr3.4:78255735-78255754 None:intergenic 35.0%
!!! TTTTAGAATGGTTACGGGTA+TGG - chr3.4:78256436-78256455 None:intergenic 35.0%
AAAGGGAATCAACCTGTAAC+GGG + chr3.4:78255750-78255769 MS.gene71529:CDS 40.0%
AAGTATGAAACAAGAGGCCT+GGG + chr3.4:78256234-78256253 MS.gene71529:intron 40.0%
AATGGTTACGGGTATGGTTA+TGG - chr3.4:78256430-78256449 None:intergenic 40.0%
ACCTAACACGTACATCATCA+TGG + chr3.4:78256290-78256309 MS.gene71529:intron 40.0%
CCGGAAAACTGTGATGAAAA+AGG + chr3.4:78255732-78255751 MS.gene71529:CDS 40.0%
CGCCCACACATAAACATAAA+AGG - chr3.4:78255873-78255892 None:intergenic 40.0%
GAGTTCAAGGCAAAGATCAT+CGG - chr3.4:78255955-78255974 None:intergenic 40.0%
GATATAACCTCTTTGCACGA+CGG + chr3.4:78256866-78256885 MS.gene71529:CDS 40.0%
GTCTAACACAAACTTGCAGA+GGG - chr3.4:78255982-78256001 None:intergenic 40.0%
GTTGACAGAAACTTTGCTCA+CGG + chr3.4:78256815-78256834 MS.gene71529:CDS 40.0%
TAGGGATAACCGGTTAACAA+TGG - chr3.4:78256518-78256537 None:intergenic 40.0%
TCTAACACAAACTTGCAGAG+GGG - chr3.4:78255981-78256000 None:intergenic 40.0%
TGTCTAACACAAACTTGCAG+AGG - chr3.4:78255983-78256002 None:intergenic 40.0%
TTAGGCCTGTGCAAAATAAC+CGG + chr3.4:78256390-78256409 MS.gene71529:CDS 40.0%
TTCTTGTTCGTGTGCTTGAA+AGG - chr3.4:78256165-78256184 None:intergenic 40.0%
TTGACATTGTGAAGACAACC+TGG + chr3.4:78256114-78256133 MS.gene71529:CDS 40.0%
! AAGATCATCGGTTAAGTCGA+TGG - chr3.4:78255943-78255962 None:intergenic 40.0%
! ACCATGATGATGTACGTGTT+AGG - chr3.4:78256294-78256313 None:intergenic 40.0%
! AGATCATCGGTTAAGTCGAT+GGG - chr3.4:78255942-78255961 None:intergenic 40.0%
! TGATGATGTACGTGTTAGGT+AGG - chr3.4:78256290-78256309 None:intergenic 40.0%
!! TCAAACCGGTTATTTTGCAC+AGG - chr3.4:78256398-78256417 None:intergenic 40.0%
ATACATACAACCAGGTCTCC+AGG - chr3.4:78256135-78256154 None:intergenic 45.0%
CAAGTACAATGCTGAGAACC+AGG + chr3.4:78256001-78256020 MS.gene71529:CDS 45.0%
CAAGTATGAAACAAGAGGCC+TGG + chr3.4:78256233-78256252 MS.gene71529:intron 45.0%
GAATTCAATACGGTTTCGCC+CGG + chr3.4:78255693-78255712 MS.gene71529:CDS 45.0%
TAACGGGATTGCAACCGAAA+CGG + chr3.4:78255766-78255785 MS.gene71529:CDS 45.0%
TACGTGTTAGGTAGGCTTCA+TGG - chr3.4:78256282-78256301 None:intergenic 45.0%
! ACAGTTTTCCGGAGAAGGTT+GGG - chr3.4:78255724-78255743 None:intergenic 45.0%
! TCATCACAGTTTTCCGGAGA+AGG - chr3.4:78255729-78255748 None:intergenic 45.0%
ACGGCGGCAAAATATGTGGA+TGG + chr3.4:78256885-78256904 MS.gene71529:CDS 50.0%
ATAACCTCTTTGCACGACGG+CGG + chr3.4:78256869-78256888 MS.gene71529:CDS 50.0%
ATGGCACATGACTTGACCTC+AGG - chr3.4:78256263-78256282 None:intergenic 50.0%
GACGGAGATGAAAACGCAAG+AGG + chr3.4:78256616-78256635 MS.gene71529:intron 50.0%
GGAGATGAAAACGCAAGAGG+AGG + chr3.4:78256619-78256638 MS.gene71529:intron 50.0%
TTCAACTCACTCCGATGACG+TGG + chr3.4:78256578-78256597 MS.gene71529:intron 50.0%
TTCGGTTGCAATCCCGTTAC+AGG - chr3.4:78255765-78255784 None:intergenic 50.0%
! CACAGTTTTCCGGAGAAGGT+TGG - chr3.4:78255725-78255744 None:intergenic 50.0%
CACGACGGCGGCAAAATATG+TGG + chr3.4:78256881-78256900 MS.gene71529:CDS 55.0%
GACGACAGAAGCTTTGCGCA+CGG + chr3.4:78256839-78256858 MS.gene71529:CDS 55.0%
GCACATGACTTGACCTCAGG+TGG - chr3.4:78256260-78256279 None:intergenic 55.0%
GTGAAGACAACCTGGAGACC+TGG + chr3.4:78256122-78256141 MS.gene71529:CDS 55.0%
TCACAGAGATGACTCCGACG+AGG + chr3.4:78256723-78256742 MS.gene71529:intron 55.0%
TGCAGAGGGGAGTGAGTTCA+AGG - chr3.4:78255968-78255987 None:intergenic 55.0%
CTCACTCCGATGACGTGGCA+CGG + chr3.4:78256583-78256602 MS.gene71529:intron 60.0%
GACAGAAGCTTTGCGCACGG+CGG + chr3.4:78256842-78256861 MS.gene71529:CDS 60.0%
TAACCGCCGTGCCACGTCAT+CGG - chr3.4:78256592-78256611 None:intergenic 60.0%
TGGCACGGCGGTTACATGGA+CGG + chr3.4:78256598-78256617 MS.gene71529:intron 60.0%
TTTGCCGCCGTCGTGCAAAG+AGG - chr3.4:78256876-78256895 None:intergenic 60.0%
ACTCCGATGACGTGGCACGG+CGG + chr3.4:78256586-78256605 MS.gene71529:intron 65.0%
CGGAGAAGGTTGGGTGACGC+CGG - chr3.4:78255715-78255734 None:intergenic 65.0%
CGGCGTCACCCAACCTTCTC+CGG + chr3.4:78255713-78255732 MS.gene71529:CDS 65.0%
CTCCGACGAGGTGTGCACGA+CGG + chr3.4:78256735-78256754 MS.gene71529:intron 65.0%
GACGTGGCACGGCGGTTACA+TGG + chr3.4:78256594-78256613 MS.gene71529:intron 65.0%
GACTTGACCTCAGGTGGCCC+AGG - chr3.4:78256254-78256273 None:intergenic 65.0%
GGAGAAGGTTGGGTGACGCC+GGG - chr3.4:78255714-78255733 None:intergenic 65.0%
CAAGAGGCCTGGGCCACCTG+AGG + chr3.4:78256244-78256263 MS.gene71529:intron 70.0%
CGCCGTCGTGCACACCTCGT+CGG - chr3.4:78256740-78256759 None:intergenic 70.0%


Chromosome Type Strat End Strand Name
chr3.4 gene 78255684 78256913 78255684 ID=MS.gene71529
chr3.4 mRNA 78255684 78256913 78255684 ID=MS.gene71529.t1;Parent=MS.gene71529
chr3.4 exon 78255684 78256022 78255684 ID=MS.gene71529.t1.exon1;Parent=MS.gene71529.t1
chr3.4 CDS 78255684 78256022 78255684 ID=cds.MS.gene71529.t1;Parent=MS.gene71529.t1
chr3.4 exon 78256095 78256235 78256095 ID=MS.gene71529.t1.exon2;Parent=MS.gene71529.t1
chr3.4 CDS 78256095 78256235 78256095 ID=cds.MS.gene71529.t1;Parent=MS.gene71529.t1
chr3.4 exon 78256386 78256420 78256386 ID=MS.gene71529.t1.exon3;Parent=MS.gene71529.t1
chr3.4 CDS 78256386 78256420 78256386 ID=cds.MS.gene71529.t1;Parent=MS.gene71529.t1
chr3.4 exon 78256811 78256913 78256811 ID=MS.gene71529.t1.exon4;Parent=MS.gene71529.t1
chr3.4 CDS 78256811 78256913 78256811 ID=cds.MS.gene71529.t1;Parent=MS.gene71529.t1
Gene Sequence

>MS.gene71529

ATGTCGATGGAATTCAATACGGTTTCGCCCGGCGTCACCCAACCTTCTCCGGAAAACTGTGATGAAAAAGGGAATCAACCTGTAACGGGATTGCAACCGAAACGGAGAAAGAAATATGAATGGGAATTGAAACGATTTGAAGATCTTGAGATTAGTGACTTCTTTATGTATGACGATGACATTAAGCCTTTTATGTTTATGTGTGGGCGATTTACCTATAAGAATAAGGCTCAGATTCTACATTGCAGTGCTGTACCCATCGACTTAACCGATGATCTTTGCCTTGAACTCACTCCCCTCTGCAAGTTTGTGTTAGACAAGTACAATGCTGAGAACCAGGTTCAACAAATTACAAGAATTATTATATATATGCATATACGTTTGTTTGAACTAATTTTTCTCCTGATTTAGGGTGCAAATTTTGTGTTTATTGACATTGTGAAGACAACCTGGAGACCTGGTTGTATGTATTACATTACCTTTCAAGCACACGAACAAGAACAAGAACAAGAAAATCCTTCCAACATCTCTGCTATAATTTTCCAAGCACAAGTATGAAACAAGAGGCCTGGGCCACCTGAGGTCAAGTCATGTGCCATGAAGCCTACCTAACACGTACATCATCATGGTAATAGTGTTGCATTAATATCATGAATTTACATCATGTTTAATCTTTTCTTGGAGATTTATAAATGCTAACAGGTCATTAGGCCTGTGCAAAATAACCGGTTTGAGTAGTAAATCCATAACCATACCCGTAACCATTCTAAAATAACCATAAATTTTAAAACCAAATATCAACCAAACCATTTAAAATGGATCGGTTATAAACCATTGTTAACCGGTTATCCCTAAAAAGAAAAAGCCCAAAAAACTATTACCAATTTTTCTGCTTTCAACTCACTCCGATGACGTGGCACGGCGGTTACATGGACGGAGATGAAAACGCAAGAGGAGGAAGAGAAAATCTAGATGCAGATCTAGTCAGTACAAATTATCTTGTTCTATATTCACACGTCGACGACGACAGAAGCTTTGCTCACAGAGATGACTCCGACGAGGTGTGCACGACGGCGACAATGATAGAAGCTTCACACACAGATTTGATGTTAAAAGCTATGTTGCAGCGACGTTGACAGAAACTTTGCTCACGGCGACGACAGAAGCTTTGCGCACGGCGGTGATATAACCTCTTTGCACGACGGCGGCAAAATATGTGGATGGTGCTAA

Protein sequence

>MS.gene71529.t1

MSMEFNTVSPGVTQPSPENCDEKGNQPVTGLQPKRRKKYEWELKRFEDLEISDFFMYDDDIKPFMFMCGRFTYKNKAQILHCSAVPIDLTDDLCLELTPLCKFVLDKYNAENQGANFVFIDIVKTTWRPGCMYYITFQAHEQEQEQENPSNISAIIFQAQVIRPVQNNRFEYDVDRNFAHGDDRSFAHGGDITSLHDGGKICGWC