AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene043331

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene043331.t1 MTR_2g089310 90.558 233 19 2 1 230 1 233 2.19e-121 344
MS.gene043331.t1 MTR_2g011450 47.586 145 49 2 1 145 1 118 2.34e-31 112
MS.gene043331.t1 MTR_4g046640 50.847 59 29 0 5 63 36 94 1.33e-12 63.2
MS.gene043331.t1 MTR_4g008050 50.000 66 33 0 3 68 6 71 3.01e-12 64.7
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene043331.t1 AT4G27310 42.197 173 56 3 1 138 1 164 9.16e-36 126
MS.gene043331.t1 AT5G54470 47.059 187 78 4 2 188 3 168 4.96e-34 121
MS.gene043331.t1 AT3G21890 56.000 50 22 0 5 54 31 80 8.81e-11 58.2

Find 61 sgRNAs with CRISPR-Local

Find 68 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GTGGATGAGGTTGGTTTGAT+AGG 0.262299 2.2:-10465542 MS.gene043331:CDS
CGGCGGTATAGCGACGTAAA+TGG 0.305299 2.2:-10465485 MS.gene043331:CDS
TTCACTTTCTTCTTGTTGCT+CGG 0.346480 2.2:+10465966 None:intergenic
TTCTTCTTGTTGCTCGGCGC+TGG 0.356031 2.2:+10465972 None:intergenic
ATGTTGGGACTGCGATTCTA+AGG 0.399501 2.2:-10466169 MS.gene043331:CDS
TGAAGAAGATGGTGATAATC+AGG 0.403542 2.2:-10465881 MS.gene043331:CDS
CGCATCGCCGCCTTTGACGA+CGG 0.405274 2.2:+10465506 None:intergenic
TTCCTCATCGGAATCGTAAT+CGG 0.408569 2.2:+10465918 None:intergenic
TGGATGAGGTTGGTTTGATA+GGG 0.423166 2.2:-10465541 MS.gene043331:CDS
CTCGGCGCTGGCACCGGCGT+TGG 0.429781 2.2:+10465984 None:intergenic
CCACCGGCTTCGAGTTCTTC+CGG 0.435713 2.2:-10465826 MS.gene043331:CDS
CGTGGAAAGCCTCCGGTGCT+AGG 0.445561 2.2:-10466074 MS.gene043331:CDS
TTGTTGCTCGGCGCTGGCAC+CGG 0.453269 2.2:+10465978 None:intergenic
CGGTAGCGATGAGTCGGTTA+CGG 0.474621 2.2:-10465806 MS.gene043331:CDS
CGACCAGGCTAGCTTATGTT+GGG 0.515990 2.2:-10466184 MS.gene043331:CDS
CGCGTTACCGAGCCTAGCAC+CGG 0.516421 2.2:+10466062 None:intergenic
CGAAGAGAGGTGGATGAGGT+TGG 0.516662 2.2:-10465551 MS.gene043331:CDS
GCCAACGCTAACTCCAACGC+CGG 0.517678 2.2:-10465997 MS.gene043331:CDS
CTCGTCCTCATCTTCCTCAT+CGG 0.523137 2.2:+10465906 None:intergenic
GACTCACAGAAAGTTCTAGC+TGG 0.526494 2.2:+10466207 None:intergenic
ACCGGCGTTGGAGTTAGCGT+TGG 0.527253 2.2:+10465996 None:intergenic
AGTCCCAACATAAGCTAGCC+TGG 0.529010 2.2:+10466181 None:intergenic
CCGACCAGGCTAGCTTATGT+TGG 0.529135 2.2:-10466185 MS.gene043331:CDS
GAGGACGAGGATGAAGAAGA+TGG 0.529527 2.2:-10465892 MS.gene043331:CDS
AACTTTCTGTGAGTCCGACC+AGG 0.531925 2.2:-10466199 MS.gene043331:CDS
ACCGGAGGCTTTCCACGGCG+TGG 0.539884 2.2:+10466080 None:intergenic
CCCACGCCGTGGAAAGCCTC+CGG 0.541657 2.2:-10466081 MS.gene043331:CDS
CGATGAGGAAGATGAGGACG+AGG 0.544127 2.2:-10465905 MS.gene043331:CDS
CGACGAGGAACCGTCGTCAA+AGG 0.547277 2.2:-10465516 MS.gene043331:CDS
GAAGAACTCGAAGCCGGTGG+TGG 0.549423 2.2:+10465829 None:intergenic
CGTCAAAGGCGGCGATGCGG+CGG 0.550222 2.2:-10465502 MS.gene043331:CDS
AACAGCGGCGCAACCACCAC+CGG 0.553693 2.2:-10465842 MS.gene043331:CDS
CATTCTCAGCCACACGATTG+AGG 0.570452 2.2:-10465455 None:intergenic
CGTAACCGACTCATCGCTAC+CGG 0.571656 2.2:+10465807 None:intergenic
TCAACGAAGAGAGGTGGATG+AGG 0.575020 2.2:-10465555 MS.gene043331:CDS
TTCTTCCGGTAGCGATGAGT+CGG 0.577433 2.2:-10465812 MS.gene043331:CDS
CGTTGGAGTTAGCGTTGGCG+TGG 0.586469 2.2:+10466001 None:intergenic
TCGTTGTGTGATAGATGCGC+CGG 0.591718 2.2:-10466036 MS.gene043331:CDS
AAAGCCTCCGGTGCTAGGCT+CGG 0.592338 2.2:-10466069 MS.gene043331:CDS
CCGGAGGCTTTCCACGGCGT+GGG 0.600004 2.2:+10466081 None:intergenic
CTAGCACCGGAGGCTTTCCA+CGG 0.603148 2.2:+10466075 None:intergenic
CGAGGAACCGTCGTCAAAGG+CGG 0.613549 2.2:-10465513 MS.gene043331:CDS
CGATTCCGATGAGGAAGATG+AGG 0.616964 2.2:-10465911 MS.gene043331:CDS
CTACCGGAAGAACTCGAAGC+CGG 0.624941 2.2:+10465823 None:intergenic
GAGATTGACATGCGTGACAG+AGG 0.627483 2.2:+10466103 None:intergenic
CCAACATAAGCTAGCCTGGT+CGG 0.628810 2.2:+10466185 None:intergenic
CGTCGTCAAAGGCGGCGATG+CGG 0.629213 2.2:-10465505 MS.gene043331:CDS
GTATAGCGACGTAAATGGAA+CGG 0.632422 2.2:-10465480 MS.gene043331:CDS
CATGTCAATCTCCCACGCCG+TGG 0.644127 2.2:-10466092 MS.gene043331:CDS
GTTACCGAGCCTAGCACCGG+AGG 0.644615 2.2:+10466065 None:intergenic
ATAGTACGGCCTCAATCGTG+TGG 0.647407 2.2:+10465446 None:intergenic
CCGGAAGAACTCGAAGCCGG+TGG 0.652243 2.2:+10465826 None:intergenic
TTGTGTGATAGATGCGCCGG+CGG 0.662123 2.2:-10466033 MS.gene043331:CDS
GTGATAATCAGGTTGTGCCG+TGG 0.677277 2.2:-10465870 MS.gene043331:CDS
GAGCAACAAGAAGAAAGTGA+AGG 0.680813 2.2:-10465964 MS.gene043331:CDS
CACCGATTACGATTCCGATG+AGG 0.696165 2.2:-10465920 MS.gene043331:CDS
TGCGCCGCTGTTGATGACCA+CGG 0.697626 2.2:+10465853 None:intergenic
TGGTTTGATAGGGTGCGACG+AGG 0.704245 2.2:-10465531 MS.gene043331:CDS
TGTGCCGTGGTCATCAACAG+CGG 0.705571 2.2:-10465857 MS.gene043331:CDS
GTGCAACGATAACCACGATG+AGG 0.723607 2.2:-10465776 MS.gene043331:CDS
ACTTAGAAATAACCTCATCG+TGG 0.742114 2.2:+10465764 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TTTTTGTTGATTTTGTTTTC+AGG - chr2.2:10466091-10466110 MS.gene043331:CDS 20.0%
!!! TTGATTTTGTTTTCAGGTTA+CGG - chr2.2:10466097-10466116 MS.gene043331:CDS 25.0%
AGGTTACGGATTCAAAAAAT+TGG - chr2.2:10466111-10466130 MS.gene043331:CDS 30.0%
! TCGTTTAGATCATGATTTTC+AGG - chr2.2:10465981-10466000 MS.gene043331:CDS 30.0%
ACTTAGAAATAACCTCATCG+TGG + chr2.2:10465933-10465952 None:intergenic 35.0%
TGAAGAAGATGGTGATAATC+AGG - chr2.2:10465813-10465832 MS.gene043331:CDS 35.0%
TTCACTTTCTTCTTGTTGCT+CGG + chr2.2:10465731-10465750 None:intergenic 35.0%
TTGGAAAAATCAACGAAGAG+AGG - chr2.2:10466130-10466149 MS.gene043331:CDS 35.0%
GAAAAATCAACGAAGAGAGG+TGG - chr2.2:10466133-10466152 MS.gene043331:CDS 40.0%
GAGCAACAAGAAGAAAGTGA+AGG - chr2.2:10465730-10465749 MS.gene043331:CDS 40.0%
GTATAGCGACGTAAATGGAA+CGG - chr2.2:10466214-10466233 MS.gene043331:CDS 40.0%
TTCCTCATCGGAATCGTAAT+CGG + chr2.2:10465779-10465798 None:intergenic 40.0%
!! TGGATGAGGTTGGTTTGATA+GGG - chr2.2:10466153-10466172 MS.gene043331:CDS 40.0%
ATGTTGGGACTGCGATTCTA+AGG - chr2.2:10465525-10465544 MS.gene043331:CDS 45.0%
CAACCAAAAAGTTAGCAGCG+TGG + chr2.2:10465552-10465571 None:intergenic 45.0%
! GACTCACAGAAAGTTCTAGC+TGG + chr2.2:10465490-10465509 None:intergenic 45.0%
!! GTGGATGAGGTTGGTTTGAT+AGG - chr2.2:10466152-10466171 MS.gene043331:CDS 45.0%
AACTTTCTGTGAGTCCGACC+AGG - chr2.2:10465495-10465514 MS.gene043331:CDS 50.0%
AGTCCCAACATAAGCTAGCC+TGG + chr2.2:10465516-10465535 None:intergenic 50.0%
CGATTCCGATGAGGAAGATG+AGG - chr2.2:10465783-10465802 MS.gene043331:CDS 50.0%
CTCGTCCTCATCTTCCTCAT+CGG + chr2.2:10465791-10465810 None:intergenic 50.0%
GAGATTGACATGCGTGACAG+AGG + chr2.2:10465594-10465613 None:intergenic 50.0%
GAGGACGAGGATGAAGAAGA+TGG - chr2.2:10465802-10465821 MS.gene043331:CDS 50.0%
GTGCAACGATAACCACGATG+AGG - chr2.2:10465918-10465937 MS.gene043331:CDS 50.0%
TCAACGAAGAGAGGTGGATG+AGG - chr2.2:10466139-10466158 MS.gene043331:CDS 50.0%
TCGTTGTGTGATAGATGCGC+CGG - chr2.2:10465658-10465677 MS.gene043331:intron 50.0%
TTCTTCCGGTAGCGATGAGT+CGG - chr2.2:10465882-10465901 MS.gene043331:CDS 50.0%
! CACCGATTACGATTCCGATG+AGG - chr2.2:10465774-10465793 MS.gene043331:CDS 50.0%
! CCAACATAAGCTAGCCTGGT+CGG + chr2.2:10465512-10465531 None:intergenic 50.0%
! GGTCCACGCTGCTAACTTTT+TGG - chr2.2:10465546-10465565 MS.gene043331:CDS 50.0%
! GTGATAATCAGGTTGTGCCG+TGG - chr2.2:10465824-10465843 MS.gene043331:CDS 50.0%
!! CGACCAGGCTAGCTTATGTT+GGG - chr2.2:10465510-10465529 MS.gene043331:CDS 50.0%
CGAAGAGAGGTGGATGAGGT+TGG - chr2.2:10466143-10466162 MS.gene043331:CDS 55.0%
CGATGAGGAAGATGAGGACG+AGG - chr2.2:10465789-10465808 MS.gene043331:CDS 55.0%
CGGCGGTATAGCGACGTAAA+TGG - chr2.2:10466209-10466228 MS.gene043331:CDS 55.0%
CGGTAGCGATGAGTCGGTTA+CGG - chr2.2:10465888-10465907 MS.gene043331:CDS 55.0%
CTACCGGAAGAACTCGAAGC+CGG + chr2.2:10465874-10465893 None:intergenic 55.0%
TGGTTTGATAGGGTGCGACG+AGG - chr2.2:10466163-10466182 MS.gene043331:CDS 55.0%
TGTGCCGTGGTCATCAACAG+CGG - chr2.2:10465837-10465856 MS.gene043331:CDS 55.0%
TTCTTCTTGTTGCTCGGCGC+TGG + chr2.2:10465725-10465744 None:intergenic 55.0%
TTGTGTGATAGATGCGCCGG+CGG - chr2.2:10465661-10465680 MS.gene043331:intron 55.0%
! CGTAACCGACTCATCGCTAC+CGG + chr2.2:10465890-10465909 None:intergenic 55.0%
!! CCGACCAGGCTAGCTTATGT+TGG - chr2.2:10465509-10465528 MS.gene043331:CDS 55.0%
CATGTCAATCTCCCACGCCG+TGG - chr2.2:10465602-10465621 MS.gene043331:intron 60.0%
CGACGAGGAACCGTCGTCAA+AGG - chr2.2:10466178-10466197 MS.gene043331:CDS 60.0%
CGAGGAACCGTCGTCAAAGG+CGG - chr2.2:10466181-10466200 MS.gene043331:CDS 60.0%
GAAGAACTCGAAGCCGGTGG+TGG + chr2.2:10465868-10465887 None:intergenic 60.0%
GCCAACGCTAACTCCAACGC+CGG - chr2.2:10465697-10465716 MS.gene043331:intron 60.0%
! AAAGCCTCCGGTGCTAGGCT+CGG - chr2.2:10465625-10465644 MS.gene043331:intron 60.0%
! ACCGGCGTTGGAGTTAGCGT+TGG + chr2.2:10465701-10465720 None:intergenic 60.0%
! CTAGCACCGGAGGCTTTCCA+CGG + chr2.2:10465622-10465641 None:intergenic 60.0%
! GGCGTGGAGTTTTCTTCCGC+CGG + chr2.2:10465680-10465699 None:intergenic 60.0%
!! CCACCGGCTTCGAGTTCTTC+CGG - chr2.2:10465868-10465887 MS.gene043331:CDS 60.0%
!! CGTTGGAGTTAGCGTTGGCG+TGG + chr2.2:10465696-10465715 None:intergenic 60.0%
!! TGCGCCGCTGTTGATGACCA+CGG + chr2.2:10465844-10465863 None:intergenic 60.0%
AACAGCGGCGCAACCACCAC+CGG - chr2.2:10465852-10465871 MS.gene043331:CDS 65.0%
CCGGAAGAACTCGAAGCCGG+TGG + chr2.2:10465871-10465890 None:intergenic 65.0%
CGCATCGCCGCCTTTGACGA+CGG + chr2.2:10466191-10466210 None:intergenic 65.0%
CGCGTTACCGAGCCTAGCAC+CGG + chr2.2:10465635-10465654 None:intergenic 65.0%
CGTCGTCAAAGGCGGCGATG+CGG - chr2.2:10466189-10466208 MS.gene043331:CDS 65.0%
CGTGGAAAGCCTCCGGTGCT+AGG - chr2.2:10465620-10465639 MS.gene043331:intron 65.0%
! GTTACCGAGCCTAGCACCGG+AGG + chr2.2:10465632-10465651 None:intergenic 65.0%
!! TTGTTGCTCGGCGCTGGCAC+CGG + chr2.2:10465719-10465738 None:intergenic 65.0%
ACCGGAGGCTTTCCACGGCG+TGG + chr2.2:10465617-10465636 None:intergenic 70.0%
CCCACGCCGTGGAAAGCCTC+CGG - chr2.2:10465613-10465632 MS.gene043331:intron 70.0%
CCGGAGGCTTTCCACGGCGT+GGG + chr2.2:10465616-10465635 None:intergenic 70.0%
CGTCAAAGGCGGCGATGCGG+CGG - chr2.2:10466192-10466211 MS.gene043331:CDS 70.0%
!!! CTCGGCGCTGGCACCGGCGT+TGG + chr2.2:10465713-10465732 None:intergenic 80.0%


Chromosome Type Strat End Strand Name
chr2.2 gene 10465457 10466259 10465457 ID=MS.gene043331
chr2.2 mRNA 10465457 10466259 10465457 ID=MS.gene043331.t1;Parent=MS.gene043331
chr2.2 exon 10465714 10466259 10465714 ID=MS.gene043331.t1.exon1;Parent=MS.gene043331.t1
chr2.2 CDS 10465714 10466259 10465714 ID=cds.MS.gene043331.t1;Parent=MS.gene043331.t1
chr2.2 exon 10465457 10465603 10465457 ID=MS.gene043331.t1.exon2;Parent=MS.gene043331.t1
chr2.2 CDS 10465457 10465603 10465457 ID=cds.MS.gene043331.t1;Parent=MS.gene043331.t1
Gene Sequence

>MS.gene043331

ATGAAAAAGAACTGCGAACTCTGCAAGCTTCCAGCTAGAACTTTCTGTGAGTCCGACCAGGCTAGCTTATGTTGGGACTGCGATTCTAAGGTCCACGCTGCTAACTTTTTGGTTGAGAGACACATGAGAACTCTCCTCTGTCACGCATGTCAATCTCCCACGCCGTGGAAAGCCTCCGGTGCTAGGCTCGGTAACGCGCTTTCGTTGTGTGATAGATGCGCCGGCGGAAGAAAACTCCACGCCAACGCTAACTCCAACGCCGGTGCCAGCGCCGAGCAACAAGAAGAAAGTGAAGGTGACAATGACAATGAAGAAGACACCGATTACGATTCCGATGAGGAAGATGAGGACGAGGATGAAGAAGATGGTGATAATCAGGTTGTGCCGTGGTCATCAACAGCGGCGCAACCACCACCGGCTTCGAGTTCTTCCGGTAGCGATGAGTCGGTTACGGTTAGCAAGTGCAACGATAACCACGATGAGGTTATTTCTAAGTTAGTTACAACGATTTCTTTGAAACGACGTCGTTTAGATCATGATTTTCAGGTAGTTAATTATTATTTTCTGTTGTAAATTAAATTACTTATTTTCTTCTGCATCTGAGTTTTCAATTTTTTCATTATTCTTTTGTTAATTTTTGTTGATTTTGTTTTCAGGTTACGGATTCAAAAAATTGGAAAAATCAACGAAGAGAGGTGGATGAGGTTGGTTTGATAGGGTGCGACGAGGAACCGTCGTCAAAGGCGGCGATGCGGCGGTATAGCGACGTAAATGGAACGGAGCATTCTCAGCCACACGATTGA
Protein sequence

>MS.gene043331.t1

MKKNCELCKLPARTFCESDQASLCWDCDSKVHAANFLVERHMRTLLCHACQSPTPWKASGARLGNALSLCDRCAGGRKLHANANSNAGASAEQQEESEGDNDNEEDTDYDSDEEDEDEDEEDGDNQVVPWSSTAAQPPPASSSSGSDESVTVSKCNDNHDEVISKLVTTISLKRRRLDHDFQVTDSKNWKNQRREVDEVGLIGCDEEPSSKAAMRRYSDVNGTEHSQPHD