AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene32999

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene32999.t1 MTR_1g016200 56.311 103 34 3 9 100 2 104 2.03e-24 90.1
MS.gene32999.t1 MTR_1g016170 62.500 48 15 1 56 100 187 234 4.86e-13 64.3
MS.gene32999.t1 MTR_7g112330 42.373 59 34 0 56 114 22 80 2.70e-11 57.0
MS.gene32999.t1 MTR_4g121110 48.276 58 25 2 54 111 28 80 5.24e-11 56.6
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene32999.t1 AT5G56860 49.231 65 29 1 25 89 203 263 6.23e-13 64.3
MS.gene32999.t1 AT4G26150 71.875 32 9 0 56 87 199 230 5.75e-11 58.5

Find 27 sgRNAs with CRISPR-Local

Find 40 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTCTTCTTTGTGGCTGGAAC+TGG 0.239072 1.1:-5933321 None:intergenic
AGTATTCGCCATTGCCCTTT+TGG 0.253039 1.1:-5933432 None:intergenic
ATGAGTATCAAGACCCTTAT+CGG 0.303482 1.1:-5933721 None:intergenic
ATACAAACACTACTCCTCTT+TGG 0.387924 1.1:+5933484 MS.gene32999:CDS
GGAAGAGGCAAAAGCCGATA+AGG 0.448770 1.1:+5933707 MS.gene32999:CDS
CAATCGAAACAAACCCTAGT+TGG 0.460017 1.1:-5933459 None:intergenic
TCTTGATACTCATAAGGAAA+AGG 0.465163 1.1:+5933731 MS.gene32999:CDS
TTGCCTCTTCCCTTCTTCGT+CGG 0.477939 1.1:-5933695 None:intergenic
CTTGATACTCATAAGGAAAA+GGG 0.489428 1.1:+5933732 MS.gene32999:CDS
TAAGGGTCTTGATACTCATA+AGG 0.492473 1.1:+5933725 MS.gene32999:CDS
ACTGAATACGAATACCCAAA+AGG 0.517161 1.1:+5933417 MS.gene32999:CDS
GAAGAGGCAAAAGCCGATAA+GGG 0.529120 1.1:+5933708 MS.gene32999:CDS
CTGAATACGAATACCCAAAA+GGG 0.529249 1.1:+5933418 MS.gene32999:CDS
ATGTGGACTCCGACGAAGAA+GGG 0.540307 1.1:+5933686 MS.gene32999:CDS
CTTTGGAGGAGTGATCCTAC+AGG 0.546346 1.1:+5933501 MS.gene32999:CDS
GGCGAATACTATATCCAACT+AGG 0.572160 1.1:+5933445 MS.gene32999:CDS
CATGTGGACTCCGACGAAGA+AGG 0.573346 1.1:+5933685 MS.gene32999:CDS
GAGTGATCCTACAGGTTCCA+AGG 0.583772 1.1:+5933509 MS.gene32999:CDS
ACTCCGACGAAGAAGGGAAG+AGG 0.589069 1.1:+5933692 MS.gene32999:CDS
CAAACACTACTCCTCTTTGG+AGG 0.592172 1.1:+5933487 MS.gene32999:CDS
GCGAATACTATATCCAACTA+GGG 0.606852 1.1:+5933446 MS.gene32999:CDS
CAGTCGTTGTGCAATGCATG+TGG 0.610062 1.1:+5933669 MS.gene32999:intron
ACGAATACCCAAAAGGGCAA+TGG 0.610371 1.1:+5933424 MS.gene32999:CDS
ACTCATAAGGAAAAGGGCAA+TGG 0.616678 1.1:+5933738 MS.gene32999:CDS
TGGCGAACGCTCATCATCTG+AGG 0.618644 1.1:+5933758 MS.gene32999:CDS
CTAATTACCTTGGAACCTGT+AGG 0.621221 1.1:-5933516 None:intergenic
GTAGGATCACTCCTCCAAAG+AGG 0.666474 1.1:-5933498 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ATAGTTAACAAGAAATATGT+TGG + chr1.1:5933644-5933663 MS.gene32999:intron 20.0%
!!! ACCAGTTTTTATTTTCTTTT+TGG - chr1.1:5933397-5933416 None:intergenic 20.0%
! GCCAAAAAGAAAATAAAAAC+TGG + chr1.1:5933393-5933412 MS.gene32999:CDS 25.0%
! TAGAGATTAACTAATTACCT+TGG - chr1.1:5933529-5933548 None:intergenic 25.0%
CTTGATACTCATAAGGAAAA+GGG + chr1.1:5933732-5933751 MS.gene32999:CDS 30.0%
TCTTGATACTCATAAGGAAA+AGG + chr1.1:5933731-5933750 MS.gene32999:CDS 30.0%
ACTGAATACGAATACCCAAA+AGG + chr1.1:5933417-5933436 MS.gene32999:CDS 35.0%
ATACAAACACTACTCCTCTT+TGG + chr1.1:5933484-5933503 MS.gene32999:CDS 35.0%
ATGAGTATCAAGACCCTTAT+CGG - chr1.1:5933724-5933743 None:intergenic 35.0%
CTGAATACGAATACCCAAAA+GGG + chr1.1:5933418-5933437 MS.gene32999:CDS 35.0%
GCGAATACTATATCCAACTA+GGG + chr1.1:5933446-5933465 MS.gene32999:CDS 35.0%
TAAGGGTCTTGATACTCATA+AGG + chr1.1:5933725-5933744 MS.gene32999:CDS 35.0%
!!! AGCAGCTTTTTTCTTCTTTG+TGG - chr1.1:5933334-5933353 None:intergenic 35.0%
ACTCATAAGGAAAAGGGCAA+TGG + chr1.1:5933738-5933757 MS.gene32999:CDS 40.0%
AGAAGAAAAAAGCTGCTGCT+AGG + chr1.1:5933337-5933356 MS.gene32999:CDS 40.0%
ATGAACCAAGAGTGAAAGCT+GGG - chr1.1:5933557-5933576 None:intergenic 40.0%
CAATCGAAACAAACCCTAGT+TGG - chr1.1:5933462-5933481 None:intergenic 40.0%
CTAATTACCTTGGAACCTGT+AGG - chr1.1:5933519-5933538 None:intergenic 40.0%
GAAGAAAAAAGCTGCTGCTA+GGG + chr1.1:5933338-5933357 MS.gene32999:CDS 40.0%
GGCGAATACTATATCCAACT+AGG + chr1.1:5933445-5933464 MS.gene32999:CDS 40.0%
!!! GCTTTTTTCTTCTTTGTGGC+TGG - chr1.1:5933330-5933349 None:intergenic 40.0%
ACGAATACCCAAAAGGGCAA+TGG + chr1.1:5933424-5933443 MS.gene32999:CDS 45.0%
CAAACACTACTCCTCTTTGG+AGG + chr1.1:5933487-5933506 MS.gene32999:CDS 45.0%
CATGAACCAAGAGTGAAAGC+TGG - chr1.1:5933558-5933577 None:intergenic 45.0%
GAAGAGGCAAAAGCCGATAA+GGG + chr1.1:5933708-5933727 MS.gene32999:CDS 45.0%
TGAACCAAGAGTGAAAGCTG+GGG - chr1.1:5933556-5933575 None:intergenic 45.0%
TTCTTCTTTGTGGCTGGAAC+TGG - chr1.1:5933324-5933343 None:intergenic 45.0%
! AGTATTCGCCATTGCCCTTT+TGG - chr1.1:5933435-5933454 None:intergenic 45.0%
! GTATTCGCCATTGCCCTTTT+GGG - chr1.1:5933434-5933453 None:intergenic 45.0%
ATGTGGACTCCGACGAAGAA+GGG + chr1.1:5933686-5933705 MS.gene32999:CDS 50.0%
CAGTCGTTGTGCAATGCATG+TGG + chr1.1:5933669-5933688 MS.gene32999:intron 50.0%
GAGTGATCCTACAGGTTCCA+AGG + chr1.1:5933509-5933528 MS.gene32999:CDS 50.0%
GGAAGAGGCAAAAGCCGATA+AGG + chr1.1:5933707-5933726 MS.gene32999:CDS 50.0%
GTAGGATCACTCCTCCAAAG+AGG - chr1.1:5933501-5933520 None:intergenic 50.0%
TTCTCCCCAGCTTTCACTCT+TGG + chr1.1:5933549-5933568 MS.gene32999:intron 50.0%
TTGCCTCTTCCCTTCTTCGT+CGG - chr1.1:5933698-5933717 None:intergenic 50.0%
! CTTTGGAGGAGTGATCCTAC+AGG + chr1.1:5933501-5933520 MS.gene32999:CDS 50.0%
ACTCCGACGAAGAAGGGAAG+AGG + chr1.1:5933692-5933711 MS.gene32999:CDS 55.0%
CATGTGGACTCCGACGAAGA+AGG + chr1.1:5933685-5933704 MS.gene32999:CDS 55.0%
TGGCGAACGCTCATCATCTG+AGG + chr1.1:5933758-5933777 MS.gene32999:CDS 55.0%


Chromosome Type Strat End Strand Name
chr1.1 gene 5933300 5933812 5933300 ID=MS.gene32999
chr1.1 mRNA 5933300 5933812 5933300 ID=MS.gene32999.t1;Parent=MS.gene32999
chr1.1 exon 5933300 5933530 5933300 ID=MS.gene32999.t1.exon1;Parent=MS.gene32999.t1
chr1.1 CDS 5933300 5933530 5933300 ID=cds.MS.gene32999.t1;Parent=MS.gene32999.t1
chr1.1 exon 5933672 5933812 5933672 ID=MS.gene32999.t1.exon2;Parent=MS.gene32999.t1
chr1.1 CDS 5933672 5933812 5933672 ID=cds.MS.gene32999.t1;Parent=MS.gene32999.t1
Gene Sequence

>MS.gene32999

ATGAGAGTAAGTAACGATGATCCAGTTCCAGCCACAAAGAAGAAAAAAGCTGCTGCTAGGGCTACAAAAAAGAAGAAAACAGCTGCTAGTGCTGCCAAAAAGAAAATAAAAACTGGTACTGAATACGAATACCCAAAAGGGCAATGGCGAATACTATATCCAACTAGGGTTTGTTTCGATTGCAATACAAACACTACTCCTCTTTGGAGGAGTGATCCTACAGGTTCCAAGGTAATTAGTTAATCTCTATTCTCCCCAGCTTTCACTCTTGGTTCATGCAAAAGTGTTATTCTATACTTATACAATGATTAATAATTTGAATATCTAGTTATATATATATATATATAGTTAACAAGAAATATGTTGGTGCAGTCGTTGTGCAATGCATGTGGACTCCGACGAAGAAGGGAAGAGGCAAAAGCCGATAAGGGTCTTGATACTCATAAGGAAAAGGGCAATGGCGAACGCTCATCATCTGAGGATGTGAAGATTAATGTTTTAATGTTCATCTGA
Protein sequence

>MS.gene32999.t1

MRVSNDDPVPATKKKKAAARATKKKKTAASAAKKKIKTGTEYEYPKGQWRILYPTRVCFDCNTNTTPLWRSDPTGSKSLCNACGLRRRREEAKADKGLDTHKEKGNGERSSSEDVKINVLMFI