AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene36239

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene36239.t1 MTR_2g103290 88.398 181 18 1 1 178 1 181 7.19e-111 313
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 31 sgRNAs with CRISPR-Local

Find 88 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GCTGAGTCTTAATCCTCATA+TGG 0.366307 2.1:+2500649 None:intergenic
TCTGCTGCTGCTACAACTAA+TGG 0.397952 2.1:-2499237 MS.gene36239:CDS
GCCATGTGCATAGTTGCATT+GGG 0.419796 2.1:+2500584 None:intergenic
TGAACATAATGAAGAGGTAG+AGG 0.427658 2.1:+2500456 None:intergenic
AACGACCTCAGAACAGCAAC+AGG 0.451715 2.1:-2500558 MS.gene36239:CDS
AAAATTCACAAACCCATATG+AGG 0.470113 2.1:-2500662 MS.gene36239:CDS
TCATTCGTCTCTATGCTGAT+TGG 0.477473 2.1:-2499059 MS.gene36239:CDS
ACTACCTCTTTACATAAGAA+TGG 0.478765 2.1:-2499129 MS.gene36239:CDS
ATGAACATTCTACAGAATCT+TGG 0.480970 2.1:+2500534 None:intergenic
AGCCATGTGCATAGTTGCAT+TGG 0.488645 2.1:+2500583 None:intergenic
CTGAGTCTTAATCCTCATAT+GGG 0.496970 2.1:+2500650 None:intergenic
CATAAGAATGGACCGTATGC+TGG 0.500563 2.1:-2499117 MS.gene36239:CDS
CGGTCCATTCTTATGTAAAG+AGG 0.523765 2.1:+2499125 None:intergenic
ACATAATGAAGAGGTAGAGG+AGG 0.543147 2.1:+2500459 None:intergenic
GTAGAGGAGGAGTTGCATGA+AGG 0.548027 2.1:+2500472 None:intergenic
TGATACAAAATGCAGAATGC+AGG 0.549025 2.1:-2499272 MS.gene36239:CDS
TCATCCTCAGCAGCAGCAGC+AGG 0.553542 2.1:-2500436 MS.gene36239:CDS
TTGGTCCTGTTGCTGTTCTG+AGG 0.555812 2.1:+2500553 None:intergenic
ATGGCTGAGGTATTTGTAGC+AGG 0.556435 2.1:+2499162 None:intergenic
CCCCAATGCAACTATGCACA+TGG 0.558064 2.1:-2500585 MS.gene36239:CDS
GTGTCCGTAGCTACAATGTC+TGG 0.558270 2.1:+2500506 None:intergenic
AGAGGTAGTTGCCGCTGTGA+TGG 0.562973 2.1:+2499143 None:intergenic
CACACCAGACATTGTAGCTA+CGG 0.572650 2.1:-2500510 MS.gene36239:CDS
TTGCATTGGGGTGCAAGAAG+AGG 0.573320 2.1:+2500597 None:intergenic
GATAGGGATTTACCAGCATA+CGG 0.594337 2.1:+2499105 None:intergenic
AGTTGCCGCTGTGATGGCTG+AGG 0.641938 2.1:+2499149 None:intergenic
TGAGGATGAACATAATGAAG+AGG 0.648497 2.1:+2500450 None:intergenic
CCATGTGCATAGTTGCATTG+GGG 0.656451 2.1:+2500585 None:intergenic
CTATGCAAAAGATTCATGCA+AGG 0.677580 2.1:-2500627 MS.gene36239:CDS
AGTTTGTGAATGCAGAACCA+GGG 0.757579 2.1:-2499296 MS.gene36239:intron
AAATACCTCAGCCATCACAG+CGG 0.800744 2.1:-2499154 MS.gene36239:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AATAAGCTAAAAACAATTTA+TGG + chr2.1:2500161-2500180 None:intergenic 15.0%
!! TTAATTAATAAGTAATGTCT+CGG - chr2.1:2499810-2499829 MS.gene36239:intron 15.0%
!! ACATAAACACTTATATGATA+TGG - chr2.1:2500276-2500295 MS.gene36239:intron 20.0%
!! TCTTAGTATTAGAACAAAAA+GGG - chr2.1:2499403-2499422 MS.gene36239:intron 20.0%
!! TTCTTAGTATTAGAACAAAA+AGG - chr2.1:2499402-2499421 MS.gene36239:intron 20.0%
!!! TTTATAGGTTTTATGTAATC+TGG - chr2.1:2499548-2499567 MS.gene36239:intron 20.0%
! AAACAACAAACACATAATGT+TGG - chr2.1:2499763-2499782 MS.gene36239:intron 25.0%
! AATAGAATATAGAACTGTGT+TGG - chr2.1:2500390-2500409 MS.gene36239:intron 25.0%
! AGTAGAAAATTGTCAAATAG+CGG + chr2.1:2500051-2500070 None:intergenic 25.0%
! TAAATGGAAAAAATGTGCAT+CGG - chr2.1:2499845-2499864 MS.gene36239:intron 25.0%
! TAATTAAGCAACCTCATAAT+CGG + chr2.1:2499797-2499816 None:intergenic 25.0%
!! CAATTTTCTACTAAATATCG+TGG - chr2.1:2500059-2500078 MS.gene36239:intron 25.0%
AAAATTCACAAACCCATATG+AGG - chr2.1:2499069-2499088 MS.gene36239:CDS 30.0%
ACTACCTCTTTACATAAGAA+TGG - chr2.1:2500602-2500621 MS.gene36239:CDS 30.0%
AGAAGTTGAAGAAAAATACG+TGG + chr2.1:2499338-2499357 None:intergenic 30.0%
AGCTTTCATGGAAATCATAT+TGG + chr2.1:2500359-2500378 None:intergenic 30.0%
ATGAACATTCTACAGAATCT+TGG + chr2.1:2499200-2499219 None:intergenic 30.0%
TGAATCACAAAAAGCTTTCA+TGG + chr2.1:2500371-2500390 None:intergenic 30.0%
TGACAAAAACACAATGCAAA+GGG - chr2.1:2500649-2500668 MS.gene36239:CDS 30.0%
!! ACTACACTAACACTACTTTT+TGG - chr2.1:2499365-2499384 MS.gene36239:intron 30.0%
!! CATTGTGTTTTTGTCAGATA+GGG + chr2.1:2500645-2500664 None:intergenic 30.0%
AAATAGACCCTAACTCATAG+GGG + chr2.1:2499881-2499900 None:intergenic 35.0%
ATCATATTGGACCTGGAATA+AGG + chr2.1:2500346-2500365 None:intergenic 35.0%
ATTAAGCTGTTTACCCAAAC+AGG - chr2.1:2500319-2500338 MS.gene36239:intron 35.0%
CAAATAGACCCTAACTCATA+GGG + chr2.1:2499882-2499901 None:intergenic 35.0%
CTATGCAAAAGATTCATGCA+AGG - chr2.1:2499104-2499123 MS.gene36239:CDS 35.0%
CTGACAAAAACACAATGCAA+AGG - chr2.1:2500648-2500667 MS.gene36239:CDS 35.0%
CTGAGTCTTAATCCTCATAT+GGG + chr2.1:2499084-2499103 None:intergenic 35.0%
GACTTCAGTTTATCTTTCGT+TGG - chr2.1:2500240-2500259 MS.gene36239:intron 35.0%
GCTGTTTGTATAAGCTATCA+TGG + chr2.1:2500196-2500215 None:intergenic 35.0%
TCAAATAGACCCTAACTCAT+AGG + chr2.1:2499883-2499902 None:intergenic 35.0%
TGAACATAATGAAGAGGTAG+AGG + chr2.1:2499278-2499297 None:intergenic 35.0%
TGAAGAAAAATACGTGGTTG+TGG + chr2.1:2499332-2499351 None:intergenic 35.0%
TGAGGATGAACATAATGAAG+AGG + chr2.1:2499284-2499303 None:intergenic 35.0%
TGATACAAAATGCAGAATGC+AGG - chr2.1:2500459-2500478 MS.gene36239:CDS 35.0%
! ATGCTCTCAATTTTGAATCG+CGG - chr2.1:2499979-2499998 MS.gene36239:intron 35.0%
! CAATTTTGAATCGCGGAAAT+TGG - chr2.1:2499986-2500005 MS.gene36239:intron 35.0%
! TCGGATTCGAGTCTTATAAA+TGG - chr2.1:2499829-2499848 MS.gene36239:intron 35.0%
! TGTTTGTGTTGGTGCTTTAT+AGG - chr2.1:2499533-2499552 MS.gene36239:intron 35.0%
!! GCATTGTGTTTTTGTCAGAT+AGG + chr2.1:2500646-2500665 None:intergenic 35.0%
ACATAATGAAGAGGTAGAGG+AGG + chr2.1:2499275-2499294 None:intergenic 40.0%
AGTTTGTGAATGCAGAACCA+GGG - chr2.1:2500435-2500454 MS.gene36239:CDS 40.0%
CACATTTGTCAGTGTTGTGT+TGG + chr2.1:2499486-2499505 None:intergenic 40.0%
CATGGAAATCATATTGGACC+TGG + chr2.1:2500353-2500372 None:intergenic 40.0%
CGGTCCATTCTTATGTAAAG+AGG + chr2.1:2500609-2500628 None:intergenic 40.0%
GATAGGGATTTACCAGCATA+CGG + chr2.1:2500629-2500648 None:intergenic 40.0%
GCTGAGTCTTAATCCTCATA+TGG + chr2.1:2499085-2499104 None:intergenic 40.0%
GCTTAATCAGTTATGGCATG+TGG - chr2.1:2499698-2499717 MS.gene36239:intron 40.0%
TCATTCGTCTCTATGCTGAT+TGG - chr2.1:2500672-2500691 MS.gene36239:CDS 40.0%
TGTGGTGAATTTAGCTAGGA+TGG - chr2.1:2499716-2499735 MS.gene36239:intron 40.0%
! ATGATTTGCCCCTATGAGTT+AGG - chr2.1:2499870-2499889 MS.gene36239:intron 40.0%
! GCAGCTTGCTTAATCAGTTA+TGG - chr2.1:2499691-2499710 MS.gene36239:intron 40.0%
! TAAAGCACCAACACAAACAC+CGG + chr2.1:2499532-2499551 None:intergenic 40.0%
! TCTGCATTTTGTATCATCCC+TGG + chr2.1:2500455-2500474 None:intergenic 40.0%
! TGATTTGCCCCTATGAGTTA+GGG - chr2.1:2499871-2499890 MS.gene36239:intron 40.0%
! TTTTGAATCGCGGAAATTGG+CGG - chr2.1:2499989-2500008 MS.gene36239:intron 40.0%
!!! TGTTGTTTTGTGCAGAAGAG+TGG + chr2.1:2500520-2500539 None:intergenic 40.0%
AAATACCTCAGCCATCACAG+CGG - chr2.1:2500577-2500596 MS.gene36239:CDS 45.0%
ACCTGGAATAAGGTCCTGTT+TGG + chr2.1:2500336-2500355 None:intergenic 45.0%
AGCCATGTGCATAGTTGCAT+TGG + chr2.1:2499151-2499170 None:intergenic 45.0%
ATAGTGTCACCATAGCGTAG+TGG + chr2.1:2500105-2500124 None:intergenic 45.0%
CACACCAGACATTGTAGCTA+CGG - chr2.1:2499221-2499240 MS.gene36239:CDS 45.0%
CATAAGAATGGACCGTATGC+TGG - chr2.1:2500614-2500633 MS.gene36239:CDS 45.0%
CATTCGATCAGTGTTGTGTC+CGG - chr2.1:2499510-2499529 MS.gene36239:intron 45.0%
CCATGTGCATAGTTGCATTG+GGG + chr2.1:2499149-2499168 None:intergenic 45.0%
CCTGGAATAAGGTCCTGTTT+GGG + chr2.1:2500335-2500354 None:intergenic 45.0%
GAGTTTGTGAATGCAGAACC+AGG - chr2.1:2500434-2500453 MS.gene36239:CDS 45.0%
GCCATGTGCATAGTTGCATT+GGG + chr2.1:2499150-2499169 None:intergenic 45.0%
GGCATGTGGTGAATTTAGCT+AGG - chr2.1:2499712-2499731 MS.gene36239:intron 45.0%
GTTCGAATTCCACTACGCTA+TGG - chr2.1:2500093-2500112 MS.gene36239:intron 45.0%
TCTGCTGCTGCTACAACTAA+TGG - chr2.1:2500494-2500513 MS.gene36239:CDS 45.0%
! ATGGCTGAGGTATTTGTAGC+AGG + chr2.1:2500572-2500591 None:intergenic 45.0%
! TGGTTCTTCTGCCGATTATG+AGG - chr2.1:2499783-2499802 MS.gene36239:intron 45.0%
!!! TTTTGTTATTAAAATAAAAT+GGG - chr2.1:2499601-2499620 MS.gene36239:intron 5.0%
!!! TTTTTGTTATTAAAATAAAA+TGG - chr2.1:2499600-2499619 MS.gene36239:intron 5.0%
AACGACCTCAGAACAGCAAC+AGG - chr2.1:2499173-2499192 MS.gene36239:CDS 50.0%
CCCAAACAGGACCTTATTCC+AGG - chr2.1:2500332-2500351 MS.gene36239:intron 50.0%
CCCCAATGCAACTATGCACA+TGG - chr2.1:2499146-2499165 MS.gene36239:CDS 50.0%
GTAGAGGAGGAGTTGCATGA+AGG + chr2.1:2499262-2499281 None:intergenic 50.0%
GTGTCCGTAGCTACAATGTC+TGG + chr2.1:2499228-2499247 None:intergenic 50.0%
GTTGTGTCCGGTGTTTGTGT+TGG - chr2.1:2499522-2499541 MS.gene36239:intron 50.0%
TAGCGGCGCTGTAGCATTAT+AGG + chr2.1:2500034-2500053 None:intergenic 50.0%
TTGCATTGGGGTGCAAGAAG+AGG + chr2.1:2499137-2499156 None:intergenic 50.0%
! TTGGTCCTGTTGCTGTTCTG+AGG + chr2.1:2499181-2499200 None:intergenic 50.0%
AGAGGTAGTTGCCGCTGTGA+TGG + chr2.1:2500591-2500610 None:intergenic 55.0%
AGTTGCCGCTGTGATGGCTG+AGG + chr2.1:2500585-2500604 None:intergenic 60.0%
TCATCCTCAGCAGCAGCAGC+AGG - chr2.1:2499295-2499314 MS.gene36239:intron 60.0%
TTCTCCTGCTGCTGCTGCTG+AGG + chr2.1:2499302-2499321 None:intergenic 60.0%


Chromosome Type Strat End Strand Name
chr2.1 gene 2499053 2500700 2499053 ID=MS.gene36239
chr2.1 mRNA 2499053 2500700 2499053 ID=MS.gene36239.t1;Parent=MS.gene36239
chr2.1 exon 2500415 2500700 2500415 ID=MS.gene36239.t1.exon1;Parent=MS.gene36239.t1
chr2.1 CDS 2500415 2500700 2500415 ID=cds.MS.gene36239.t1;Parent=MS.gene36239.t1
chr2.1 exon 2499053 2499303 2499053 ID=MS.gene36239.t1.exon2;Parent=MS.gene36239.t1
chr2.1 CDS 2499053 2499303 2499053 ID=cds.MS.gene36239.t1;Parent=MS.gene36239.t1
Gene Sequence

>MS.gene36239

ATGGATTCAGAAGCTGAAAATTCACAAACCCATATGAGGATTAAGACTCAGCTATGCAAAAGATTCATGCAAGGAACGTGTCCTCTTCTTGCACCCCAATGCAACTATGCACATGGCTACAACGACCTCAGAACAGCAACAGGACCAAGATTCTGTAGAATGTTCATGCACACCAGACATTGTAGCTACGGACACAACTGTCGTTTCCTTCATGCAACTCCTCCTCTACCTCTTCATTATGTTCATCCTCAGCAGCAGCAGCAGGAGAACTTTTCTCCACAACCACGTATTTTTCTTCAACTTCTTTCATTTACTACACTAACACTACTTTTTGGTCTTGTTTGTTCATTTCTTAGTATTAGAACAAAAAGGGTTTTCTTTTCTGTAGCATCGACACATTTGATCAAAAGTGTGTTTGTCAGTTCTTAAACCAACACAACACTGACAAATGTGAATACATTCGATCAGTGTTGTGTCCGGTGTTTGTGTTGGTGCTTTATAGGTTTTATGTAATCTGGTGAATTTTGTGCTTGTTTAATAATTTTTTTTTTTGTTATTAAAATAAAATGGGTTTTTTATTTTTTTTCTAAACATTATTACTTGAACTGTGAAATTGTGTTATTGTATGATCTAGTTCTGCAGCTTGCTTAATCAGTTATGGCATGTGGTGAATTTAGCTAGGATGGCATACTGTTAAAATATTTCAATAAAAACAACAAACACATAATGTTGGTTCTTCTGCCGATTATGAGGTTGCTTAATTAATAAGTAATGTCTCGGATTCGAGTCTTATAAATGGAAAAAATGTGCATCGGAGATGATTTGCCCCTATGAGTTAGGGTCTATTTGAATTGACTTATTTGAGTTTATTTACTGACATAAAATATCGTGAGATTGTTTGTAAGAGTTTATGAAAACAAATTAAAATGCTCTCAATTTTGAATCGCGGAAATTGGCGGTCTGTTCAATTTCTGCTATCCTATAATGCTACAGCGCCGCTATTTGACAATTTTCTACTAAATATCGTGGAACAATAGTTTGTTCGAATTCCACTACGCTATGGTGACACTATAATTGCTATTTGACAACACTGTTTATGACATATCCATAAATTGTTTTTAGCTTATTTTTATAAGCTCTCCATGATAGCTTATACAAACAGCTTATAGTATATATGAAAACAACATGACTTCAGTTTATCTTTCGTTGGAAAAATAGTTTATACATAAACACTTATATGATATGGACTTATGCTATGAGTGTTTAATTAAGCTGTTTACCCAAACAGGACCTTATTCCAGGTCCAATATGATTTCCATGAAAGCTTTTTGTGATTCAATAGAATATAGAACTGTGTTGGTGTAAGTAAATTTTGACTTGAGAGTTTGTGAATGCAGAACCAGGGATGATACAAAATGCAGAATGCAGGATCATGCAAACTTCTGCTGCTGCTACAACTAATGGCCACTCTTCTGCACAAAACAACACAACGCAATTGCAAACTTATAGCTCTACTCCTGCTACAAATACCTCAGCCATCACAGCGGCAACTACCTCTTTACATAAGAATGGACCGTATGCTGGTAAATCCCTATCTGACAAAAACACAATGCAAAGGGTCATTCGTCTCTATGCTGATTGGATTTAA
Protein sequence

>MS.gene36239.t1

MDSEAENSQTHMRIKTQLCKRFMQGTCPLLAPQCNYAHGYNDLRTATGPRFCRMFMHTRHCSYGHNCRFLHATPPLPLHYVHPQQQQQENFSPQPQPGMIQNAECRIMQTSAAATTNGHSSAQNNTTQLQTYSSTPATNTSAITAATTSLHKNGPYAGKSLSDKNTMQRVIRLYADWI