AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene059622

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene059622.t1 MTR_6g087770 93.617 47 3 0 1 47 1 47 2.56e-27 94.0
MS.gene059622.t1 MTR_2g101850 72.340 47 13 0 1 47 1 47 9.20e-21 77.4
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene059622.t1 AT1G52245 74.468 47 12 0 1 47 1 47 2.96e-21 78.6
MS.gene059622.t1 AT3G16120 70.213 47 14 0 1 47 1 47 3.24e-17 68.6
MS.gene059622.t1 AT3G16120 70.213 47 14 0 1 47 1 47 3.24e-17 68.6

Find 8 sgRNAs with CRISPR-Local

Find 52 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TGTGATTGTAGATCAATTGC+TGG 0.453871 6.2:+87527506 MS.gene059622:CDS
CTAAAGATGTTGGAAGGAAA+AGG 0.470654 6.2:+87527398 None:intergenic
GCTTGAATTTGCATCTTCAA+AGG 0.513495 6.2:-87527443 None:intergenic
AAGCAACTAAAGATGTTGGA+AGG 0.603964 6.2:+87527392 None:intergenic
AATTGCTGGTAATATCAAGA+AGG 0.615321 6.2:+87527520 MS.gene059622:CDS
GTTGGAAGGAAAAGGTGTGG+TGG 0.639264 6.2:+87527406 MS.gene059622:CDS
AGCTTGAGAAGCAAATGACA+TGG 0.664039 6.2:-87527465 None:intergenic
GATGTTGGAAGGAAAAGGTG+TGG 0.753253 6.2:+87527403 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! CAATAAAAATAAAAATTTTG+GGG + chr6.2:87528163-87528182 MS.gene059622:intron 10.0%
!!! GTCAATAAAAATAAAAATTT+TGG + chr6.2:87528161-87528180 MS.gene059622:intron 10.0%
!! CTAAACAAATTATTTGTATT+TGG - chr6.2:87527776-87527795 None:intergenic 15.0%
!! GTAGCTAAAAAAATATTATT+GGG + chr6.2:87528109-87528128 MS.gene059622:intron 15.0%
!! TAATTATTTGCAAATGAATT+TGG + chr6.2:87528081-87528100 MS.gene059622:intron 15.0%
!! TAGCTAAAAAAATATTATTG+GGG + chr6.2:87528110-87528129 MS.gene059622:intron 15.0%
!! TGAAAATATTAGAATGAATT+TGG - chr6.2:87527625-87527644 None:intergenic 15.0%
!!! CAAATACAAATAATTTGTTT+AGG + chr6.2:87527774-87527793 MS.gene059622:intron 15.0%
!!! TTTATTTTTATTGACTCATT+AGG - chr6.2:87528156-87528175 None:intergenic 15.0%
!! AATGTACAATTAGTATAAAC+AGG - chr6.2:87527709-87527728 None:intergenic 20.0%
!! GGTAGCTAAAAAAATATTAT+TGG + chr6.2:87528108-87528127 MS.gene059622:intron 20.0%
!!! GAAAATCACTCAATTTTTTT+GGG - chr6.2:87527586-87527605 None:intergenic 20.0%
! AAATTGTGTTGTGAGTAAAT+AGG - chr6.2:87528293-87528312 None:intergenic 25.0%
! ACTAATTGTACATTTCTTTG+TGG + chr6.2:87527715-87527734 MS.gene059622:intron 25.0%
! TGAATTTGGATTTATGAGAT+TGG - chr6.2:87527611-87527630 None:intergenic 25.0%
! TTTCTATTCAATAAAGCAAG+AGG + chr6.2:87528409-87528428 MS.gene059622:intron 25.0%
!!! GGAAAATCACTCAATTTTTT+TGG - chr6.2:87527587-87527606 None:intergenic 25.0%
!!! TTTTTTCAACGTAGACAAAT+AGG + chr6.2:87527903-87527922 MS.gene059622:intron 25.0%
AATTGCTGGTAATATCAAGA+AGG + chr6.2:87527520-87527539 MS.gene059622:CDS 30.0%
ATTTGGATTTATGAGATTGG+TGG - chr6.2:87527608-87527627 None:intergenic 30.0%
GAATATTACGAAGATTCTTG+AGG - chr6.2:87528240-87528259 None:intergenic 30.0%
TTTGCAAATGAATTTGGTTG+AGG + chr6.2:87528087-87528106 MS.gene059622:intron 30.0%
! AAGCTAGAGAAATTTTTACG+AGG + chr6.2:87527747-87527766 MS.gene059622:intron 30.0%
! ACAATCCTTTGTTTCTCATA+TGG + chr6.2:87528318-87528337 MS.gene059622:intron 30.0%
! AGCTAGAGAAATTTTTACGA+GGG + chr6.2:87527748-87527767 MS.gene059622:intron 30.0%
! CAATCCTTTGTTTCTCATAT+GGG + chr6.2:87528319-87528338 MS.gene059622:intron 30.0%
ATAACGAATAGAATGACCAG+AGG - chr6.2:87528352-87528371 None:intergenic 35.0%
CCATGGATACAAAAGTTTGT+TGG - chr6.2:87527682-87527701 None:intergenic 35.0%
GCTTGAATTTGCATCTTCAA+AGG - chr6.2:87527446-87527465 None:intergenic 35.0%
GTAACCCATATGAGAAACAA+AGG - chr6.2:87528326-87528345 None:intergenic 35.0%
TAGTATAAACAGGAGATCCA+TGG - chr6.2:87527699-87527718 None:intergenic 35.0%
TGTGATTGTAGATCAATTGC+TGG + chr6.2:87527506-87527525 MS.gene059622:CDS 35.0%
! CCAACAAACTTTTGTATCCA+TGG + chr6.2:87527679-87527698 MS.gene059622:intron 35.0%
! CTAGAGAAATTTTTACGAGG+GGG + chr6.2:87527750-87527769 MS.gene059622:intron 35.0%
! GCTAGAGAAATTTTTACGAG+GGG + chr6.2:87527749-87527768 MS.gene059622:intron 35.0%
AGCTTGAGAAGCAAATGACA+TGG - chr6.2:87527468-87527487 None:intergenic 40.0%
GTACATTTCTTTGTGGACAG+CGG + chr6.2:87527722-87527741 MS.gene059622:intron 40.0%
! TCATATGGGTTACAAACCTC+TGG + chr6.2:87528333-87528352 MS.gene059622:intron 40.0%
AAGCTACCCCATCCTTTCAA+AGG + chr6.2:87528192-87528211 MS.gene059622:intron 45.0%
AGCTACCCCATCCTTTCAAA+GGG + chr6.2:87528193-87528212 MS.gene059622:intron 45.0%
TGTTGGAATCTCAGCGAGTT+CGG - chr6.2:87527665-87527684 None:intergenic 45.0%
TTGAAAGGATGGGGTAGCTT+TGG - chr6.2:87528192-87528211 None:intergenic 45.0%
! CGATTCCCTTTGAAAGGATG+GGG - chr6.2:87528201-87528220 None:intergenic 45.0%
! GCGATTCCCTTTGAAAGGAT+GGG - chr6.2:87528202-87528221 None:intergenic 45.0%
! TCTTGAGGTGTCCACAAACA+GGG - chr6.2:87528225-87528244 None:intergenic 45.0%
! TTCTTGAGGTGTCCACAAAC+AGG - chr6.2:87528226-87528245 None:intergenic 45.0%
!!! TCAATAAAAATAAAAATTTT+GGG + chr6.2:87528162-87528181 MS.gene059622:intron 5.0%
! CTTGAGGTGTCCACAAACAG+GGG - chr6.2:87528224-87528243 None:intergenic 50.0%
! GGCGATTCCCTTTGAAAGGA+TGG - chr6.2:87528203-87528222 None:intergenic 50.0%
! GTTGGAAGGAAAAGGTGTGG+TGG + chr6.2:87527406-87527425 MS.gene059622:CDS 50.0%
AAGGGAATCGCCCCTGTTTG+TGG + chr6.2:87528211-87528230 MS.gene059622:intron 55.0%
CAGGGGCGATTCCCTTTGAA+AGG - chr6.2:87528207-87528226 None:intergenic 55.0%


Chromosome Type Strat End Strand Name
chr6.2 gene 87527404 87528442 87527404 ID=MS.gene059622
chr6.2 mRNA 87527404 87528442 87527404 ID=MS.gene059622.t1;Parent=MS.gene059622
chr6.2 exon 87527404 87527541 87527404 ID=MS.gene059622.t1.exon1;Parent=MS.gene059622.t1
chr6.2 CDS 87527404 87527541 87527404 ID=cds.MS.gene059622.t1;Parent=MS.gene059622.t1
chr6.2 exon 87528425 87528442 87528425 ID=MS.gene059622.t1.exon2;Parent=MS.gene059622.t1
chr6.2 CDS 87528425 87528442 87528425 ID=cds.MS.gene059622.t1;Parent=MS.gene059622.t1
Gene Sequence

>MS.gene059622

ATGTTGGAAGGAAAAGGTGTGGTGGAAGAAACAGATATGCCTTTGAAGATGCAAATTCAAGCCATGTCATTTGCTTCTCAAGCTCTTGATCTCTATGATGTTTGTGATTGTAGATCAATTGCTGGTAATATCAAGAAGGTACATTACTTTTAACACTTGTGAAAATTTTACTCTATATACCCAAAAAAATTGAGTGATTTTCCACCAATCTCATAAATCCAAATTCATTCTAATATTTTCAAGAAACAAAACTCTTATCCGAACTCGCTGAGATTCCAACAAACTTTTGTATCCATGGATCTCCTGTTTATACTAATTGTACATTTCTTTGTGGACAGCGGCGAAGCTAGAGAAATTTTTACGAGGGGGCCAAATACAAATAATTTGTTTAGGTAAAAAAAAACTTATATATTTTAAAATATTATATATTAAATTTAAAAGTTAAGTATGTTTAATCTCTAACTTTTTTTTTCAACGTATCTTTCTAAAAGAATTTTTTTTTTTTCAACGTAGACAAATAGGTTATTTGCATGAAATTATCGTCTATTATGTTTGACTATTGATAGTTTTTATTGCTAAAAATGCTTTCTTTATAGTTGTTGTAGAGAACGAAATGTCAAAATAAGACAAATAAGTTTATTAATCAAGTAATAATTTTTTAATCTTTTAATTTATGCTAATTATTTGCAAATGAATTTGGTTGAGGTAGCTAAAAAAATATTATTGGGGTAGCTAGCTATATTAATATACCTAATGAGTCAATAAAAATAAAAATTTTGGGGTAGCCAAAGCTACCCCATCCTTTCAAAGGGAATCGCCCCTGTTTGTGGACACCTCAAGAATCTTCGTAATATTCGTGCTAATCTTCTTACGTGCTTGATGAAATCCTATTTACTCACAACACAATTTATATCACAATCCTTTGTTTCTCATATGGGTTACAAACCTCTGGTCATTCTATTCGTTATTTATGCTATACAAGCTTAGCATGCATAATATTGATATTTTCTATTCAATAAAGCAAGAGGTGTTTAACTAA
Protein sequence

>MS.gene059622.t1

MLEGKGVVEETDMPLKMQIQAMSFASQALDLYDVCDCRSIAGNIKKQEVFN