AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene036817

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene036817.t1 MTR_4g113940 56.757 259 39 4 1 186 12 270 1.34e-89 264
MS.gene036817.t1 MTR_4g113890 58.952 229 40 4 1 185 12 230 4.39e-81 241
MS.gene036817.t1 MTR_4g113860 34.551 301 87 5 1 191 12 312 2.43e-47 157
MS.gene036817.t1 MTR_4g113970 38.017 242 57 6 1 150 12 252 2.81e-36 127
MS.gene036817.t1 MTR_3g050390 36.652 221 89 4 20 191 15 233 1.44e-34 122
MS.gene036817.t1 MTR_3g466460 57.627 59 22 1 138 193 46 104 3.54e-15 69.7
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene036817.t1 AT3G19360 30.153 262 74 7 36 189 116 376 5.63e-23 95.1
MS.gene036817.t1 AT3G19360 30.153 262 74 7 36 189 116 376 5.63e-23 95.1

Find 49 sgRNAs with CRISPR-Local

Find 86 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CCACCTAGCTTCTGCAAATT+TGG 0.182814 8.1:+12657373 None:intergenic
CCAAGTATACGCTTCTTCTT+AGG 0.280007 8.1:+12656652 None:intergenic
AGCCAGATCAATCGTATTTA+CGG 0.289560 8.1:-12656619 MS.gene036817:CDS
CTCTGGAAACACACCTCATT+TGG 0.330065 8.1:-12656565 MS.gene036817:CDS
AATTTACAGTTATCTCTATA+TGG 0.333739 8.1:+12657247 None:intergenic
TCAATCGTATTTACGGTGAT+TGG 0.347052 8.1:-12656612 MS.gene036817:CDS
CATACCGGATATTGTTCCTT+TGG 0.350886 8.1:-12657077 MS.gene036817:CDS
CCTAAGAAGAAGCGTATACT+TGG 0.373101 8.1:-12656652 MS.gene036817:CDS
TGAACAATAATGACTTCAAA+AGG 0.385432 8.1:-12657603 MS.gene036817:CDS
AGACTAAGCTGTGTCGCAAT+TGG 0.427484 8.1:-12657103 MS.gene036817:CDS
AGCAAGCAAGGGGCACTTAT+CGG 0.435970 8.1:-12657127 MS.gene036817:CDS
AGATTTGGTGCTTGTAGAAA+CGG 0.437088 8.1:-12657445 MS.gene036817:CDS
ACGGTGATTGGATTGATGAT+TGG 0.443878 8.1:-12656600 MS.gene036817:CDS
CAACGAAGATCAACTGCAGC+TGG 0.445811 8.1:-12657344 MS.gene036817:CDS
TCCTTGTTTATAGGCAGAGC+AGG 0.451853 8.1:-12656715 MS.gene036817:intron
CATTCCAAAGGAACAATATC+CGG 0.460353 8.1:+12657073 None:intergenic
CTAATAATTTGGAAGGCAGC+AGG 0.471854 8.1:-12657160 MS.gene036817:intron
AGCTTCTGCAAATTTGGTGG+TGG 0.473172 8.1:+12657379 None:intergenic
CACCGTAAATACGATTGATC+TGG 0.481235 8.1:+12656617 None:intergenic
GGGCTGTGAACAAGCAAGCA+AGG 0.482646 8.1:-12657139 MS.gene036817:CDS
ATGTACCCGACTTGTGGAAA+AGG 0.484051 8.1:-12656686 MS.gene036817:CDS
TGTGCAAGAAGTATTGCAAT+GGG 0.488339 8.1:-12657279 MS.gene036817:CDS
CTCTTTGCTCATGATGAAGA+AGG 0.508905 8.1:-12657044 MS.gene036817:intron
CCTAGCTTCTGCAAATTTGG+TGG 0.512657 8.1:+12657376 None:intergenic
GGCTGTGAACAAGCAAGCAA+GGG 0.513346 8.1:-12657138 MS.gene036817:CDS
TTCTGAATGTACCCGACTTG+TGG 0.526232 8.1:-12656692 MS.gene036817:CDS
TGCAGTTGATCTTCGTTGCA+CGG 0.530704 8.1:+12657349 None:intergenic
ATCATGGAGCTGAAGAGATA+AGG 0.532117 8.1:-12657405 MS.gene036817:CDS
AGGAGGGCATATCAATGCAT+TGG 0.539478 8.1:+12657564 None:intergenic
GAACAATAATGACTTCAAAA+GGG 0.552156 8.1:-12657602 MS.gene036817:CDS
TGTCGCAATTGGAAGCATAC+CGG 0.563682 8.1:-12657092 MS.gene036817:CDS
CTGTGCAAGAAGTATTGCAA+TGG 0.572239 8.1:-12657280 MS.gene036817:CDS
TGTTTCCAGAGCATAACAAA+AGG 0.581785 8.1:+12656577 None:intergenic
AATAATGACTTCAAAAGGGA+AGG 0.582018 8.1:-12657598 MS.gene036817:CDS
GAAGAATGCTTATCCAAATG+AGG 0.582982 8.1:+12656552 None:intergenic
TAATAATTTGGAAGGCAGCA+GGG 0.584634 8.1:-12657159 MS.gene036817:intron
CACATCAATGCATCAGAAGG+AGG 0.586467 8.1:+12657547 None:intergenic
TTGTTCAATGAAGTGAATTG+CGG 0.591801 8.1:+12657619 None:intergenic
AACGAAGATCAACTGCAGCT+GGG 0.593604 8.1:-12657343 MS.gene036817:CDS
CCACCAAATTTGCAGAAGCT+AGG 0.604649 8.1:-12657376 MS.gene036817:CDS
AAAGAGACAGTTCATTCCAA+AGG 0.613697 8.1:+12657061 None:intergenic
GGTCACATCAATGCATCAGA+AGG 0.614755 8.1:+12657544 None:intergenic
ACATCAATGCATCAGAAGGA+GGG 0.627126 8.1:+12657548 None:intergenic
CTAAGAAGAAGCGTATACTT+GGG 0.628540 8.1:-12656651 MS.gene036817:CDS
GCTGTGAACAAGCAAGCAAG+GGG 0.637136 8.1:-12657137 MS.gene036817:CDS
CCAAATTTGCAGAAGCTAGG+TGG 0.641093 8.1:-12657373 MS.gene036817:CDS
CAAGAAGTATTGCAATGGGG+AGG 0.655957 8.1:-12657275 MS.gene036817:CDS
TTCAATGAAGTGAATTGCGG+CGG 0.670436 8.1:+12657622 None:intergenic
GTGCAAGAAGTATTGCAATG+GGG 0.763140 8.1:-12657278 MS.gene036817:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAGATGAAAAAATCATACAA+AGG - chr8.1:12656880-12656899 MS.gene036817:intron 20.0%
!! AATTTACAGTTATCTCTATA+TGG + chr8.1:12656945-12656964 None:intergenic 20.0%
!!! CAATAACTCATTTTGATTAT+TGG - chr8.1:12657171-12657190 MS.gene036817:intron 20.0%
! AAAAATTGCAACTTTGATCA+TGG - chr8.1:12656768-12656787 MS.gene036817:intron 25.0%
! ACTTATCGGAACTAATAATT+TGG - chr8.1:12657018-12657037 MS.gene036817:intron 25.0%
! GAACAATAATGACTTCAAAA+GGG - chr8.1:12656587-12656606 MS.gene036817:CDS 25.0%
! TGAACAATAATGACTTCAAA+AGG - chr8.1:12656586-12656605 MS.gene036817:CDS 25.0%
!!! CTCATTTTGATTATTGGTTT+TGG - chr8.1:12657177-12657196 MS.gene036817:intron 25.0%
!!! TGTTTCATGTTTGATTTGAA+TGG - chr8.1:12657369-12657388 MS.gene036817:CDS 25.0%
AATAATGACTTCAAAAGGGA+AGG - chr8.1:12656591-12656610 MS.gene036817:CDS 30.0%
ATCGGAACTAATAATTTGGA+AGG - chr8.1:12657022-12657041 MS.gene036817:intron 30.0%
TAAGTACTCTCTTGATTTCA+AGG + chr8.1:12657003-12657022 None:intergenic 30.0%
TTGTTCAATGAAGTGAATTG+CGG + chr8.1:12656573-12656592 None:intergenic 30.0%
! ATGATTCCATCCTTGTTTAT+AGG - chr8.1:12657465-12657484 MS.gene036817:intron 30.0%
!! GAAATCAAGAGAGTACTTAT+CGG - chr8.1:12657004-12657023 MS.gene036817:intron 30.0%
AAAGAGACAGTTCATTCCAA+AGG + chr8.1:12657131-12657150 None:intergenic 35.0%
AGCCAGATCAATCGTATTTA+CGG - chr8.1:12657570-12657589 MS.gene036817:CDS 35.0%
ATTTGTACCGAGTTCAGATT+TGG - chr8.1:12656729-12656748 MS.gene036817:intron 35.0%
CATTCCAAAGGAACAATATC+CGG + chr8.1:12657119-12657138 None:intergenic 35.0%
TAATAATTTGGAAGGCAGCA+GGG - chr8.1:12657030-12657049 MS.gene036817:intron 35.0%
TCAATCGTATTTACGGTGAT+TGG - chr8.1:12657577-12657596 MS.gene036817:CDS 35.0%
TGCAAAAATGTTCCTTCCTA+AGG - chr8.1:12657430-12657449 MS.gene036817:CDS 35.0%
TGTTTCCAGAGCATAACAAA+AGG + chr8.1:12657615-12657634 None:intergenic 35.0%
! AGGAACATTTTTGCAAGACA+AGG + chr8.1:12657425-12657444 None:intergenic 35.0%
! ATTTTTGCAAGACAAGGCAA+AGG + chr8.1:12657419-12657438 None:intergenic 35.0%
! CTAAGAAGAAGCGTATACTT+GGG - chr8.1:12657538-12657557 MS.gene036817:intron 35.0%
! TCATTTTCCATCAGAACCTT+AGG + chr8.1:12657449-12657468 None:intergenic 35.0%
! TTTTTGCAAGACAAGGCAAA+GGG + chr8.1:12657418-12657437 None:intergenic 35.0%
!! AGATTTGGTGCTTGTAGAAA+CGG - chr8.1:12656744-12656763 MS.gene036817:intron 35.0%
!! TGATTTGTTTGATTGAGGCA+AGG + chr8.1:12656685-12656704 None:intergenic 35.0%
!! TGCTCTGATTTGTTTGATTG+AGG + chr8.1:12656690-12656709 None:intergenic 35.0%
!! TGTGCAAGAAGTATTGCAAT+GGG - chr8.1:12656910-12656929 MS.gene036817:intron 35.0%
ACAAGCACCAAATCTGAACT+CGG + chr8.1:12656739-12656758 None:intergenic 40.0%
ACATCAATGCATCAGAAGGA+GGG + chr8.1:12656644-12656663 None:intergenic 40.0%
ATCATGGAGCTGAAGAGATA+AGG - chr8.1:12656784-12656803 MS.gene036817:intron 40.0%
ATGAAGATCCTGCACAGTTT+AGG - chr8.1:12656970-12656989 MS.gene036817:intron 40.0%
CACCGTAAATACGATTGATC+TGG + chr8.1:12657575-12657594 None:intergenic 40.0%
CATACCGGATATTGTTCCTT+TGG - chr8.1:12657112-12657131 MS.gene036817:CDS 40.0%
CCAAGTATACGCTTCTTCTT+AGG + chr8.1:12657540-12657559 None:intergenic 40.0%
CTAATAATTTGGAAGGCAGC+AGG - chr8.1:12657029-12657048 MS.gene036817:intron 40.0%
CTCTTTGCTCATGATGAAGA+AGG - chr8.1:12657145-12657164 MS.gene036817:CDS 40.0%
TGAAGATCCTGCACAGTTTA+GGG - chr8.1:12656971-12656990 MS.gene036817:intron 40.0%
TTCAATGAAGTGAATTGCGG+CGG + chr8.1:12656570-12656589 None:intergenic 40.0%
TTTCCATCAGAACCTTAGGA+AGG + chr8.1:12657445-12657464 None:intergenic 40.0%
! ACGGTGATTGGATTGATGAT+TGG - chr8.1:12657589-12657608 MS.gene036817:CDS 40.0%
! CCTAAGAAGAAGCGTATACT+TGG - chr8.1:12657537-12657556 MS.gene036817:intron 40.0%
! CTTCTTCCTTTTCCACAAGT+CGG + chr8.1:12657512-12657531 None:intergenic 40.0%
! TTCTTCCTTTTCCACAAGTC+GGG + chr8.1:12657511-12657530 None:intergenic 40.0%
!! CTGTGCAAGAAGTATTGCAA+TGG - chr8.1:12656909-12656928 MS.gene036817:intron 40.0%
!! GTGCAAGAAGTATTGCAATG+GGG - chr8.1:12656911-12656930 MS.gene036817:intron 40.0%
!!! ATTGGCCTTTTGTTATGCTC+TGG - chr8.1:12657607-12657626 MS.gene036817:CDS 40.0%
AACGAAGATCAACTGCAGCT+GGG - chr8.1:12656846-12656865 MS.gene036817:intron 45.0%
AAGGCAAAGGGAAAACCAGT+AGG + chr8.1:12657406-12657425 None:intergenic 45.0%
ACCTGCTCTGCCTATAAACA+AGG + chr8.1:12657478-12657497 None:intergenic 45.0%
ACTGTGCAGGATCTTCATGA+AGG + chr8.1:12656968-12656987 None:intergenic 45.0%
AGACTAAGCTGTGTCGCAAT+TGG - chr8.1:12657086-12657105 MS.gene036817:CDS 45.0%
ATGGAAAATGCTCCTCCTAC+TGG - chr8.1:12657388-12657407 MS.gene036817:CDS 45.0%
CACATCAATGCATCAGAAGG+AGG + chr8.1:12656645-12656664 None:intergenic 45.0%
CCAAATTTGCAGAAGCTAGG+TGG - chr8.1:12656816-12656835 MS.gene036817:intron 45.0%
CCACCAAATTTGCAGAAGCT+AGG - chr8.1:12656813-12656832 MS.gene036817:intron 45.0%
CCACCTAGCTTCTGCAAATT+TGG + chr8.1:12656819-12656838 None:intergenic 45.0%
CCTAGCTTCTGCAAATTTGG+TGG + chr8.1:12656816-12656835 None:intergenic 45.0%
GAATCATCCCTAAACTGTGC+AGG + chr8.1:12656981-12657000 None:intergenic 45.0%
GCTCTGCCTATAAACAAGGA+TGG + chr8.1:12657474-12657493 None:intergenic 45.0%
GGTCACATCAATGCATCAGA+AGG + chr8.1:12656648-12656667 None:intergenic 45.0%
TGCAGTTGATCTTCGTTGCA+CGG + chr8.1:12656843-12656862 None:intergenic 45.0%
! AGCTTCTGCAAATTTGGTGG+TGG + chr8.1:12656813-12656832 None:intergenic 45.0%
! AGGAGGGCATATCAATGCAT+TGG + chr8.1:12656628-12656647 None:intergenic 45.0%
! ATGTACCCGACTTGTGGAAA+AGG - chr8.1:12657503-12657522 MS.gene036817:intron 45.0%
! CTCTGGAAACACACCTCATT+TGG - chr8.1:12657624-12657643 MS.gene036817:CDS 45.0%
! GTTCCTTCCTAAGGTTCTGA+TGG - chr8.1:12657439-12657458 MS.gene036817:CDS 45.0%
! TCCTTGTTTATAGGCAGAGC+AGG - chr8.1:12657474-12657493 MS.gene036817:intron 45.0%
! TGTCGCAATTGGAAGCATAC+CGG - chr8.1:12657097-12657116 MS.gene036817:CDS 45.0%
! TTCTGAATGTACCCGACTTG+TGG - chr8.1:12657497-12657516 MS.gene036817:intron 45.0%
!! CAAGAAGTATTGCAATGGGG+AGG - chr8.1:12656914-12656933 MS.gene036817:intron 45.0%
CAACGAAGATCAACTGCAGC+TGG - chr8.1:12656845-12656864 MS.gene036817:intron 50.0%
CATTGATGTGACCTCCTCCA+AGG - chr8.1:12656655-12656674 MS.gene036817:CDS 50.0%
GCAAAGGGAAAACCAGTAGG+AGG + chr8.1:12657403-12657422 None:intergenic 50.0%
GCTGTGAACAAGCAAGCAAG+GGG - chr8.1:12657052-12657071 MS.gene036817:CDS 50.0%
GGCTGTGAACAAGCAAGCAA+GGG - chr8.1:12657051-12657070 MS.gene036817:CDS 50.0%
!! AGCAAGCAAGGGGCACTTAT+CGG - chr8.1:12657062-12657081 MS.gene036817:CDS 50.0%
GATGTGACCTCCTCCAAGGA+TGG - chr8.1:12656659-12656678 MS.gene036817:CDS 55.0%
GATTGAGGCAAGGCCATCCT+TGG + chr8.1:12656675-12656694 None:intergenic 55.0%
GGGCTGTGAACAAGCAAGCA+AGG - chr8.1:12657050-12657069 MS.gene036817:CDS 55.0%
TGAGGCAAGGCCATCCTTGG+AGG + chr8.1:12656672-12656691 None:intergenic 60.0%
GGCAAGGCCATCCTTGGAGG+AGG + chr8.1:12656669-12656688 None:intergenic 65.0%


Chromosome Type Strat End Strand Name
chr8.1 gene 12656561 12657650 12656561 ID=MS.gene036817
chr8.1 mRNA 12656561 12657650 12656561 ID=MS.gene036817.t1;Parent=MS.gene036817
chr8.1 exon 12657550 12657650 12657550 ID=MS.gene036817.t1.exon1;Parent=MS.gene036817.t1
chr8.1 CDS 12657550 12657650 12657550 ID=cds.MS.gene036817.t1;Parent=MS.gene036817.t1
chr8.1 exon 12657254 12657465 12657254 ID=MS.gene036817.t1.exon2;Parent=MS.gene036817.t1
chr8.1 CDS 12657254 12657465 12657254 ID=cds.MS.gene036817.t1;Parent=MS.gene036817.t1
chr8.1 exon 12657045 12657167 12657045 ID=MS.gene036817.t1.exon3;Parent=MS.gene036817.t1
chr8.1 CDS 12657045 12657167 12657045 ID=cds.MS.gene036817.t1;Parent=MS.gene036817.t1
chr8.1 exon 12656561 12656724 12656561 ID=MS.gene036817.t1.exon4;Parent=MS.gene036817.t1
chr8.1 CDS 12656561 12656724 12656561 ID=cds.MS.gene036817.t1;Parent=MS.gene036817.t1
Gene Sequence

>MS.gene036817

ATGTCACCGCCGCAATTCACTTCATTGAACAATAATGACTTCAAAAGGGAAGGAACTTCTCATTCCAATGCATTGATATGCCCTCCTTCTGATGCATTGATGTGACCTCCTCCAAGGATGGCCTTGCCTCAATCAAACAAATCAGAGCACATTTTTTACAAAACACGAATTTGTACCGAGTTCAGATTTGGTGCTTGTAGAAACGGAAAAAATTGCAACTTTGATCATGGAGCTGAAGAGATAAGGCAACCACCACCAAATTTGCAGAAGCTAGGTGGTCCGTGCAACGAAGATCAACTGCAGCTGGGAAATCAAGTTGAAGATGAAAAAATCATACAAAGGATGAAACTGTGCAAGAAGTATTGCAATGGGGAGGAATGTCCATATAGAGATAACTGTAAATTCCTTCATGAAGATCCTGCACAGTTTAGGGATGATTCCTTGAAATCAAGAGAGTACTTATCGGAACTAATAATTTGGAAGGCAGCAGGGCTGTGAACAAGCAAGCAAGGGGCACTTATCGGAAGACTAAGCTGTGTCGCAATTGGAAGCATACCGGATATTGTTCCTTTGGAATGAACTGTCTCTTTGCTCATGATGAAGAAGGTAACAATAACTCATTTTGATTATTGGTTTTGGTTTTATCATATTCATATAATTCTATTGCTTTATTTTGTTTAGTTATATAAAATATGTTTTTTTCATTTTCTAGATGATGTGTAGAATGTCATTTTCTGTGATATGATGTGCAAACTACAGTGTTTGAATGCTTTGAATGTGTGTCATTTTGTTGTTGTGTTGTGTATGATGTTTCATGTTTGATTTGAATGGAAAATGCTCCTCCTACTGGTTTTCCCTTTGCCTTGTCTTGCAAAAATGTTCCTTCCTAAGGTTCTGATGGAAAATGATTCCATCCTTGTTTATAGGCAGAGCAGGTTCTGAATGTACCCGACTTGTGGAAAAGGAAGAAGAGCAGCCTAAGAAGAAGCGTATACTTGGGTTGAAATTCAGCCAGATCAATCGTATTTACGGTGATTGGATTGATGATTGGCCTTTTGTTATGCTCTGGAAACACACCTCATTTGGATAA
Protein sequence

>MS.gene036817.t1

MSPPQFTSLNNNDFKREGTSHSNALICPPSDALIFGACRNGKNCNFDHGAEEIRQPPPNLQKLGGPCNEDQLQLGNQVEDEKIIQRMKLCKKYCNGEECPYRDNCSRAVNKQARGTYRKTKLCRNWKHTGYCSFGMNCLFAHDEEGRAGSECTRLVEKEEEQPKKKRILGLKFSQINRIYGDWIDDWPFVMLWKHTSFG