AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene70821

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene70821.t1 MTR_1g080910 90.210 143 7 2 1 140 1 139 8.74e-73 214
MS.gene70821.t1 MTR_1g080910 88.462 104 5 2 1 101 1 100 6.52e-44 140
MS.gene70821.t1 MTR_7g115180 70.707 99 24 2 47 140 46 144 7.08e-41 133
MS.gene70821.t1 MTR_7g115180 68.919 74 21 1 47 118 46 119 5.03e-27 97.8
MS.gene70821.t1 MTR_1g100220 40.260 77 45 1 49 125 75 150 9.29e-11 58.2
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene70821.t1 AT5G28750 55.652 115 43 3 27 136 31 142 2.95e-36 122
MS.gene70821.t1 AT5G52440 52.083 48 23 0 60 107 85 132 3.48e-11 59.3

Find 31 sgRNAs with CRISPR-Local

Find 45 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ACGCTTTGTGCTTCTGTTTC+TGG 0.042249 1.2:-61269273 None:intergenic
CCAACTTCGGGCAATTTCTT+AGG 0.195754 1.2:-61269374 None:intergenic
TCTGGTTCTGGTTCTGGTTC+TGG 0.213224 1.2:-61269255 None:intergenic
TCTGTTTCTGGTTCTGGTTC+TGG 0.213548 1.2:-61269261 None:intergenic
TGTGCTTCTGTTTCTGGTTC+TGG 0.214615 1.2:-61269267 None:intergenic
CATTATTGTCTTGATCTTCT+TGG 0.219177 1.2:-61269810 None:intergenic
GAAATTTCTTCAGTAGAATT+AGG 0.222712 1.2:-61269775 None:intergenic
CCCGAGCTTGTTGTTATTGC+AGG 0.253511 1.2:+61269329 MS.gene70821:CDS
GCCGATGCTGCGACCAACTT+CGG 0.342708 1.2:-61269387 None:intergenic
TTTACTTGCAACGCCTTCTT+CGG 0.349544 1.2:+61269296 MS.gene70821:CDS
AAGTGATGTATTGTTAGAAT+TGG 0.354759 1.2:-61269219 None:intergenic
CCGATGCTGCGACCAACTTC+GGG 0.355688 1.2:-61269386 None:intergenic
TAAGAAGGATAAGGTGGAAT+AGG 0.383721 1.2:-61269192 None:intergenic
GTTAGAATTGGAAGCTAAGA+AGG 0.407354 1.2:-61269207 None:intergenic
GTGGAATAGGATGAAGAGAT+TGG 0.421445 1.2:-61269179 None:intergenic
GCGAATTAAAGAAGAAGAAA+GGG 0.424605 1.2:-61269147 None:intergenic
CTTCTTCTTTAATTCGCCCT+AGG 0.426973 1.2:+61269153 MS.gene70821:CDS
GGCGAATTAAAGAAGAAGAA+AGG 0.452383 1.2:-61269148 None:intergenic
AACTGTCAAAAGCTTCCAAC+AGG 0.455252 1.2:+61269412 MS.gene70821:CDS
CCCGAAGTTGGTCGCAGCAT+CGG 0.463383 1.2:+61269386 MS.gene70821:CDS
CCTAAGAAATTGCCCGAAGT+TGG 0.474122 1.2:+61269374 MS.gene70821:CDS
ATTGGAAGCTAAGAAGGATA+AGG 0.493246 1.2:-61269201 None:intergenic
TGAAACCTTGTAGGCAGCAA+AGG 0.513076 1.2:+61269726 MS.gene70821:intron
TGCAACGCCTTCTTCGGATT+AGG 0.521226 1.2:+61269302 MS.gene70821:CDS
TCCTGCAATAACAACAAGCT+CGG 0.534091 1.2:-61269330 None:intergenic
CAATAATGTTTCTAGTACAA+AGG 0.541741 1.2:+61269825 MS.gene70821:CDS
ATGAAGAGATTGGAAGCCTA+GGG 0.550257 1.2:-61269169 None:intergenic
GATGAAGAGATTGGAAGCCT+AGG 0.550349 1.2:-61269170 None:intergenic
CCTGCAATAACAACAAGCTC+GGG 0.555493 1.2:-61269329 None:intergenic
GGAAGCTAAGAAGGATAAGG+TGG 0.578078 1.2:-61269198 None:intergenic
GGGCACGCCTAATCCGAAGA+AGG 0.614059 1.2:-61269309 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TAAAATTGAAATTGTTTTAT+AGG + chr1.2:61269598-61269617 MS.gene70821:intron 10.0%
!!! CAAATTTTTATTGTTTGTTT+GGG + chr1.2:61269688-61269707 MS.gene70821:intron 15.0%
!! GCAATTTCTTATCTAATTAA+CGG + chr1.2:61269509-61269528 MS.gene70821:intron 20.0%
!! TTATCATAAGAATGAGAAAA+TGG - chr1.2:61269440-61269459 None:intergenic 20.0%
!!! GCAAATTTTTATTGTTTGTT+TGG + chr1.2:61269687-61269706 MS.gene70821:intron 20.0%
! AAGTGATGTATTGTTAGAAT+TGG - chr1.2:61269222-61269241 None:intergenic 25.0%
! GAAATTTCTTCAGTAGAATT+AGG - chr1.2:61269778-61269797 None:intergenic 25.0%
!!! ATTAGATTTTGAAACCTTGT+AGG + chr1.2:61269717-61269736 MS.gene70821:intron 25.0%
!!! ATTAGGTTCCTTTTTTAACT+CGG - chr1.2:61269761-61269780 None:intergenic 25.0%
!!! CAATAATGTTTCTAGTACAA+AGG + chr1.2:61269825-61269844 MS.gene70821:CDS 25.0%
ATGTAGAACTCCTATATGTT+AGG - chr1.2:61269487-61269506 None:intergenic 30.0%
CATTATTGTCTTGATCTTCT+TGG - chr1.2:61269813-61269832 None:intergenic 30.0%
GCGAATTAAAGAAGAAGAAA+GGG - chr1.2:61269150-61269169 None:intergenic 30.0%
TCATTCGTTGTATTTGAATG+AGG + chr1.2:61269642-61269661 MS.gene70821:intron 30.0%
!! ATTTGTTGTGCCTAACATAT+AGG + chr1.2:61269474-61269493 MS.gene70821:intron 30.0%
AATGAGAAAATGGAACCTGT+TGG - chr1.2:61269430-61269449 None:intergenic 35.0%
ATTGGAAGCTAAGAAGGATA+AGG - chr1.2:61269204-61269223 None:intergenic 35.0%
GGCGAATTAAAGAAGAAGAA+AGG - chr1.2:61269151-61269170 None:intergenic 35.0%
GTTAGAATTGGAAGCTAAGA+AGG - chr1.2:61269210-61269229 None:intergenic 35.0%
TAAGAAGGATAAGGTGGAAT+AGG - chr1.2:61269195-61269214 None:intergenic 35.0%
! GTTTGAGACCGAGTTAAAAA+AGG + chr1.2:61269750-61269769 MS.gene70821:CDS 35.0%
AACTGTCAAAAGCTTCCAAC+AGG + chr1.2:61269412-61269431 MS.gene70821:CDS 40.0%
ATGAAGAGATTGGAAGCCTA+GGG - chr1.2:61269172-61269191 None:intergenic 40.0%
CTTCTTCTTTAATTCGCCCT+AGG + chr1.2:61269153-61269172 MS.gene70821:CDS 40.0%
GTGGAATAGGATGAAGAGAT+TGG - chr1.2:61269182-61269201 None:intergenic 40.0%
TCCTGCAATAACAACAAGCT+CGG - chr1.2:61269333-61269352 None:intergenic 40.0%
TTTACTTGCAACGCCTTCTT+CGG + chr1.2:61269296-61269315 MS.gene70821:CDS 40.0%
AAACTCCTTTGCTGCCTACA+AGG - chr1.2:61269734-61269753 None:intergenic 45.0%
ACGCTTTGTGCTTCTGTTTC+TGG - chr1.2:61269276-61269295 None:intergenic 45.0%
CCAACTTCGGGCAATTTCTT+AGG - chr1.2:61269377-61269396 None:intergenic 45.0%
CCTAAGAAATTGCCCGAAGT+TGG + chr1.2:61269374-61269393 MS.gene70821:CDS 45.0%
CCTGCAATAACAACAAGCTC+GGG - chr1.2:61269332-61269351 None:intergenic 45.0%
GATGAAGAGATTGGAAGCCT+AGG - chr1.2:61269173-61269192 None:intergenic 45.0%
GGAAGCTAAGAAGGATAAGG+TGG - chr1.2:61269201-61269220 None:intergenic 45.0%
TGAAACCTTGTAGGCAGCAA+AGG + chr1.2:61269726-61269745 MS.gene70821:intron 45.0%
!! TCTGTTTCTGGTTCTGGTTC+TGG - chr1.2:61269264-61269283 None:intergenic 45.0%
!! TGTGCTTCTGTTTCTGGTTC+TGG - chr1.2:61269270-61269289 None:intergenic 45.0%
TGCAACGCCTTCTTCGGATT+AGG + chr1.2:61269302-61269321 MS.gene70821:CDS 50.0%
!! CCCGAGCTTGTTGTTATTGC+AGG + chr1.2:61269329-61269348 MS.gene70821:CDS 50.0%
!! TCTGGTTCTGGTTCTGGTTC+TGG - chr1.2:61269258-61269277 None:intergenic 50.0%
!!! GGAGTCGCTGCTCTTGTTTT+CGG + chr1.2:61269350-61269369 MS.gene70821:CDS 50.0%
CCGATGCTGCGACCAACTTC+GGG - chr1.2:61269389-61269408 None:intergenic 60.0%
GCCGATGCTGCGACCAACTT+CGG - chr1.2:61269390-61269409 None:intergenic 60.0%
GGGCACGCCTAATCCGAAGA+AGG - chr1.2:61269312-61269331 None:intergenic 60.0%
! CCCGAAGTTGGTCGCAGCAT+CGG + chr1.2:61269386-61269405 MS.gene70821:CDS 60.0%


Chromosome Type Strat End Strand Name
chr1.2 gene 61269131 61269858 61269131 ID=MS.gene70821
chr1.2 mRNA 61269131 61269858 61269131 ID=MS.gene70821.t1;Parent=MS.gene70821
chr1.2 exon 61269131 61269433 61269131 ID=MS.gene70821.t1.exon1;Parent=MS.gene70821.t1
chr1.2 CDS 61269131 61269433 61269131 ID=cds.MS.gene70821.t1;Parent=MS.gene70821.t1
chr1.2 exon 61269739 61269858 61269739 ID=MS.gene70821.t1.exon2;Parent=MS.gene70821.t1
chr1.2 CDS 61269739 61269858 61269739 ID=cds.MS.gene70821.t1;Parent=MS.gene70821.t1
Gene Sequence

>MS.gene70821

ATGGAGACAACACTTTCCCTTTCTTCTTCTTTAATTCGCCCTAGGCTTCCAATCTCTTCATCCTATTCCACCTTATCCTTCTTAGCTTCCAATTCTAACAATACATCACTTCTCTTGAAGAAAGCCAGAACCAGAACCAGAACCAGAAACAGAAGCACAAAGCGTTTTACTTGCAACGCCTTCTTCGGATTAGGCGTGCCCGAGCTTGTTGTTATTGCAGGAGTCGCTGCTCTTGTTTTCGGTCCTAAGAAATTGCCCGAAGTTGGTCGCAGCATCGGCAAAACTGTCAAAAGCTTCCAACAGGTTCCATTTTCTCATTCTTATGATAAGTTGCATTTTTTTTATTTGTTGTGCCTAACATATAGGAGTTCTACATTTGCAATTTCTTATCTAATTAACGGATCATATTTTTTTTAAATAATCGCATAAAATTTTGTAACATGTATATCTATCTCAAATTAGTCGCGTAAAATTGAAATTGTTTTATAGGTTCATTTGTATTTGTACTTACTCATTCGTTGTATTTGAATGAGGAGTTTCTAATAATTCAGTTGAAGCAAATTTTTATTGTTTGTTTGGGTTACTTATTAGATTTTGAAACCTTGTAGGCAGCAAAGGAGTTTGAGACCGAGTTAAAAAAGGAACCTAATTCTACTGAAGAAATTTCTGTTGCGAATGACCAAGAAGATCAAGACAATAATGTTTCTAGTACAAAGGATAGTGTATGA
Protein sequence

>MS.gene70821.t1

METTLSLSSSLIRPRLPISSSYSTLSFLASNSNNTSLLLKKARTRTRTRNRSTKRFTCNAFFGLGVPELVVIAGVAALVFGPKKLPEVGRSIGKTVKSFQQAAKEFETELKKEPNSTEEISVANDQEDQDNNVSSTKDSV