AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene049873


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 36 sgRNAs with CRISPR-Local

Find 42 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CAATTGCCATAACCTCTTTA+AGG 0.113717 4.3:-40945063 None:intergenic
CATTGAACTGATGCACATTC+TGG 0.222910 4.3:+40945123 MS.gene049873:CDS
CAATCACTCACTCCTTCAAT+TGG 0.356642 4.3:-40945495 None:intergenic
ATTCCAGTGCCTATATGAAT+AGG 0.375180 4.3:-40945534 None:intergenic
CTGATCTATGATACCATATC+TGG 0.377324 4.3:-40945158 None:intergenic
CAAGGGCCTTAAAGAGGTTA+TGG 0.402001 4.3:+40945057 MS.gene049873:CDS
ATGGCAATTGAAGGGGTTGA+TGG 0.404455 4.3:+40945076 MS.gene049873:CDS
TAGCAGATATGATGACTGTC+AGG 0.404647 4.3:+40945239 MS.gene049873:CDS
TATCTGCTAGAAGCATAATA+TGG 0.411824 4.3:-40945225 None:intergenic
CGATGCATCCTTGCGTGGGA+AGG 0.413910 4.3:+40945467 MS.gene049873:CDS
GGAATTGAGGCTGCCAGATA+TGG 0.414804 4.3:+40945145 MS.gene049873:CDS
TCAAACTAGGGTCAAGTCCT+TGG 0.415181 4.3:+40945363 MS.gene049873:intron
ATGGGTAAACCTATTCATAT+AGG 0.444116 4.3:+40945525 MS.gene049873:CDS
ATTGAACTGATGCACATTCT+GGG 0.456174 4.3:+40945124 MS.gene049873:CDS
AGTGAGTGATTGCATAATCA+TGG 0.458045 4.3:+40945506 MS.gene049873:CDS
AAAGAGGTTATGGCAATTGA+AGG 0.469543 4.3:+40945067 MS.gene049873:CDS
AAGACATGGAATTCAAAAGA+TGG 0.509948 4.3:+40945392 MS.gene049873:CDS
CATCAGCAAGGGCCTTAAAG+AGG 0.511065 4.3:+40945051 None:intergenic
TTCCATGTCTTGTCATTCCA+AGG 0.514932 4.3:-40945380 None:intergenic
AAACCTATTCATATAGGCAC+TGG 0.516311 4.3:+40945531 MS.gene049873:CDS
AAGAGGTTATGGCAATTGAA+GGG 0.518619 4.3:+40945068 MS.gene049873:CDS
TTCAATGATATGATTAGTAA+CGG 0.524631 4.3:-40945107 None:intergenic
GGGAAGGGTGACCCAATTGA+AGG 0.525487 4.3:+40945483 MS.gene049873:CDS
TGGCAATTGAAGGGGTTGAT+GGG 0.534884 4.3:+40945077 MS.gene049873:CDS
AGAGGTTATGGCAATTGAAG+GGG 0.537047 4.3:+40945069 MS.gene049873:CDS
AATCACTCACTCCTTCAATT+GGG 0.539564 4.3:-40945494 None:intergenic
GATGCATCCTTGCGTGGGAA+GGG 0.543229 4.3:+40945468 MS.gene049873:CDS
GATGCACATTCTGGGAATTG+AGG 0.567345 4.3:+40945132 MS.gene049873:CDS
AGACATGGAATTCAAAAGAT+GGG 0.582691 4.3:+40945393 MS.gene049873:CDS
GTGAGTGATTGCATAATCAT+GGG 0.585359 4.3:+40945507 MS.gene049873:CDS
GTCCTTGGAATGACAAGACA+TGG 0.589188 4.3:+40945378 MS.gene049873:CDS
TGGGTCACCCTTCCCACGCA+AGG 0.590838 4.3:-40945475 None:intergenic
CAGTATACAATGAAACAGCA+TGG 0.633424 4.3:+40945184 MS.gene049873:CDS
AGCAGATATGATGACTGTCA+GGG 0.641689 4.3:+40945240 MS.gene049873:CDS
TATAGGCACTGGAATGATCG+AGG 0.686172 4.3:+40945542 MS.gene049873:CDS
GAATGATCGAGGTCAAACAA+AGG 0.700498 4.3:+40945553 MS.gene049873:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! GTTATTTGAAAATTACTATA+AGG + chr4.3:40945266-40945285 MS.gene049873:intron 15.0%
!! TTATGTGATTTATCAAACTA+GGG + chr4.3:40945351-40945370 MS.gene049873:intron 20.0%
!! TTCAATGATATGATTAGTAA+CGG - chr4.3:40945110-40945129 None:intergenic 20.0%
!! TTTATGTGATTTATCAAACT+AGG + chr4.3:40945350-40945369 MS.gene049873:intron 20.0%
!!! GACTTGTAATTTAAACTTTT+TGG - chr4.3:40945292-40945311 None:intergenic 20.0%
! ATATTTATCACAAACACACA+TGG - chr4.3:40945315-40945334 None:intergenic 25.0%
! TATTTATCACAAACACACAT+GGG - chr4.3:40945314-40945333 None:intergenic 25.0%
AAGACATGGAATTCAAAAGA+TGG + chr4.3:40945392-40945411 MS.gene049873:CDS 30.0%
AGACATGGAATTCAAAAGAT+GGG + chr4.3:40945393-40945412 MS.gene049873:CDS 30.0%
ATGGGTAAACCTATTCATAT+AGG + chr4.3:40945525-40945544 MS.gene049873:CDS 30.0%
! TATCTGCTAGAAGCATAATA+TGG - chr4.3:40945228-40945247 None:intergenic 30.0%
AAACCTATTCATATAGGCAC+TGG + chr4.3:40945531-40945550 MS.gene049873:CDS 35.0%
AAAGAGGTTATGGCAATTGA+AGG + chr4.3:40945067-40945086 MS.gene049873:CDS 35.0%
AAGAGGTTATGGCAATTGAA+GGG + chr4.3:40945068-40945087 MS.gene049873:CDS 35.0%
AATCACTCACTCCTTCAATT+GGG - chr4.3:40945497-40945516 None:intergenic 35.0%
AGTGAGTGATTGCATAATCA+TGG + chr4.3:40945506-40945525 MS.gene049873:CDS 35.0%
ATTCCAGTGCCTATATGAAT+AGG - chr4.3:40945537-40945556 None:intergenic 35.0%
ATTGAACTGATGCACATTCT+GGG + chr4.3:40945124-40945143 MS.gene049873:CDS 35.0%
CAATTGCCATAACCTCTTTA+AGG - chr4.3:40945066-40945085 None:intergenic 35.0%
CAGTATACAATGAAACAGCA+TGG + chr4.3:40945184-40945203 MS.gene049873:CDS 35.0%
CTGATCTATGATACCATATC+TGG - chr4.3:40945161-40945180 None:intergenic 35.0%
GTGAGTGATTGCATAATCAT+GGG + chr4.3:40945507-40945526 MS.gene049873:CDS 35.0%
AGAGGTTATGGCAATTGAAG+GGG + chr4.3:40945069-40945088 MS.gene049873:CDS 40.0%
AGCAGATATGATGACTGTCA+GGG + chr4.3:40945240-40945259 MS.gene049873:CDS 40.0%
CAATCACTCACTCCTTCAAT+TGG - chr4.3:40945498-40945517 None:intergenic 40.0%
CATTGAACTGATGCACATTC+TGG + chr4.3:40945123-40945142 MS.gene049873:CDS 40.0%
TAGCAGATATGATGACTGTC+AGG + chr4.3:40945239-40945258 MS.gene049873:CDS 40.0%
TTCCATGTCTTGTCATTCCA+AGG - chr4.3:40945383-40945402 None:intergenic 40.0%
ATGGCAATTGAAGGGGTTGA+TGG + chr4.3:40945076-40945095 MS.gene049873:CDS 45.0%
CAAGGGCCTTAAAGAGGTTA+TGG + chr4.3:40945057-40945076 MS.gene049873:CDS 45.0%
GTCCTTGGAATGACAAGACA+TGG + chr4.3:40945378-40945397 MS.gene049873:CDS 45.0%
TCAAACTAGGGTCAAGTCCT+TGG + chr4.3:40945363-40945382 MS.gene049873:intron 45.0%
! GATGCACATTCTGGGAATTG+AGG + chr4.3:40945132-40945151 MS.gene049873:CDS 45.0%
! TGGCAATTGAAGGGGTTGAT+GGG + chr4.3:40945077-40945096 MS.gene049873:CDS 45.0%
! TTTTCGATGCATCCTTGCGT+GGG + chr4.3:40945463-40945482 MS.gene049873:CDS 45.0%
!! TATAGGCACTGGAATGATCG+AGG + chr4.3:40945542-40945561 MS.gene049873:CDS 45.0%
GGAATTGAGGCTGCCAGATA+TGG + chr4.3:40945145-40945164 MS.gene049873:CDS 50.0%
! CTTTTCGATGCATCCTTGCG+TGG + chr4.3:40945462-40945481 MS.gene049873:CDS 50.0%
GATGCATCCTTGCGTGGGAA+GGG + chr4.3:40945468-40945487 MS.gene049873:CDS 55.0%
GGGAAGGGTGACCCAATTGA+AGG + chr4.3:40945483-40945502 MS.gene049873:CDS 55.0%
CGATGCATCCTTGCGTGGGA+AGG + chr4.3:40945467-40945486 MS.gene049873:CDS 60.0%
TGGGTCACCCTTCCCACGCA+AGG - chr4.3:40945478-40945497 None:intergenic 65.0%


Chromosome Type Strat End Strand Name
chr4.3 gene 40945057 40945574 40945057 ID=MS.gene049873
chr4.3 mRNA 40945057 40945574 40945057 ID=MS.gene049873.t1;Parent=MS.gene049873
chr4.3 exon 40945057 40945261 40945057 ID=MS.gene049873.t1.exon1;Parent=MS.gene049873.t1
chr4.3 CDS 40945057 40945261 40945057 ID=cds.MS.gene049873.t1;Parent=MS.gene049873.t1
chr4.3 exon 40945372 40945574 40945372 ID=MS.gene049873.t1.exon2;Parent=MS.gene049873.t1
chr4.3 CDS 40945372 40945574 40945372 ID=cds.MS.gene049873.t1;Parent=MS.gene049873.t1
Gene Sequence

>MS.gene049873

CAAGGGCCTTAAAGAGGTTATGGCAATTGAAGGGGTTGATGGGCATAAAACCGTTACTAATCATATCATTGAACTGATGCACATTCTGGGAATTGAGGCTGCCAGATATGGTATCATAGATCAGATACAGTATACAATGAAACAGCATGGAATGAGCATAGACGTACGCCATATTATGCTTCTAGCAGATATGATGACTGTCAGGGTGAGTTATTTGAAAATTACTATAAGGCCAAAAAGTTTAAATTACAAGTCCCATGTGTGTTTGTGATAAATATGTAGATTTCTACTCATTTATGTGATTTATCAAACTAGGGTCAAGTCCTTGGAATGACAAGACATGGAATTCAAAAGATGGGCAGAAGTGCATTAATGCTTGCATCATTTGAGAGTTCAACAGACTATCTTTTCGATGCATCCTTGCGTGGGAAGGGTGACCCAATTGAAGGAGTGAGTGATTGCATAATCATGGGTAAACCTATTCATATAGGCACTGGAATGATCGAGGTCAAACAAAG

Protein sequence

>MS.gene049873.t1

QGPURGYGNURGUWAUNRYUSYHUTDAHSGNUGCQIWYHRSDTVYNETAWNEHRRTPYYASSRYDDCQGSSPWNDKTWNSKDGQKCINACIIUEFNRLSFRCILAWEGUPNURSEULHNHGUTYSYRHWNDRGQTK