AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene25704


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene25704.t1 MTR_3g082420 79.736 227 36 4 3 224 1 222 3.98e-123 348
MS.gene25704.t1 MTR_3g082340 69.264 231 56 4 1 224 1 223 3.49e-104 300
MS.gene25704.t1 MTR_3g080680 46.305 203 96 5 30 224 2 199 2.40e-45 150
MS.gene25704.t1 MTR_3g083030 42.105 228 104 11 9 223 17 229 1.74e-35 125
MS.gene25704.t1 MTR_3g083050 39.565 230 108 10 1 223 1 206 1.19e-31 115
MS.gene25704.t1 MTR_3g083080 38.462 169 91 5 59 223 46 205 1.48e-25 99.4
MS.gene25704.t1 MTR_8g461300 38.278 209 105 8 24 223 5 198 6.58e-24 94.7
MS.gene25704.t1 MTR_4g055800 38.889 144 71 4 68 207 143 273 3.38e-19 84.3
MS.gene25704.t1 MTR_3g083150 34.783 230 124 10 1 223 1 211 1.12e-17 78.6
MS.gene25704.t1 MTR_3g086030 39.091 110 62 2 40 145 1 109 8.31e-13 64.3
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 69 sgRNAs with CRISPR-Local

Find 77 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CCGAAATCGGAACCGGAATT+AGG 0.217000 3.3:+69272125 MS.gene25704:CDS
CGCGGTTTGGGTTTGGATTC+GGG 0.220683 3.3:-69272161 None:intergenic
CTCCTCCCGCGGTTTGGGTT+TGG 0.249105 3.3:-69272168 None:intergenic
CCGCGGTTTGGGTTTGGATT+CGG 0.250476 3.3:-69272162 None:intergenic
CCTAATTCCGGTTCCGATTT+CGG 0.259504 3.3:-69272125 None:intergenic
GACACCTCCTCCCGCGGTTT+GGG 0.274746 3.3:-69272173 None:intergenic
TTCCGATTCCTTTCCCGGTT+CGG 0.295282 3.3:-69272087 None:intergenic
TCCTTTCCCGGTTCGGAATT+CGG 0.295778 3.3:-69272080 None:intergenic
CAACTTTCCAGGCTCAAGTA+TGG 0.302357 3.3:+69272827 MS.gene25704:CDS
GGACACCTCCTCCCGCGGTT+TGG 0.311576 3.3:-69272174 None:intergenic
TCCTGTTCCGATCCTAATTC+CGG 0.325855 3.3:-69272137 None:intergenic
CCCTGCTTTAACAACTTTCC+AGG 0.345313 3.3:+69272816 MS.gene25704:CDS
GGAACCGAAACGGCCGAAAT+CGG 0.376767 3.3:+69272112 MS.gene25704:CDS
CCGCCACATAACAGTGTTCT+TGG 0.391644 3.3:-69272474 None:intergenic
GGTTCCGATTTCGGCCGTTT+CGG 0.408652 3.3:-69272116 None:intergenic
TTCCGAACCGGGAAAGGAAT+CGG 0.417366 3.3:+69272085 MS.gene25704:CDS
TCGATACTCACACGGAAAGC+TGG 0.427552 3.3:+69272039 MS.gene25704:CDS
TGAACTCTCCCTGCTTGCAT+TGG 0.445183 3.3:+69272542 MS.gene25704:CDS
ATAGAAAAGTCACTCAACTT+TGG 0.446397 3.3:-69272206 None:intergenic
GCCTGGAAAGTTGTTAAAGC+AGG 0.451262 3.3:-69272817 None:intergenic
GAAGCGGCCGAATTCCGAAC+CGG 0.466533 3.3:+69272073 MS.gene25704:CDS
ATCGGTTATGAAGAGGGGTT+GGG 0.467286 3.3:-69272499 None:intergenic
GCCGAATTCCGAACCGGGAA+AGG 0.476664 3.3:+69272079 MS.gene25704:CDS
ACCGGGAAAGGAATCGGAAA+AGG 0.477636 3.3:+69272091 MS.gene25704:CDS
TTTGTGTTGCAGAATGTCAA+TGG 0.481116 3.3:+69272013 None:intergenic
ACCGGAATTAGGATCGGAAC+AGG 0.482569 3.3:+69272136 MS.gene25704:CDS
TGTAATATTCCAATGCAAGC+AGG 0.487476 3.3:-69272551 None:intergenic
GAAACGGCCGAAATCGGAAC+CGG 0.494140 3.3:+69272118 MS.gene25704:CDS
CACCGTCCCATACTTGAGCC+TGG 0.497315 3.3:-69272834 None:intergenic
TAACAGTGTTCTTGGCGGAC+GGG 0.498416 3.3:-69272466 None:intergenic
AAGCGGCCGAATTCCGAACC+GGG 0.499700 3.3:+69272074 MS.gene25704:CDS
ACTTGATGAAACTCAAATGT+TGG 0.500719 3.3:-69272697 None:intergenic
CATCGGTTATGAAGAGGGGT+TGG 0.502034 3.3:-69272500 None:intergenic
TTATCACACATATATATGTA+AGG 0.511583 3.3:-69272248 None:intergenic
AACAGTGTTCTTGGCGGACG+GGG 0.511969 3.3:-69272465 None:intergenic
ATCAGCAATACCAACATCAT+AGG 0.513179 3.3:-69272731 None:intergenic
ATCTTCATCGGTTATGAAGA+GGG 0.524106 3.3:-69272505 None:intergenic
AACTTTCCAGGCTCAAGTAT+GGG 0.533504 3.3:+69272828 MS.gene25704:CDS
CGAATCCAAACCCAAACCGC+GGG 0.537433 3.3:+69272163 MS.gene25704:CDS
CGATACTCACACGGAAAGCT+GGG 0.542297 3.3:+69272040 MS.gene25704:CDS
CAGGGAGAGTTCATCAAGAG+TGG 0.544597 3.3:-69272532 None:intergenic
AGGGAGAGTTCATCAAGAGT+GGG 0.550261 3.3:-69272531 None:intergenic
CAAACCCAAACCGCGGGAGG+AGG 0.554321 3.3:+69272169 MS.gene25704:CDS
ACTCAACTTTGGATCTTCAT+CGG 0.555138 3.3:-69272195 None:intergenic
AAGAGTGGGGCGATCTTCAT+CGG 0.559401 3.3:-69272517 None:intergenic
ATAACAGTGTTCTTGGCGGA+CGG 0.562366 3.3:-69272467 None:intergenic
ATCCAAACCCAAACCGCGGG+AGG 0.562389 3.3:+69272166 MS.gene25704:CDS
TATGATGTTGGTATTGCTGA+TGG 0.567223 3.3:+69272733 MS.gene25704:CDS
CTTGCATTGGAATATTACAA+TGG 0.578867 3.3:+69272555 MS.gene25704:CDS
AATCGGAAAAGGAACCGAAA+CGG 0.587324 3.3:+69272102 MS.gene25704:CDS
TCATCGGACACCTCCTCCCG+CGG 0.588030 3.3:-69272179 None:intergenic
GTAATATTCCAATGCAAGCA+GGG 0.591856 3.3:-69272550 None:intergenic
CCACATAACAGTGTTCTTGG+CGG 0.600956 3.3:-69272471 None:intergenic
CCTGGAAAGTTGTTAAAGCA+GGG 0.605506 3.3:-69272816 None:intergenic
ATCGGAACCGGAATTAGGAT+CGG 0.612901 3.3:+69272130 MS.gene25704:CDS
AGTTGTTAAAGCAGGGCTGT+CGG 0.619352 3.3:-69272809 None:intergenic
CCGCCAAGAACACTGTTATG+TGG 0.619826 3.3:+69272471 MS.gene25704:CDS
GATCTTCATCGGTTATGAAG+AGG 0.624382 3.3:-69272506 None:intergenic
GTCAAGTGTACCTATGATGT+TGG 0.629074 3.3:+69272721 MS.gene25704:CDS
TCTTCATCGGTTATGAAGAG+GGG 0.634517 3.3:-69272504 None:intergenic
TTCCAGGCTCAAGTATGGGA+CGG 0.638739 3.3:+69272832 MS.gene25704:CDS
ACAGTGTTCTTGGCGGACGG+GGG 0.652393 3.3:-69272464 None:intergenic
CCGAATCCAAACCCAAACCG+CGG 0.656141 3.3:+69272162 MS.gene25704:CDS
TAAACTCATGAAGAAACTAG+AGG 0.657097 3.3:+69272286 MS.gene25704:CDS
GGGAGAGTTCATCAAGAGTG+GGG 0.657488 3.3:-69272530 None:intergenic
GCTGGGAAGAAAGTTTGAAG+CGG 0.688820 3.3:+69272057 MS.gene25704:CDS
CCAAGAACACTGTTATGTGG+CGG 0.693885 3.3:+69272474 MS.gene25704:CDS
AATGGAATTCGATACTCACA+CGG 0.710555 3.3:+69272031 MS.gene25704:CDS
GAGCATCTAGAGCGTTCTCG+CGG 0.715724 3.3:+69272320 MS.gene25704:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! GTTCTTCTTAATTAATTATT+AGG + chr3.3:69272672-69272691 MS.gene25704:intron 15.0%
!! CAATGGAAAAAATAATAATC+AGG + chr3.3:69272572-69272591 MS.gene25704:CDS 20.0%
!! TTATCACACATATATATGTA+AGG - chr3.3:69272251-69272270 None:intergenic 20.0%
!!! TAATTAATTTTGATTCATCC+TGG + chr3.3:69272413-69272432 MS.gene25704:intron 20.0%
ACTTGATGAAACTCAAATGT+TGG - chr3.3:69272700-69272719 None:intergenic 30.0%
ATAGAAAAGTCACTCAACTT+TGG - chr3.3:69272209-69272228 None:intergenic 30.0%
CTTGCATTGGAATATTACAA+TGG + chr3.3:69272555-69272574 MS.gene25704:CDS 30.0%
TAAACTCATGAAGAAACTAG+AGG + chr3.3:69272286-69272305 MS.gene25704:CDS 30.0%
!! GAAGTGTCTTCTTTTGATAT+TGG - chr3.3:69272790-69272809 None:intergenic 30.0%
!!! TGATATTGGTTTTGCTTGAA+AGG - chr3.3:69272776-69272795 None:intergenic 30.0%
AATGGAATTCGATACTCACA+CGG + chr3.3:69272031-69272050 MS.gene25704:CDS 35.0%
ACTCAACTTTGGATCTTCAT+CGG - chr3.3:69272198-69272217 None:intergenic 35.0%
ATCAGCAATACCAACATCAT+AGG - chr3.3:69272734-69272753 None:intergenic 35.0%
GTAATATTCCAATGCAAGCA+GGG - chr3.3:69272553-69272572 None:intergenic 35.0%
TATGATGTTGGTATTGCTGA+TGG + chr3.3:69272733-69272752 MS.gene25704:CDS 35.0%
TGTAATATTCCAATGCAAGC+AGG - chr3.3:69272554-69272573 None:intergenic 35.0%
! ATCTTCATCGGTTATGAAGA+GGG - chr3.3:69272508-69272527 None:intergenic 35.0%
AACTTTCCAGGCTCAAGTAT+GGG + chr3.3:69272828-69272847 MS.gene25704:CDS 40.0%
AATCGGAAAAGGAACCGAAA+CGG + chr3.3:69272102-69272121 MS.gene25704:CDS 40.0%
CCTGGAAAGTTGTTAAAGCA+GGG - chr3.3:69272819-69272838 None:intergenic 40.0%
GTCAAGTGTACCTATGATGT+TGG + chr3.3:69272721-69272740 MS.gene25704:CDS 40.0%
! GATCTTCATCGGTTATGAAG+AGG - chr3.3:69272509-69272528 None:intergenic 40.0%
! TCTTCATCGGTTATGAAGAG+GGG - chr3.3:69272507-69272526 None:intergenic 40.0%
ACACCTGTATTGTGTTGTCC+AGG - chr3.3:69272434-69272453 None:intergenic 45.0%
AGGGAGAGTTCATCAAGAGT+GGG - chr3.3:69272534-69272553 None:intergenic 45.0%
AGTTGTTAAAGCAGGGCTGT+CGG - chr3.3:69272812-69272831 None:intergenic 45.0%
ATAACAGTGTTCTTGGCGGA+CGG - chr3.3:69272470-69272489 None:intergenic 45.0%
ATAGACGCGTACGTACACTT+AGG - chr3.3:69272346-69272365 None:intergenic 45.0%
ATCGGAACCGGAATTAGGAT+CGG + chr3.3:69272130-69272149 MS.gene25704:CDS 45.0%
ATCGGTTATGAAGAGGGGTT+GGG - chr3.3:69272502-69272521 None:intergenic 45.0%
CAACTTTCCAGGCTCAAGTA+TGG + chr3.3:69272827-69272846 MS.gene25704:CDS 45.0%
CATCCTGGACAACACAATAC+AGG + chr3.3:69272428-69272447 MS.gene25704:intron 45.0%
CCAAGAACACTGTTATGTGG+CGG + chr3.3:69272474-69272493 MS.gene25704:CDS 45.0%
CCACATAACAGTGTTCTTGG+CGG - chr3.3:69272474-69272493 None:intergenic 45.0%
CCCTGCTTTAACAACTTTCC+AGG + chr3.3:69272816-69272835 MS.gene25704:CDS 45.0%
CCTAATTCCGGTTCCGATTT+CGG - chr3.3:69272128-69272147 None:intergenic 45.0%
GCCTGGAAAGTTGTTAAAGC+AGG - chr3.3:69272820-69272839 None:intergenic 45.0%
GCTGGGAAGAAAGTTTGAAG+CGG + chr3.3:69272057-69272076 MS.gene25704:CDS 45.0%
TCCTGTTCCGATCCTAATTC+CGG - chr3.3:69272140-69272159 None:intergenic 45.0%
! TCCTTTTCCGATTCCTTTCC+CGG - chr3.3:69272095-69272114 None:intergenic 45.0%
AAGAGTGGGGCGATCTTCAT+CGG - chr3.3:69272520-69272539 None:intergenic 50.0%
ACCGGAATTAGGATCGGAAC+AGG + chr3.3:69272136-69272155 MS.gene25704:CDS 50.0%
ACCGGGAAAGGAATCGGAAA+AGG + chr3.3:69272091-69272110 MS.gene25704:CDS 50.0%
CAGGGAGAGTTCATCAAGAG+TGG - chr3.3:69272535-69272554 None:intergenic 50.0%
CCGAAATCGGAACCGGAATT+AGG + chr3.3:69272125-69272144 MS.gene25704:CDS 50.0%
CCGCCAAGAACACTGTTATG+TGG + chr3.3:69272471-69272490 MS.gene25704:CDS 50.0%
CCGCCACATAACAGTGTTCT+TGG - chr3.3:69272477-69272496 None:intergenic 50.0%
CGATACTCACACGGAAAGCT+GGG + chr3.3:69272040-69272059 MS.gene25704:CDS 50.0%
GGGAGAGTTCATCAAGAGTG+GGG - chr3.3:69272533-69272552 None:intergenic 50.0%
TCGATACTCACACGGAAAGC+TGG + chr3.3:69272039-69272058 MS.gene25704:CDS 50.0%
TGAACTCTCCCTGCTTGCAT+TGG + chr3.3:69272542-69272561 MS.gene25704:CDS 50.0%
TTCCAGGCTCAAGTATGGGA+CGG + chr3.3:69272832-69272851 MS.gene25704:CDS 50.0%
TTCCGAACCGGGAAAGGAAT+CGG + chr3.3:69272085-69272104 MS.gene25704:CDS 50.0%
TTCCGATTCCTTTCCCGGTT+CGG - chr3.3:69272090-69272109 None:intergenic 50.0%
! CATCGGTTATGAAGAGGGGT+TGG - chr3.3:69272503-69272522 None:intergenic 50.0%
! TAACAGTGTTCTTGGCGGAC+GGG - chr3.3:69272469-69272488 None:intergenic 50.0%
!! TCCTTTCCCGGTTCGGAATT+CGG - chr3.3:69272083-69272102 None:intergenic 50.0%
CCGAATCCAAACCCAAACCG+CGG + chr3.3:69272162-69272181 MS.gene25704:CDS 55.0%
CGAATCCAAACCCAAACCGC+GGG + chr3.3:69272163-69272182 MS.gene25704:CDS 55.0%
GAAACGGCCGAAATCGGAAC+CGG + chr3.3:69272118-69272137 MS.gene25704:CDS 55.0%
GGAACCGAAACGGCCGAAAT+CGG + chr3.3:69272112-69272131 MS.gene25704:CDS 55.0%
GGTTCCGATTTCGGCCGTTT+CGG - chr3.3:69272119-69272138 None:intergenic 55.0%
! AACAGTGTTCTTGGCGGACG+GGG - chr3.3:69272468-69272487 None:intergenic 55.0%
! CCGCGGTTTGGGTTTGGATT+CGG - chr3.3:69272165-69272184 None:intergenic 55.0%
! CGCGGTTTGGGTTTGGATTC+GGG - chr3.3:69272164-69272183 None:intergenic 55.0%
! GAGCATCTAGAGCGTTCTCG+CGG + chr3.3:69272320-69272339 MS.gene25704:CDS 55.0%
AAGCGGCCGAATTCCGAACC+GGG + chr3.3:69272074-69272093 MS.gene25704:CDS 60.0%
ATCCAAACCCAAACCGCGGG+AGG + chr3.3:69272166-69272185 MS.gene25704:CDS 60.0%
CACCGTCCCATACTTGAGCC+TGG - chr3.3:69272837-69272856 None:intergenic 60.0%
GAAGCGGCCGAATTCCGAAC+CGG + chr3.3:69272073-69272092 MS.gene25704:CDS 60.0%
GCCGAATTCCGAACCGGGAA+AGG + chr3.3:69272079-69272098 MS.gene25704:CDS 60.0%
! ACAGTGTTCTTGGCGGACGG+GGG - chr3.3:69272467-69272486 None:intergenic 60.0%
CAAACCCAAACCGCGGGAGG+AGG + chr3.3:69272169-69272188 MS.gene25704:CDS 65.0%
GACACCTCCTCCCGCGGTTT+GGG - chr3.3:69272176-69272195 None:intergenic 65.0%
TCATCGGACACCTCCTCCCG+CGG - chr3.3:69272182-69272201 None:intergenic 65.0%
! CTCCTCCCGCGGTTTGGGTT+TGG - chr3.3:69272171-69272190 None:intergenic 65.0%
GGACACCTCCTCCCGCGGTT+TGG - chr3.3:69272177-69272196 None:intergenic 70.0%


Chromosome Type Strat End Strand Name
chr3.3 gene 69272026 69272900 69272026 ID=MS.gene25704
chr3.3 mRNA 69272026 69272900 69272026 ID=MS.gene25704.t1;Parent=MS.gene25704
chr3.3 exon 69272026 69272349 69272026 ID=MS.gene25704.t1.exon1;Parent=MS.gene25704.t1
chr3.3 CDS 69272026 69272349 69272026 ID=cds.MS.gene25704.t1;Parent=MS.gene25704.t1
chr3.3 exon 69272450 69272593 69272450 ID=MS.gene25704.t1.exon2;Parent=MS.gene25704.t1
chr3.3 CDS 69272450 69272593 69272450 ID=cds.MS.gene25704.t1;Parent=MS.gene25704.t1
chr3.3 exon 69272694 69272900 69272694 ID=MS.gene25704.t1.exon3;Parent=MS.gene25704.t1
chr3.3 CDS 69272694 69272900 69272694 ID=cds.MS.gene25704.t1;Parent=MS.gene25704.t1
Gene Sequence

>MS.gene25704

ATGTCAATGGAATTCGATACTCACACGGAAAGCTGGGAAGAAAGTTTGAAGCGGCCGAATTCCGAACCGGGAAAGGAATCGGAAAAGGAACCGAAACGGCCGAAATCGGAACCGGAATTAGGATCGGAACAGGAACCCGAATCCAAACCCAAACCGCGGGAGGAGGTGTCCGATGAAGATCCAAAGTTGAGTGACTTTTCTATCTATGATGACGACGACGAGCCTTACATATATATGTGTGATAAATTTGTGTATAAGAATAAACTCATGAAGAAACTAGAGGAAGCAGATAATGAGCATCTAGAGCGTTCTCGCGGCCTAAGTGTACGTACGCGTCTATCTATCTATTTCATTTTTGTTTTCAATTTACTGTTTCACTCTCTTAATTAATTAATTTTGATTCATCCTGGACAACACAATACAGGTGTACGATGTTCTCCCCCGTCCGCCAAGAACACTGTTATGTGGCGGTACCCAACCCCTCTTCATAACCGATGAAGATCGCCCCACTCTTGATGAACTCTCCCTGCTTGCATTGGAATATTACAATGGAAAAAATAATAATCAGGTTCAATACTTAATACTTAAATGAAGAGAATGAATGAATATTGTATGTTGTTTATTCATTAGCTAGACTAAACTAATTGTTCTTCTTAATTAATTATTAGGCTCCAACATTTGAGTTTCATCAAGTTGTCAAGTGTACCTATGATGTTGGTATTGCTGATGGAAATATGTTTTACATTACCTTTCAAGCAAAACCAATATCAAAAGAAGACACTTCCGACAGCCCTGCTTTAACAACTTTCCAGGCTCAAGTATGGGACGGTGATGATAAATCACGTAATGTCATAAAGTGCGCCATTAAAATCTAA

Protein sequence

>MS.gene25704.t1

MSMEFDTHTESWEESLKRPNSEPGKESEKEPKRPKSEPELGSEQEPESKPKPREEVSDEDPKLSDFSIYDDDDEPYIYMCDKFVYKNKLMKKLEEADNEHLERSRGLSVYDVLPRPPRTLLCGGTQPLFITDEDRPTLDELSLLALEYYNGKNNNQAPTFEFHQVVKCTYDVGIADGNMFYITFQAKPISKEDTSDSPALTTFQAQVWDGDDKSRNVIKCAIKI